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1. Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

Author

Andrea M. Chiariello, Alex Abraham, Simona Bianco, Andrea Esposito, Andrea Fontana, Francesca Vercellone, Mattia Conte, and Mario Nicodemi

Subjects
Science
Abstract

Abstract SARS-CoV-2 can re-structure chromatin organization and alter the epigenomic landscape of the host genome, but the mechanisms that produce such changes remain unclear. Here, we use polymer physics to investigate how the chromatin of the host genome is re-organized upon infection with SARS-CoV-2. We show that re-structuring of A/B compartments can be explained by a re-modulation of intra-compartment homo-typic affinities, which leads to the weakening of A-A interactions and the enhancement of A-B mixing. At the TAD level, re-arrangements are physically described by a reduction in the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and a spread in space of the TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon response, such as DDX58 or IFIT, becomes more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysing the time trajectories of pairwise gene-enhancer and higher-order contacts reveals that this variability derives from increased fluctuations in the chromatin dynamics of infected cells. This suggests that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time.

Published
2024
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2. Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding

Author

Mattia Conte, Ehsan Irani, Andrea M. Chiariello, Alex Abraham, Simona Bianco, Andrea Esposito, and Mario Nicodemi

Subjects
Science
Abstract

Two main mechanisms have been proposed to shape 3D genome architecture - loop extrusion and phase separation. Here the authors combine these mechanisms in polymer models in a manner that best fits 3D genome, based on both Hi-C and super-resolution locus imaging data, proposing that these two physical processes can indeed coexist simultaneously within cells to define loops and TADs.

Published
2022
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3. Heterogeneous migration routes of DNA triplet repeat slip-outs

Author

Simona Bianco, Tianyu Hu, Oliver Henrich, and Steven W. Magennis

Subjects
Physics, QC1-999, Biology (General), QH301-705.5
Abstract

It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role. It was recently shown that three-way DNA junctions containing slip-out hairpins of CAG or CTG repeats and contiguous triplet repeats in the adjacent duplex displayed single-molecule FRET (smFRET) dynamics that were ascribed to both local conformational motions and longer-range branch migration. Here we explore these so-called ''mobile'' slip-out structures through a detailed kinetic analysis of smFRET trajectories and coarse-grained modeling. Despite the apparent structural simplicity, with six FRET states resolvable, most smFRET states displayed biexponential dwell-time distributions, attributed to structural heterogeneity and overlapping FRET states. Coarse-grained modeling for a (GAC)10 repeat slip-out included trajectories that corresponded to a complete round of branch migration; the structured free energy landscape between slippage events supports the dynamical complexity observed by smFRET. A hairpin slip-out with 40 CAG repeats, which is above the repeat length required for disease in several triplet repeat disorders, displayed smFRET dwell times that were on average double those of 3WJs with 10 repeats. The rate of secondary-structure rearrangement via branch migration, relative to particular DNA processing pathways, may be an important factor in the expansion of triplet repeat expansion diseases.

Published
2022
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4. Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

Author

Mattia Conte, Luca Fiorillo, Simona Bianco, Andrea M. Chiariello, Andrea Esposito, and Mario Nicodemi

Subjects
Science
Abstract

The molecular and physical mechanisms underlying chromatin folding at the single DNA molecule level remain poorly understood. Here, the authors use polymer modeling to investigate the conformations of two 2Mb-wide DNA loci in normal and cohesin depleted cells, and provide evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules.

Published
2020
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5. Polymer Models of Chromatin Imaging Data in Single Cells

Author

Mattia Conte, Andrea M. Chiariello, Alex Abraham, Simona Bianco, Andrea Esposito, Mario Nicodemi, Tommaso Matteuzzi, and Francesca Vercellone

Subjects
chromosome architecture, multiplexed FISH imaging, polymer physics, machine learning, computer simulations, Industrial engineering. Management engineering, T55.4-60.8, Electronic computers. Computer science, QA75.5-76.95
Abstract

Recent super-resolution imaging technologies enable tracing chromatin conformation with nanometer-scale precision at the single-cell level. They revealed, for example, that human chromosomes fold into a complex three-dimensional structure within the cell nucleus that is essential to establish biological activities, such as the regulation of the genes. Yet, to decode from imaging data the molecular mechanisms that shape the structure of the genome, quantitative methods are required. In this review, we consider models of polymer physics of chromosome folding that we benchmark against multiplexed FISH data available in human loci in IMR90 fibroblast cells. By combining polymer theory, numerical simulations and machine learning strategies, the predictions of the models are validated at the single-cell level, showing that chromosome structure is controlled by the interplay of distinct physical processes, such as active loop-extrusion and thermodynamic phase-separation.

Published
2022
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6. Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

Author

Irene Salamon, Simone Serio, Simona Bianco, Christina Pagiatakis, Silvia Crasto, Andrea M. Chiariello, Mattia Conte, Paola Cattaneo, Luca Fiorillo, Arianna Felicetta, Elisa di Pasquale, Paolo Kunderfranco, Mario Nicodemi, Roberto Papait, and Gianluigi Condorelli

Subjects
Biological Sciences, Molecular Biology, Molecular Mechanism of Gene Regulation, Science
Abstract

Summary: Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries. In the present work, we describe two eRNAs transcribed from the enhancer of Nkx2-5—a gene specifying a master cardiomyogenic lineage transcription factor (TF)—which we call Intergenic Regulatory Element Nkx2-5 Enhancers (IRENEs). The IRENEs are encoded, respectively, on the same strand (SS) and in the divergent direction (div) respect to the nearby gene. Of note, these two eRNAs have opposing roles in the regulation of Nkx2-5: IRENE-SS acts as a canonical promoter of transcription, whereas IRENE-div represses the activity of the enhancer through recruitment of the histone deacetylase sirtuin 1. Thus, we have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription.

Published
2020
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7. Using Rheology to Understand Transient and Dynamic Gels

Author

Simona Bianco, Santanu Panja, and Dave J. Adams

Subjects
gel, rheology, transient, dissipative, dynamic, Science, Chemistry, QD1-999, Inorganic chemistry, QD146-197, General. Including alchemy, QD1-65
Abstract

Supramolecular gels can be designed such that pre-determined changes in state occur. For example, systems that go from a solution (sol) state to a gel state and then back to a sol state can be prepared using chemical processes to control the onset and duration of each change of state. Based on this, more complex systems such as gel-to-sol-to-gel and gel-to-gel-to-gel systems can be designed. Here, we show that we can provide additional insights into such systems by using rheological measurements at varying values of frequency or strain during the evolution of the systems. Since the different states are affected to different degrees by the frequency and/or strain applied, this allows us to better understand and follow the changes in state in such systems.

Published
2022
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8. A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells

Author

Andrea M. Chiariello, Simona Bianco, A. Marieke Oudelaar, Andrea Esposito, Carlo Annunziatella, Luca Fiorillo, Mattia Conte, Alfonso Corrado, Antonella Prisco, Martin S.C. Larke, Jelena M. Telenius, Renato Sciarretta, Francesco Musella, Veronica J. Buckle, Douglas R. Higgs, Jim R. Hughes, and Mario Nicodemi

Subjects
Biology (General), QH301-705.5
Abstract

Summary: We investigate the three-dimensional (3D) conformations of the α-globin locus at the single-allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer physics models and high-resolution Capture-C data. Model predictions are validated against independent fluorescence in situ hybridization (FISH) data measuring pairwise distances, and Tri-C data identifying three-way contacts. The architecture is rearranged during the transition from ESCs to erythroid cells, associated with the activation of the globin genes. We find that in ESCs, the spatial organization conforms to a highly intermingled 3D structure involving non-specific contacts, whereas in erythroid cells the α-globin genes and their enhancers form a self-contained domain, arranged in a folded hairpin conformation, separated from intermingling flanking regions by a thermodynamic mechanism of micro-phase separation. The flanking regions are rich in convergent CTCF sites, which only marginally participate in the erythroid-specific gene-enhancer contacts, suggesting that beyond the interaction of CTCF sites, multiple molecular mechanisms cooperate to form an interacting domain. : Chiariello et al. use polymer physics models to infer the 3D conformations of the murine α-globin locus. In the transition from ESCs to erythroid cells, the locus rearranges from an inactive highly intermingled conformation to an active, hairpin-shaped structure, marked by cell-specific three-way contacts accurately predicted by the models. Keywords: globin loci, higher-order chromatin organization, polymer physics, gene regulation

Published
2020
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9. A Polymer Physics Investigation of the Architecture of the Murine Orthologue of the 7q11.23 Human Locus

Author

Andrea M. Chiariello, Andrea Esposito, Carlo Annunziatella, Simona Bianco, Luca Fiorillo, Antonella Prisco, and Mario Nicodemi

Subjects
polymer physics, chromatin, Neuroscience, congenital disease, 7q11.23 locus, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

In the last decade, the developments of novel technologies, such as Hi-C or GAM methods, allowed to discover that chromosomes in the nucleus of mammalian cells have a complex spatial organization, encompassing the functional contacts between genes and regulators. In this work, we review recent progresses in chromosome modeling based on polymer physics to understand chromatin structure and folding mechanisms. As an example, we derive in mouse embryonic stem cells the full 3D structure of the Bmp7 locus, a genomic region that plays a key role in osteoblastic differentiation. Next, as an application to Neuroscience, we present the first 3D model for the mouse orthologoue of the Williams–Beuren syndrome 7q11.23 human locus. Deletions and duplications of the 7q11.23 region generate neurodevelopmental disorders with multi-system involvement and variable expressivity, and with autism. Understanding the impact of such mutations on the rewiring of the interactions of genes and regulators could be a new key to make sense of their related diseases, with potential applications in biomedicine.

Published
2017
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14. Lung ultrasonography performed by nephrologist: COVID-19 as an opportunity to reveal ultrasound's full potential and usefulness in the dialysis room

Author

Federica N Vigotti, Carlo Di Benedetto, Fabrizio Fop, Simona Bianco, Donatella Bilucaglia, and Giulio Cesano

Subjects
Transplantation, Nephrology
Abstract

BackgroundInterest in point-of-care ultrasound (POCUS) and lung ultrasound (LUS) is growing in the nephrology and dialysis field, and the number of nephrologists skilled in what is proving to be the “5th pillar of bedside physical examination” is increasing. Patients on hemodialysis (HD) are at high risk of contracting severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) and developing coronavirus disease 2019 (COVID-19) serious complications. Despite this, to our knowledge there are no studies to date that show the role of LUS in this setting, while there are many in the emergency room, where LUS proved to be an important tool, providing risk stratification and guiding management strategies and resource allocation. Therefore, it is not clear whether the usefulness and cut-offs of LUS highlighted in studies in the general population are reliable in dialysis, or whether variations, precautions and adjustments to this specific situation are necessary.MethodsThis was a 1-year monocentric prospective observational cohort study of 56 HD patients with COVID-19. Patients underwent a monitoring protocol that included at first evaluation bedside LUS, using a 12-scan scoring system, by the same nephrologist. All data were prospectively and systematically collected. Outcomes. hospitalization rate, combined outcome [non-invasive ventilation (NIV + death)], mortality. Descriptive variables are presented as medians (interquartile range), or percentage. Univariate and multivariate analysis, as well as Kaplan–Meier (K-M) survival curves, were carried out. P was fixed at .05.ResultsMedian age was 78 years, 90% had at least one comorbidity (46% diabetics), 55% were hospitalized and 23% deaths. Median duration of disease was 23 days (14–34). A LUS score ≥11 represented a 13-fold risk of hospitalization, a 16.5-fold risk of combined outcome (NIV + death) vs risk factors such as age [odds ratio (OR) 1.6], diabetes (OR 1.2), male sex (OR 1.3) and obesity (OR 1.25), and a 7.7-fold risk of mortality. In the logistic regression, LUS score ≥11 is associated with the combined outcome with a hazard ratio (HR) of 6.1 vs inflammations indices such as CRP ≥9 mg/dL (HR 5.5) and interleukin-6 (IL-6) ≥62 pg/mL (HR 5.4). In K-M curves, survival drops significantly with LUS score above 11.ConclusionsIn our experience of COVID-19 HD patients, LUS appeared to be an effective and easy tool, predicting the need for NIV and mortality better than “classic” known COVID-19 risk factors such as age, diabetes, male sex and obesity, and even better than inflammations indices such as CRP and IL-6. These results are consistent with those of the studies in the emergency room setting, but with a lower LUS score cut-off (11 vs 16–18). This is probably due to the higher global frailty and peculiarity of HD population, and emphasizes how nephrologists should themselves use LUS and POCUS as a part of their everyday clinical practice, adapting it to the peculiarity of the HD ward.

Published
2022
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15. Empagliflozin in Patients with Chronic Kidney Disease

Author

Herrington, William G, Staplin, Natalie, Wanner, Christoph, Green, Jennifer B, Hauske, Sibylle J, Emberson, Jonathan R, Preiss, David, Judge, Parminder, Mayne, Kaitlin J, Ng, Sarah Y A, Sammons, Emily, Zhu, Doreen, Hill, Michael, Stevens, Will, Wallendszus, Karl, Brenner, Susanne, Cheung, Alfred K, Liu, Zhi-Hong, Li, Jing, Hooi, Lai Seong, Liu, Wen, Kadowaki, Takashi, Nangaku, Masaomi, Levin, Adeera, Cherney, David, Maggioni, Aldo P, Pontremoli, Roberto, Deo, Rajat, Goto, Shinya, Rossello, Xavier, Tuttle, Katherine R, Steubl, Dominik, Petrini, Michaela, Massey, Dan, Eilbracht, Jens, Brueckmann, Martina, Landray, Martin J, Baigent, Colin, Haynes, Richard, The EMPA-KIDNEY Collaborative Group: Colin Baigent, Martin J Landray, Christoph Wanner, William G Herrington, Richard Haynes, Jennifer B Green, Sibylle J Hauske, Martina Brueckmann, Mark Hopley, Maximillian von-Eynatten, Jyothis George, Susanne Brenner, Alfred K Cheung, David Preiss, Zhi-Hong Liu, Jing Li, Laiseong Hooi, Wen Liu, Takashi Kadowaki, Masaomi Nangaku, Adeera Levin, David Cherney, Roberto Pontremoli, Aldo P Maggioni, Natalie Staplin, Jonathan Emberson, Stefan Hantel, Shinya Goto, Rajat Deo, Katherine R Tuttle, Michael Hill, Parminder Judge, Kaitlin J Mayne, Sarah Y A Ng, Xavier Rossello, Emily Sammons, Doreen Zhu, Peter Sandercock, Rudolf Bilous, Charles Herzog, Paul Whelton, Janet Wittes, Derrick Bennett, Patricia Achiri, Chrissie Ambrose, Cristina Badin, Jill Barton, Richard Brown, Andy Burke, Sebastian Butler, Rejive Dayanandan, Pia Donaldson, Robert Dykas, Lucy Fletcher, Kate Frederick, Hannah Kingston, Mo Gray, Emily Harding, Akiko Hashimoto, Lyn Howie, Susan Hurley, Ryonfa Lee, Nik Luker, Kevin Murphy, Mariko Nakahara, John Nolan, Michelle Nunn, Sorcha Mulligan, Akiko Omata, Sandra Pickworth, YanRu Qiao, Shraddha Shah, Karen Taylor, Alison Timadjer, Monique Willett, Liz Wincott, Qin Yan, Hui Yu, Louise Bowman, Fang Chen, Robert Clarke, Michelle Goonasekera, Waseem Karsan, Marion Mafham, Christina Reith, Mohammed Zayed, Ritva Ellison, Rowan Moys, Will Stevens, Kevin Verdel, Karl Wallendszus, Chris Bowler, Anna Brewer, Andy Measor, Guanguo Cui, Charles Daniels, Angela Field, Bob Goodenough, Ashley Lawson, Youcef Mostefai, Dheeptha Radhakrishnan, Samee Syed, Shuang Xia, Ruth Adewuyi-Dalton, Thomas Arnold, Anne-Marie Beneat, Anoushka Bhatt, Chloe Bird, Andrew Breach, Laura Brown, Mark Caple, Tatyana Chavagnon, Karen Chung, Sarah Clark, Luminita Condurache, Katarzyna Eichstadt, Marta Espino Obrero, Scarlett Forest, Helen French, Nick Goodwin, Andrew Gordon, Joanne Gordon, Cat Guest, Tina Harding, Michal Hozak, Matthew Lacey, David MacLean, Louise Messinger, Stewart Moffat, Martin Radley, Claire Shenton, Sarah Tipper, Jon Tyler, Lesley Weaving, James Wheeler, Elissa Williams, Tim Williams, Hamish Woodhouse, Angela Chamberlain, Jo Chambers, Joanne Davies, Denise Donaldson, Pati Faria-Shayler, Denise Fleming-Brown, Jennifer Ingell, Carol Knott, Anna Liew, Helen Lochhead, Juliette Meek, Isabel Rodriguez-Bachiller, Andrea Wilson, Patrick Zettergren, Rach AitSadi, Ian Barton, Alex Baxter, Yonghong Bu, Lukasz Danel, Sonja Grotjahn, Rijo Kurien, Michael Lay, Archie Maskill, Aleksandra Murawska, Rachel Raff, Allen Young, Rebecca Sardell, Vladimir Cejka, Marcela Fajardo-Moser, Christian Hartner, Doris Poehler, Janina Renner, Franziska Scheidemantel, Miya Bryant, Anita Hepditch, Cassandra Johnson, Erin Latore, Yolanda Miller, Lauren Price, Merilee Whalen, Ashleigh Wheeler, Jenny Ingell, Yu An, Yinghua Chen, Peiling Chen, Hao Dai, Hong Du, Fang Feng, Qing Guo, Libo Hou, Wuhanbilige Hundei, Binbin Jin, Yan Li, Jiamin Liu, Xia Song, Yanping Wang, Yanwu Yu, Ning Zhang, Lingshan Zhao, Hui Zhong, Cheng Beng Goh, Ye Mun Low, Soon Yi Sor, Farah Hanis Zulkipli, Sarojini Sivanandam, Natsuki Arai, Ai Fukasawa, Mizue Furukawa, Keisuke Habuki, Shoko Hayashi, Wakako Isari, Saki Kanegae, Maria Kawai, Reiki Kobayashi, Takako Kuramae, Chika Kuribayashi, Sawako Maeno, Satoshi Masumoto, Tomoko Morisaki, Minoru Oda, Kazue Sawada, Kenta Sugamori, Ayana Tatsuzawa, Aiko Tomita, Kazuyuki Yuasa, Hiroko Inazawa, Amanda Axler, Kerri Gallo, Ester Baldini, Barbara Bartolomei Mecatti, Francesca Bianchini, Martina Ceseri, Laura Cipressa, Gianna Fabbri, Andrea Lorimer, Donata Lucci, Sharang Ghavampour, Anja Knoppe, Hans Schmidt-Gurtler, Hubert Dumann, Sybille Merscher, Margret Patecki, Georg Rainer Schlieper, Anke Torp, Bianca Weber, Maja Zietz, Bernd Hohenstein, Urs Benck, Diliana Draganova, Thomas Weinreich, Lothar Wolf, Jasmine Gaidu, Hanna Reiner, Mandy Visnjic, Daniel Steffl, Marie Breitenfeldt, Annette Kraemer-Guth, Christine Braun, Simone Hagge, Michael Schomig, Stephan Matthias, Dominik Stoffler, Beate Schumacher, Thomas Sitter, Louise Fuessl, Julia Krappe, Jerome Loutan, Volker Vielhauer, Luciano Andriaccio, Magdalena Maurer, Bernhard Winkelmann, Martin Dursch, Linda Seifert, Linda Tenbusch, Julia Weinmann-Menke, Simone Boedecker, Wiebke Kaluza-Schilling, Daniel Kraus, Carina Krieger, Margit Schmude, Anne Schreiber, Ewelina Eckrich, Diethelm Tschope, Abdulwahab Arbi, Young Lee-Barkey, Bernd Stratmann, Natalie Prib, Sina Rolfsmeier, Irina Schneider, Lars Rump, Johannes Stegbauer, Christine Pötz, Mara Schemmelmann, Claudia Schmidt, Michael Koch, Sendogan Aker, Annika Küpper, Manuela Martin, Thiemo Pfab, Christian Albert, Michael Haase, Barbara Zander, Claudia Schneider-Danwitz, Wolfgang Seeger, Wolf-Adam Seeger, Britta Zemann, Christoph Stellbrink, Kristin Marx, Ekaterina Stellbrink, Britta Brettschneider, Stephanie Watson, Marion Iselt, Gerhard Klausmann, Inga-Nadine Kummer, Auguste Kutschat, Simone Streitenberger, Matthias Girndt, Silke Markau, Ina Girakossyan, Claudia Hanf, Joachim Beige, Ralph Wendt, Ulrike Schmidt, Andreas Schneider, Roland Veelken, Claudia Donhauser, Luis Becker, Nexhat Miftari, Ricarda Wolfling, Sarah Morlok, Christian Hugo, Alexander Paliege, Jens Passauer, Julian Stumpf, Annegret Fleischer, Kerstin Haaser, Bernhard Kraemer, Jan Jochims, Bernd Kruger, Claudia Foellinger, Anastassiya Reisler, Frank Strutz, Stefan Haack, Ursula Hohenstatt, Martin Busch, Konstantin Herfurth, Gunter Wolf, Rainer Paul, Hermann Haller, Jessica Kaufeld, Jan Menne, Elisabeth Bahlmann-Kroll, Angela Bergner, Horst Weihprecht, Aydin Er, Florian Sonntag, Elif Turan, Michael Wittmann, Franziska Klauser, Eva Voigt, Volker Schettler, Egbert Schulz, Madlen Rohnstock, Elke Schettler, Bernd Schroppel, Rene van Erp, Martin Kachele, Ulla Ludwig, Lena Schulte-Kemna, Waltraud Kmietschak, Elke Preiss, Martina Ruocco, Gunnar Heine, Martin Brzoska, Sebastian Gabel, Christina Büttner, Asma Sabarai, Bernhard Banas, Tobias Bergler, Yvonne Ehrl, Franz Putz, Antonia Schuster, Stefanie Kuhn, Torsten Schramm, Stefan Degenhardt, Gerhard Schmidt, Lea Weiland, Ulrike Giebeln-Hudnell, Jan Kielstein, Gabriele Eden, Brigitte Fuchs, Gina Morig, Manuela Winkler, Harald Darius, Charalampos Kriatselis, Carl-Philipp Roesch, Astrid Maselli, Dominik Alscher, Markus Ketteler, Moritz Schanz, Severin Schricker, Bianka Rettenmaier, Andrea Schwab, Pablo Pergola, Irene Leal, Melissa Cagle, Anna Romo, Anthony Torres, Sucharit Joshi, Kulli Barrett, Alexis Africano, Vicki Dodds, Dorleena Gowen, Ashlee Morris, Juan Fernandez, Guillermo Jimenez, Ricardo Viera, Kendaling Bruce, Ryan Barrios, Maylin Garcia, Kerelyn Garcia, Iradis Leal, David Tietjen, David Bains, Carlo Castillo, Genielle Brewer, Justin Davis, Natalie Freking, Brittany Golson, Sally Ham, Jesslyn Roesch, Pusadee Suchinda, Shameem Beigh, Usah Lilavivat, Joyce Bilton, Kim Bocchicchia, Jeffrey Turner, Neera Dahl, Aldo Peixoto, Yasemin Kavak, Lauren Liberti, Hari Nair, Nicolas Page, Stephanie Rosenberg, Kathryn Simmons, Tamara Isakova, Rebecca Frazier, Rupal Mehta, Anand Srivastava, Patrick Fox, Jonathan Hecktman, Alexander Hodakowski, Carlos Martinez, Rachel Phillips, Alexis Stevenson, Reem Mustafa, Kyle Jansson, Cassandra Kimber, Jason Stubbs, Ahmad Tuffaha, Sri Yarlagadda, Debbie Griffin, Elisabeth Laundy, Zhuo Tang, Radica Alicic, Ann Cooper, Lisa Davis, Ashwini Gore, Rebecca Goldfaden, Leslie Harvill, Lisa Hichkad, Barry Johns, Thomas Jones, Kayla Merritt, Jennifer Sheldon, Jennifer Stanfield, Lindsay Alexander, Kaitlyn Preston, Lindsey Wood, Rajesh Pradhan, Roger DeRaad, Kelli McIntosh, Louis Raymond, Michael Shepperd, Susan McLaughlin, Mary Seifert, Andrew Shepherd, Joseph Aiello, William Durham, Laurie Loudermilk, John Manley, Sabrina Burnette, Stephanie Evans, Tara Johnson, Lance Sloan, Judy Ann Acosta, Stacy Gillham, Katia Sloan, SueAnn Squyres, Michael Rocco, Amret Hawfield, Ben Bagwell, Lauren Richmond, Joseph Soufer, Subha Clarke, Amanda Aliu, Kristine Calabrese, Amanda Davis, Veronica Poma, Tracy Spinola, James Magee, Ricardo Silva, Rushab Choksi, Lorraine Dajani, John Evans, Anil George, Prasanth Krish, Gerard Martins, Mae Sheikh-Ali, David Sutton, Freda Driver, Abraham Hanburry, Laura Hume, Amber Hurst, Matthew Taddeo, Marla Turner, Veronica Yousif, Srinivasan Beddhu, Laith Al-Rabadi, Nikita Abraham, Amalia Caamano, Judy Carle, Victoria Gonce, Kaitlyn Staylor, Na Zhou, Shweta Bansal, Manoj Bhattarai, Kumar Sharma, Subrata Debnath, Aliseiya Garza, Chakradhar Velagapudi, Sergio Rovner, Javier Almeida, Pablo Casares, Verlaine Stewart-Ray, Rene Almaraz, Renata Dayrell, Ana Moncada, Ricardo Pulido, Roxana Rodriquez, Wasim Deeb, Kathryn DeGoursey, Rodel Gloria, Trevor Greene, Robert Miller, Edward Pereira, Miguel Roura, Debbie Domingo, Sasha Dorestin, William Hodge, Cathy Jackson, Deborah Lund, Katrina Taylor, Kenneth Boren, Brittany Cleveland, Sandra Gaiser, Mandeep Sahani, Logan Aldrich, Exodus Edmerson, Edmond Limon, Cole Valletta, Patricia Vasquez, Christopher Provenzano, Navkiranjot Brar, Heather Henderson, Bellovich Keith, Qur Khai, Quresh Khairullah, Gail Makos, Joel Topf, Sherry Gasko, Rosemarie Henschel, Kaitlin Knapp, Teresa Kozlowski, Paula LaFleur, Ashwathy Varughese, Hui Xue, Patricia Wu, Olga Arechiga, Shan Darbeau, Michael Fechter, Stephanie Martinez, Lenita Hanson, Nyla Cooper, Arelis Madera, Jay Cadorna, Rita Sheridan, Helen Sparks, Bradley Eilerman, Susanne Bodine, Wael Eid, Rebecca Flora, Amber Avery, Cashmere Hardy, Mihaela Biscoveanu, Steven Nagelberg, Tracey Cummins, Frederic Rahbari-Oskoui, Anju Oommen, Zohreh Forghani, Stacie Hitchcock, Darya Hosein, Diane Watkins, Minesh Patel, Anthony Lambert, Elizabeth Newman, Autumn Wood, Tammy Ross, Stephany Topping, Jeffrey Mulhern, Lorna Murphy, Ann Vasseur, Gregory Greenwood, Alexander Hadley, Denise Laurienti, Christopher Marshall, Nicholas McLean, Scott Satko, Brandy Caudill, Jacob Maris, Janice Rogers, Cindy Vanhoy, George Thomas, Georges Nakhoul, John O'Toole, Jonathan Taliercio, Leslie Cooperman, Marina Markovic, Barbara Tucky, Devasmita Dev, Alia Hasan, Hima Yalamanchili, Namita Jain, Lesley McNeil, Eric Wines, Jean Park, Adline Ghazi, Mia Hamm, Tejas Patel, Amy Mottl, Emily Chang, Vimal Derebail, Emmie Cole, Anne Froment, Sara Kelley, Jordan Osmond Foster, Vahid Mahabadi, Golriz Jafari, Anita Kamarzarian, Wendy Arriaga, Daisy Arteaga, Rosario Machicado, Genesis Naverrete, Prashant Kumar, Imran Nazeer, Karina Urquia, Tammi Glider, Vickie Jones, Savannah Rucker, Jennifer Wiley, Rahul Pandey, Jesus Arroyo, Harish Pariani, Mohammad Ahmad, Shahin Mozaffari, Erika Perez, Matthew Budoff, Sion Roy, Divya Birudaraju, Ahmed Ghanem, Sajad Hamal, Stephen Aronoff, Elisa Joye Petr, Richard Sachson, Jaime Wiebel, Sana Akram, Laurie Jones, Curtis Knight, Maurie Tarlac, Shahbaz Ahmed, Harold Szerlip, Akinwande Akinfolarin, Ankit Mehta, Shana Camp, Cindy Castro, Zanaida Cooper, Jessica Terry, Ahmed Awad, Bhavya Kothapalli, Ryan Lustig, Serine Alfaress, Hyder Jasim, Mary Parrigon, Dennis Karounos, Sadiq Ahmed, Maggie Berry, Ruth Oremus, Carlos Hernandez-Cassis, Elias Ugwu, Nazia Junejo, Nancy Suazo, Mark Segal, Amir Kazory, Sherry Brown, Tristan Daniels, Sofia Dayi, Renee Hogan, Kathy McCray, Jennifer Stickley, Mahboob Rahman, Mirela Dobre, Lavinia Negrea, Aparna Padiyar, Nishigandha Pradhan, Arash Rashidi, Nagaraju Sarabu, Vicki Donley, Tricia Young, Godson Oguchi, Judepatricks Onyema, Kahla Damianik, Jack Dienes, Judith Plummer-Morgan, Marilyn Roman, Mauver Skipper, Stacey-Ann Villaruel, Krystle Williams, Danny Sugimoto, Jeffrey Dugas, Ismeal Ahmed, Jamie Bhairoo, Dolores Rijos, Huzaifa Salim, Madita Gavrila, Kathryn Lafferty, Ria Rabara, Sally Ruse, Maria Weetman, James Bushnell, Albert Power, Alison Jenkins, Stefanie Jones, Amanda Scott, Cath Byrne, Mark Jesky, Alison Cowley, Emma McHaffie, Holly Waterfall, Jo Taylor, Laura Bough, Thomas Phillips, Barbara Winter-Goodwin, Sui Phin Kon, Iain MacDougall, Eirini Lioudaki, Sapna Shah, Claire Sharpe, Francisco Aguilar, Abegail Hernandez Pena, Conception Pugay, Amelia Te, Hugh Finn, Wasim Hanif, Samiul Mostafa, Alice Aitken, Katharine Draxlbauer, Evelina Grobovaite, Jennifer Kearney, Theresa McCarthy, Giorgio Gentile, Duncan Browne, Palanichamy Chellamuthu, Tabinda 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Cipressa, Laura, Fabbri, Gianna, Lorimer, Andrea, Lucci, Donata, Ghavampour, Sharang, Knoppe, Anja, Schmidt-Gurtler, Han, Dumann, Hubert, Merscher, Sybille, Patecki, Margret, Rainer Schlieper, Georg, Torp, Anke, Weber, Bianca, Zietz, Maja, Hohenstein, Bernd, Benck, Ur, Draganova, Diliana, Weinreich, Thoma, Wolf, Lothar, Gaidu, Jasmine, Reiner, Hanna, Visnjic, Mandy, Steffl, Daniel, Breitenfeldt, Marie, Kraemer-Guth, Annette, Braun, Christine, Hagge, Simone, Schomig, Michael, Matthias, Stephan, Stoffler, Dominik, Schumacher, Beate, Sitter, Thoma, Fuessl, Louise, Krappe, Julia, Loutan, Jerome, Vielhauer, Volker, Andriaccio, Luciano, Maurer, Magdalena, Winkelmann, Bernhard, Dursch, Martin, Seifert, Linda, Tenbusch, Linda, Weinmann-Menke, Julia, Boedecker, Simone, Kaluza-Schilling, Wiebke, Kraus, Daniel, Krieger, Carina, Schmude, Margit, Schreiber, Anne, Eckrich, Ewelina, Tschope, Diethelm, Arbi, Abdulwahab, Lee-Barkey, Young, Stratmann, Bernd, Prib, Natalie, Rolfsmeier, Sina, Schneider, 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Herfurth, Konstantin, Wolf, Gunter, Paul, Rainer, Haller, Hermann, Kaufeld, Jessica, Menne, Jan, Bahlmann-Kroll, Elisabeth, Bergner, Angela, Weihprecht, Horst, Er, Aydin, Sonntag, Florian, Turan, Elif, Wittmann, Michael, Klauser, Franziska, Voigt, Eva, Schettler, Volker, Schulz, Egbert, Rohnstock, Madlen, Schettler, Elke, Schroppel, Bernd, van Erp, Rene, Kachele, Martin, Ludwig, Ulla, Schulte-Kemna, Lena, Kmietschak, Waltraud, Preiss, Elke, Ruocco, Martina, Heine, Gunnar, Brzoska, Martin, Gabel, Sebastian, Büttner, Christina, Sabarai, Asma, Banas, Bernhard, Bergler, Tobia, Ehrl, Yvonne, Putz, Franz, Schuster, Antonia, Kuhn, Stefanie, Schramm, Torsten, Degenhardt, Stefan, Schmidt, Gerhard, Weiland, Lea, Giebeln-Hudnell, Ulrike, Kielstein, Jan, Eden, Gabriele, Fuchs, Brigitte, Morig, Gina, Winkler, Manuela, Darius, Harald, Kriatselis, Charalampo, Roesch, Carl-Philipp, Maselli, Astrid, Alscher, Dominik, Ketteler, Marku, Schanz, Moritz, Schricker, Severin, Rettenmaier, Bianka, Schwab, Andrea, Pergola, Pablo, Leal, Irene, Cagle, Melissa, Romo, Anna, Torres, Anthony, Joshi, Sucharit, Barrett, Kulli, Africano, Alexi, Dodds, Vicki, Gowen, Dorleena, Morris, Ashlee, Fernandez, Juan, Jimenez, Guillermo, Viera, Ricardo, Bruce, Kendaling, Barrios, Ryan, Garcia, Maylin, Garcia, Kerelyn, Leal, Iradi, Tietjen, David, Bains, David, Castillo, Carlo, Brewer, Genielle, Davis, Justin, Freking, Natalie, Golson, Brittany, Ham, Sally, Roesch, Jesslyn, Suchinda, Pusadee, Beigh, Shameem, Lilavivat, Usah, Bilton, Joyce, Bocchicchia, Kim, Turner, Jeffrey, Dahl, Neera, Peixoto, Aldo, Kavak, Yasemin, Liberti, Lauren, Nair, Hari, Page, Nicola, Rosenberg, Stephanie, Simmons, Kathryn, Isakova, Tamara, Frazier, Rebecca, Mehta, Rupal, Srivastava, Anand, Fox, Patrick, Hecktman, Jonathan, Hodakowski, Alexander, Martinez, Carlo, Phillips, Rachel, Stevenson, Alexi, Mustafa, Reem, Jansson, Kyle, Kimber, Cassandra, Stubbs, Jason, Tuffaha, Ahmad, Yarlagadda, Sri, Griffin, Debbie, Laundy, Elisabeth, Tang, Zhuo, Alicic, Radica, Cooper, Ann, Davis, Lisa, Gore, Ashwini, Goldfaden, Rebecca, Harvill, Leslie, Hichkad, Lisa, Johns, Barry, Jones, Thoma, Merritt, Kayla, Sheldon, Jennifer, Stanfield, Jennifer, Alexander, Lindsay, Preston, Kaitlyn, Wood, Lindsey, Pradhan, Rajesh, Deraad, Roger, Mcintosh, Kelli, Raymond, Loui, Shepperd, Michael, Mclaughlin, Susan, Seifert, Mary, Shepherd, Andrew, Aiello, Joseph, Durham, William, Loudermilk, Laurie, Manley, John, Burnette, Sabrina, Evans, Stephanie, Johnson, Tara, Sloan, Lance, Ann Acosta, Judy, Gillham, Stacy, Sloan, Katia, Squyres, Sueann, Rocco, Michael, Hawfield, Amret, Bagwell, Ben, Richmond, Lauren, Soufer, Joseph, Clarke, Subha, Aliu, Amanda, Calabrese, Kristine, Davis, Amanda, Poma, Veronica, Spinola, Tracy, Magee, Jame, Silva, Ricardo, Choksi, Rushab, Dajani, Lorraine, Evans, John, George, Anil, Krish, Prasanth, Martins, Gerard, Sheikh-Ali, Mae, Sutton, David, Driver, Freda, Hanburry, Abraham, Hume, Laura, Hurst, Amber, Taddeo, Matthew, Turner, Marla, Yousif, Veronica, Beddhu, Srinivasan, Al-Rabadi, Laith, Abraham, Nikita, Caamano, Amalia, Carle, Judy, Gonce, Victoria, Staylor, Kaitlyn, Zhou, Na, Bansal, Shweta, Bhattarai, Manoj, Sharma, Kumar, Debnath, Subrata, Garza, Aliseiya, Velagapudi, Chakradhar, Rovner, Sergio, Almeida, Javier, Casares, Pablo, Stewart-Ray, Verlaine, Almaraz, Rene, Dayrell, Renata, Moncada, Ana, Pulido, Ricardo, Rodriquez, Roxana, Deeb, Wasim, Degoursey, Kathryn, Gloria, Rodel, Greene, Trevor, Miller, Robert, Pereira, Edward, Roura, Miguel, Domingo, Debbie, Dorestin, Sasha, Hodge, William, Jackson, Cathy, Lund, Deborah, Taylor, Katrina, Boren, Kenneth, Cleveland, Brittany, Gaiser, Sandra, Sahani, Mandeep, Aldrich, Logan, Edmerson, Exodu, Limon, Edmond, Valletta, Cole, Vasquez, Patricia, Provenzano, Christopher, Brar, Navkiranjot, Henderson, Heather, Keith, Bellovich, Khai, Qur, Khairullah, Quresh, Makos, Gail, Topf, Joel, Gasko, Sherry, Henschel, Rosemarie, Knapp, Kaitlin, Kozlowski, Teresa, Lafleur, Paula, Varughese, Ashwathy, Xue, Hui, Wu, Patricia, Arechiga, Olga, Darbeau, Shan, Fechter, Michael, Martinez, Stephanie, Hanson, Lenita, Cooper, Nyla, Madera, Areli, Cadorna, Jay, Sheridan, Rita, Sparks, Helen, Eilerman, Bradley, Bodine, Susanne, Eid, Wael, Flora, Rebecca, Avery, Amber, Hardy, Cashmere, Biscoveanu, Mihaela, Nagelberg, Steven, Cummins, Tracey, Rahbari-Oskoui, Frederic, Oommen, Anju, Forghani, Zohreh, Hitchcock, Stacie, Hosein, Darya, Watkins, Diane, Patel, Minesh, Lambert, Anthony, Newman, Elizabeth, Wood, Autumn, Ross, Tammy, Topping, Stephany, Mulhern, Jeffrey, Murphy, Lorna, Vasseur, Ann, Greenwood, Gregory, Hadley, Alexander, Laurienti, Denise, Marshall, Christopher, Mclean, Nichola, Satko, Scott, Caudill, Brandy, Maris, Jacob, Rogers, Janice, Vanhoy, Cindy, Thomas, George, Nakhoul, George, O'Toole, John, Taliercio, Jonathan, Cooperman, Leslie, Markovic, Marina, Tucky, Barbara, Dev, Devasmita, Hasan, Alia, Yalamanchili, Hima, Jain, Namita, Mcneil, Lesley, Wines, Eric, Park, Jean, Ghazi, Adline, Hamm, Mia, Patel, Teja, Mottl, Amy, Chang, Emily, Derebail, Vimal, Cole, Emmie, Froment, Anne, Kelley, Sara, Osmond Foster, Jordan, Mahabadi, Vahid, Jafari, Golriz, Kamarzarian, Anita, Arriaga, Wendy, Arteaga, Daisy, Machicado, Rosario, Naverrete, Genesi, Kumar, Prashant, Nazeer, Imran, Urquia, Karina, Glider, Tammi, Jones, Vickie, Rucker, Savannah, Wiley, Jennifer, Pandey, Rahul, Arroyo, Jesu, Pariani, Harish, Ahmad, Mohammad, Mozaffari, Shahin, Perez, Erika, Budoff, Matthew, Roy, Sion, Birudaraju, Divya, Ghanem, Ahmed, Hamal, Sajad, Aronoff, Stephen, Joye Petr, Elisa, Sachson, Richard, Wiebel, Jaime, Akram, Sana, Jones, Laurie, Knight, Curti, Tarlac, Maurie, Ahmed, Shahbaz, Szerlip, Harold, Akinfolarin, Akinwande, Mehta, Ankit, Camp, Shana, Castro, Cindy, Cooper, Zanaida, Terry, Jessica, Awad, Ahmed, Kothapalli, Bhavya, Lustig, Ryan, Alfaress, Serine, Jasim, Hyder, Parrigon, Mary, Karounos, Denni, Ahmed, Sadiq, Berry, Maggie, Oremus, Ruth, Hernandez-Cassis, Carlo, Ugwu, Elia, Junejo, Nazia, Suazo, Nancy, Segal, Mark, Kazory, Amir, Brown, Sherry, Daniels, Tristan, Dayi, Sofia, Hogan, Renee, Mccray, Kathy, Stickley, Jennifer, Rahman, Mahboob, Dobre, Mirela, Negrea, Lavinia, Padiyar, Aparna, Pradhan, Nishigandha, Rashidi, Arash, Sarabu, Nagaraju, Donley, Vicki, Young, Tricia, Oguchi, Godson, Onyema, Judepatrick, Damianik, Kahla, Dienes, Jack, Plummer-Morgan, Judith, Roman, Marilyn, Skipper, Mauver, Villaruel, Stacey-Ann, Williams, Krystle, Sugimoto, Danny, Dugas, Jeffrey, Ahmed, Ismeal, Bhairoo, Jamie, Rijos, Dolore, Salim, Huzaifa, Gavrila, Madita, Lafferty, Kathryn, Rabara, Ria, Ruse, Sally, Weetman, Maria, Bushnell, Jame, Power, Albert, Jenkins, Alison, Jones, Stefanie, Scott, Amanda, Byrne, Cath, Jesky, Mark, Cowley, Alison, Mchaffie, Emma, Waterfall, Holly, Taylor, Jo, Bough, Laura, Phillips, Thoma, Winter-Goodwin, Barbara, Phin Kon, Sui, Macdougall, Iain, Lioudaki, Eirini, Shah, Sapna, Sharpe, Claire, Aguilar, Francisco, Hernandez Pena, Abegail, Pugay, Conception, Te, Amelia, Finn, Hugh, Hanif, Wasim, Mostafa, Samiul, Aitken, Alice, Draxlbauer, Katharine, Grobovaite, Evelina, Kearney, Jennifer, Mccarthy, Theresa, Gentile, Giorgio, Browne, Duncan, Chellamuthu, Palanichamy, Dugal, Tabinda, Chant, Terri, Jones, Laura, Laity, Emily, Miners, Megan, Muir, Jame, Swanson, Elizabeth, Frankel, Andrew, Tomlinson, Jame, Alegata, Marlon, Almasarwah, Rashid, Apostolidi, Anthoula, Vourvou, Maria, Walters, Thoma, Taal, Maarten, Dukka, Hari, Kolhe, Nitin, Mcdonald, Carly, White, Kelly, Ugni, Shiva, Gunda, Smita, Oluyombo, Rotimi, Brindle, Vicki, Coutts, Ping, Fuller, Tracy, Nadar, Evelyn, Ramadoss, Suresh, Motherwell, Nichola, Pajak, Susannah, Tonks, Louise, Bhandari, Sunil, Bodington, Richard, Hazara, Adil, Fellowes, Dominic, Wong, Christopher, Goldsmith, Christopher, Barnes, Sherald, Bennett, Ann, Burston, Claire, Hope, Samantha, Hunt, Nicola, Kurian, Lini, Fish, Richard, Farrugia, Daniela, Lee, Judy, Sadler, Emma, Turner, Hannah, Hill, Christopher, Brown, Henry, Masengu, Agne, Maxwell, Peter, Bleakley, Nina, Murtagh, Hugh, Petchey, William, Yiu, Vivian, Kellett, Joanne, Williams, Angharad, Clarke, Helen, Carnall, Victoria, Benyon, Sarah, Blake, Caroline, Estcourt, Stephanie, Piper, Jane, Morgan, Neal, Hutchinson, Carolyn, Mckinley, Teresa, Woodman, Alastair, Graham, Judi, Leonard, Niall, Smyth, John, Adell, Vicki, Hagan, Samantha, Caplin, Ben, Oomatia, Amin, Damian, Eleanor, Sobande, Toluleyi, Doulton, Tim, Delaney, Michael, Montasser, Mahmoud, Hansen, Jenny, Loader, David, Moon, Angela, Morris, France, Sinha, Smeeta, Chukwu, Chukwuma, Hudson, Amy, Campbell, Diane, Kershaw, Melanie, Whittaker, Stephanie, Irtiza-Ali, Ayesha, Ghalli, Farid, Nosseir, Heba, Leslie, Allison, Trivedi, Kate, Fraser, Donald, Alhadj Ali, Mohammad, Griffin, Sian, Latif, Farah, Witczak, Justyna, Wonnacott, Alexa, Jeffers, Lynda, Webley, Yvette, Phelan, Paul, Miller-Hodges, Eve, Geddes, Ailsa, Glenwright, Margaret, Hunter, Amy, Pickett, Thoma, Moriarty, Jim, Hill, Linda, Tyler, Amanda, Ayub, Waqar, Evans, Gail, Hewins, Sue, Hewitt, Davina, Read, Kerry, Bell, Samira, Cosgrove, Leanne, Craik, Rachel, Murray, Shona, Bhandary, Nitin, Coles, Holly, Easow, Rashmi, Joseph, Maya, Khwaja, Arif, Jackson, Yvonne, Mbuyisa, Angeline, Sellars, Rachel, Chitalia, Nihil, Mohandas, Cynthia, Gherman, Anca, Kamundi, Charlotte, Olufuwa, Olumide, Mccafferty, Kieran, Adeleke, Adedolapo, Healy, Cara, Jeyarajah, Damini, Kinsella-Perks, Edward, Smith, Richard, Camilleri, Brian, Buckman, Carol, Finch, Jenny, Rivers, Vanessa, Connor, Andrew, Carr, Sheila, Shainberg, Lisa, Lewington, Andrew, Baker, Richard, Dorey, Suzannah, Tobin, Kay, Wheatley, Rosalyn, Banerjee, Debasish, Hull, Richard, Abat, Sharirose, Paul, Riny, Karim, Mahzuz, Htet, Zay, Tufail, Saad, Varma, Ravi, Convery, Karen, Fottrell-Gould, Deirdre, Hudig, Lisa, Tropman, Emily, Abdul-Samad, Thahir, Grace, Anne, Phipps, Marie, Suckling, Rebecca, Somalanka, Subash, Sood, Bhrigu, Swift, Pauline, Acheampong, Sarah, Ansu, Kwame, Augustin, Martia, Sampson, Anna, Vinall, Lynn, Wren, Kim, Wanninayake, Shamila, Wooding, Nichola, Edwards, Heather, Owen, Lydia, Bolton, Stephanie, Carson, Marion, Matthews, Michael, Brunskill, Nigel, Jesus-Silva, Jorge, Howson, Alex, Quashie-Akponeware, Mary, Tindall, Hilary, Nethaji, Chidambaram, Eldon, Helen, Patel, Rajan, Mark, Patrick, Rankin, Alastair, Sullivan, Michael, Forsyth, Kirsty, Mcdougall, Rowan, Dasgupta, Tanaji, Davies, Louisa, Ryder, Maggie, Grimmer, Philip, Macdonald, Clare, Webster, Mary, Newcastle, Newcastle, Ellam, Timothy, Wong, Edwin, Meshykhi, Christine, Webster, Andrea, Wilson, Peter, Vilar, Enric, Berdeprado, Jocelyn, Doctolero, Eunice, Wilkinson, Lily, Mccarroll, Frank, Ammar, Hesham, Kuan, Ying, Moran, Conor, Shivashankar, Girish, Campbell, Ryan, Glowski, Deborah, Mcdermott, Paula, Ali, Amar, Patel, Zuber, Bond, Christine, Whalley, Gillian, Zhang, Haitao, Yang, Liu, Zhang, Lihua, Kan, Tingting, Zhu, Ling, Zhao, Jinghong, Hou, Weiping, Wu, Jing, Cheng, Hong, Bian, Weijing, Zhao, Zhirui, Shao, Fengmin, Cao, Huixia, Jiao, Xiaojing, Niu, Peiyuan, Niu, Jianying, Chen, Yu, Zhang, Lihong, Zhu, Shenglang, Lin, Haiyan, Yao, Shaopeng, Chen, Jiehui, Jiang, Ying, Hu, Ying, Xiao, Huaying, Yang, Fuye, Zhang, Xinzhou, Guo, Baochun, Jin, Qiu, Liu, Lixia, Xiao, Xiangcheng, Xie, Yanyun, Meng, Ting, Xu, Chuanwen, Huang, Jie, Xu, Yanmei, Kong, Weixin, Wang, Xiaoliang, Liu, Qianpan, Wang, Xueying, Gao, Ming, Hu, Xiumei, Lu, Ying, Wang, Li, Peng, Kun, Wang, Wei, Gong, Qiuhong, Cai, Jianfang, Li, Xiaojue, Liu, Xuejiao, Zhou, Shuhan, Liu, Hong, Weng, Yao, Tang, Shuai, Yao, Yao, Zhao, Shi, Cheng, Chen, Wei, Wei, Li, Na, Aqashiah Mazlan, Sadanah, Zubaidah Bahtar, Alia, Katiman, Elliyyin, Othman, Noraini, Mushahar, Lily, Mazlan, Nurdiana, Sharafina Safiee, Nur, Ramasamy, Sarasa, Seng Wong, Hin, Ahmad Rosdi, Hajar, Zhao Zhi Tan, Esther, Fan Tay, Ju, Seng Teng, Kok, Yahaya, Hasnah, Jiun Liu, Wen, Wee Ee, Lik, Kay Leong Khoo, Kenneth, Mohd Yusoff, Yuana, Safhan Mohamad Nor, Fariz, Kamil Ahmad, Mohd, Ramli Seman, Mohd, Hui Hong Tan, Clare, Lui Sian Ngu, Laura, Yoke May Chan, Jaime, Peji, Javelin, Loong Loh, Chek, Yan Lee, Yee, Ramanaidu, Sridhar, Mean Thong, Kah, Hong Wong, Yik, Junus, Suria, Hua Ching, Chen, Faisal Asmee, Mohammad, Ruziana Ku Md Razi, Ku, Leong Low, Chun, Sze Bing Sim, Christopher, Duan Tham, Zhang, Kamila Abdullah, Noor, Meng Chen, Tai, Chieh Chan, Yong, Chang, Eason, Yean Kang, Huan, Quan Lee, Kai, Ann Lee, Sue, Kheng Lee, Aik, Vinathan, Jeevika, Abdul Cader, Rizna, Mustafar, Ruslinda, Kamaruzaman, Lydia, Mohd, Rozita, Ismail, Rahimah, Men Leong, Chong, Koon Low, Chee, Wei Wong, Liang, Adnan, Norlezah, Ibrahim, Sabariah, Zaimi Abdul Wahab, Mohamad, Bavanandan, Sunita, Shen Lim, Yik, Hazlina Wan Mohamad, Wan, Munirah Jaafar, Siti, Ashykeen Mohd Fauzi, Nur, Sudin, Aziee, Kun Lim, Soo, Chung Gan, Chye, Hing, Albert, Ahmad Faizal Alaidin Razali, Wan, Fong Liew, Yew, Bao Tyng Chan, Chelsia, Chih Cheng, Mei, Chen Ong, Yu, Meng Ong, Loke, Amalina Mohamed Affandi, Farah, Rahmat, Korina, Chai Peng, Ban, Amat, Masayu, Hadafi Ahmad, Nuzaimin, Yee Mah, Doo, Loon Tye, Yi, Azhari, Zaid, Nabilah Mohamad Zaini, Siti, Aidil Musa, Mohd, Ahmad Miswan, Norazinizah, Ramli, Rafizanur, Aziah Ahmad, Nor, Leong Goh, Bak, Izah Ahmad, Nurul, Huda Ibrahim, Fairol, Jian Ng, Tze, Shanmuganathan, Malini, Lian Tay, Li, Harun, Zaiha, Ramli, Salmi, 'Ain Yusof, Nurul, Abd Rahman, Rossenizal, Iqbal Abdul Hafidz, Muhammad, Hidayati Mohd Sharif, Nur, Yasmoon Awang, Irda, Nakashima, Eitaro, Imamine, Rui, Minatoguchi, Makiko, Miura, Yukari, Nakaoka, Miduki, Suzuki, Yoshiki, Yoshikawa, Hitomi, Shin, Koki, Fujita, Kanae, Iwasa, Misuzu, Sasajima, Haruka, Sato, Airi, Hamamoto, Yoshiyuki, Fujita, Yuki, Haraguchi, Takuya, Hyo, Takanori, Izumi, Kiyohiro, Komiya, Toshiyuki, Kubota, Sodai, Kurose, Takeshi, Kuwata, Hitoshi, Nakatani, Susumu, Oishi, Kaori, Okamoto, Saki, Okamura, Kaori, Takeoka, Jun, Tanaka, Nagaaki, Tanigaki, Katsuya, Toda, Naohiro, Watanabe, Koin, Komori, Hiromi, Kumuji, Rika, Takesada, Asako, Tanaka, Aya, Maruyama, Shoichi, Hasegawa, Tomonori, Ishiguro, Akiko, Ishimoto, Takuji, Ito, Kazuhiro, Kamimura, Yutaka, Kato, Noritoshi, Kato, Sawako, Kojima, Hiroshi, Kosugi, Tomoki, Maeda, Kayaho, Mizuno, Masasi, Saito, Shoji, Sato, Hitomi, Sato, Yuka, Suzuki, Yasuhiro, Tanaka, Akihito, Yasuda, Yoshinari, Hasegawa, Fujiko, Hayashi, Maiko, Higashi, Shizuka, Shimamura, Kaho, Sumi, Momoko, Tajima, Kazuki, Unekawa, Chimaki, Wakayama, Kana, Wakita, Yukiko, Otani, Takatoshi, Imai, Ayako, Kawashima, Sayaka, Kogure, Eri, Sato, Tomoe, Takezawa, Misato, Yoshida, Shinya, Araki, Hideo, Katsuda, Yuko, Konishi, Masahiro, Matsunaga, Takahiro, Oe, Masashi, Ogane, Kunihiro, Sakai, Masato, Takahashi, Tomoko, Yamano, Takahiro, Yokoyama, Takuya, Ito, Hitomi, Katayama, Masayo, Kuroda, Emi, Ikeda, Toru, Kojo, Takuma, Yoshidome, Etsuo, Mizumachi, Rieko, Yamamoto, Akane, Yamasaki, Narihisa, Yamasaki, Yoshihiko, Wada, Jun, Eguchi, Jun, Higuchi, Chigusa, Katayama, Akihiro, Kinomura, Masaru, Kitagawa, Masashi, Kitamura, Shinji, Miyamoto, Satoshi, Morinaga, Hiroshi, Nakatsuka, Atsuko, Nojima, Ichiro, Shikata, Kenichi, Sugiyama, Hitoshi, Tanabe, Katsuyuki, Tsuji, Kenji, Uchida, Haruhito, Watanabe, Mayu, Hashimoto, Chie, Kato, Takahiro, Yamamoto, Sayaka, Wada, Takehiko, Fukagawa, Masafumi, Hamano, Naoto, Koizumi, Masahiro, Komaba, Hirotaka, Nakagawa, Yosuke, Iwamoto, Michiyo, Masutani, Kosuke, Katanosaka, Akane, Kiyota, Mayu, Uchi, Hikari, Ueda, Yuka, Yamamoto, Sonoka, Nagasu, Hajime, Itano, Seiji, Iwakura, Tsukasa, Kadoya, Hiroyuki, Kanda, Eiichiro, Kashihara, Naoki, Kidokoro, Kengo, Kondo, Megumi, Sasaki, Tamaki, Satoh, Minoru, Tokuyama, Atsuyuki, Umeno, Reina, Wada, Yoshihisa, Yamamoto, Toshiya, Yamanouchi, Yu, Abe, Masumi, Inukai, Yoko, Ogawa, Wataru, Asahara, Shunichiro, Fujii, Hideki, Goto, Shunsuke, Hirota, Yushi, Hosooka, Tetsuya, Kono, Keiji, Nishi, Shinichi, Okada, Yuko, Sakaguchi, Kazuhiko, Sugawara, Kenji, Takahashi, Michiko, Takai, Tomoko, Tamori, Yoshikazu, Watanabe, Kentaro, Kitajima, Miyu, Nishi, Misaki, Wada, Junko, Ito, Yasuhiko, Kamiya, Hideki, Asai, Akimasa, Asai, Nao, Asano, Saeko, Banno, Shogo, Ejima, Yohei, Hase, Hanako, Hayami, Tomohide, Himeno, Tatsuhito, Ishikawa, Takahiro, Ito, Mayumi, Iwagaitsu, Shiho, Kasagi, Rina, Kato, Yoshiro, Kato, Makoto, Kato, Koichi, Katsuno, Takayuki, Kawai, Miyuka, Kinashi, Hiroshi, Kondo, Masaki, Koshino, Masako, Matsuoka, Naoya, Morishita, Yoshiaki, Motegi, Mikio, Nakamura, Jiro, Shimoda, Hiromi, Sugiyama, Hirokazu, Tsunekawa, Shin, Yamaguchi, Makoto, Takahashi, Kazuyo, Watada, Hirotaka, Funayama, Takashi, Furukawa, Yasuhiko, Gohda, Tomohito, Goto, Hiromasa, Kaga, Hideyoshi, Kanaguchi, Yasuhiko, Kanazawa, Akio, Kaneko, Kayo, Kano, Toshiki, Kihara, Masao, Kimura, Shogo, Kobayashi, Takashi, Maiguma, Masayuki, Makita, Yuko, Mano, Satoshi, Mita, Tomoya, Miyatsuka, Takeshi, Murakoshi, Maki, Muto, Masahiro, Nakata, Masami, Nakata, Junichiro, Nishida, Yuya, Nohara, Nao, Ogihara, Takeshi, Sato, Daisuke, Sato, Junko, Sato, Hiroaki, Suzuki, Yusuke, Suzuki, Ruka, Suzuki, Hitoshi, Takagi, Miyuki, Tamura, Yoshifumi, Uchida, Toyoyoshi, Ueda, Seiji, Asawa, Miki, Miyaji, Minako, Nagashima, Eri, Shibata, Yoshie, Yanagisawa, Eri, Yamauchi, Toshimasa, Hirakawa, Yosuke, Nishi, Hiroshi, Shojima, Nobuhiro, Horikawa, Satoko, Nakayama, Yukiko, Yamada, Naoko, Omori, Yuki, Yano, Shintaro, Ioka, Miyabi, Kuwabara, Nahoko, Nagano, Remi, Nozawa, Megumi, Osawa, Yumi, Maegawa, Hiroshi, Kume, Shinji, Araki, Shinichi, Miyazawa, Itsuko, Morino, Katsutaro, Kawai, Ikuko, Sobata, Masumi, Takaoka, Motoko, Iwaita, Yasushi, Udagawa, Takashi, Inamori, Ami, Kawase, Aya, Yamanaka, Aya, Shimano, Hitoshi, Fujita, Akiko, Iwasaki, Hitoshi, Kai, Hirayasu, Osaki, Yoshinori, Saito, Chie, Sekiya, Motohiro, Tsunoda, Ryoya, Yamagata, Kunihiro, Nakamura, Rikako, Yamada, Aiko, Ohsugi, Mitsuru, Awazawa, Motoharu, Bouchi, Ryotaro, Hashimoto, Shota, Hashimoto, Makiko, Hisatake, Tomoko, Ihana, Noriko, Ishizuka, Koko, Izumi, Kazuo, Kajio, Hiroshi, Kobayashi, Michi, Kodani, Noriko, Maruyama, Koji, Matsumoto, Michihiro, Matsushita, Maya, Nakamura, Tomoka, Sugiyama, Takehiro, Tanabe, Akiyo, Terakawa, Aiko, Ueki, Kojiro, Orimo, Yuko, Ozawa, Takako, Takahira, Eriko, Yamasaki, Yoshimitsu, Haneda, Masakazu, Tomita, Tadahiro, Akimoto, Saori, Fujimoto, Akihiro, Ishihara, Kenji, Murakami, Chiho, Nishiyama, Akiyo, Toyonaga, Yukiko, Uozumi, Kana, Yamaji, Yukihiro, Shigehara, Tetsuya, Okajyo, Jun, Shimizu, Yukihiro, Iwasaki, Shingo, Fukao, Yuki, Furusho, Megumi, Nunokawa, Shintaro, Katagiri, Hideki, Izumi, Tomohito, Kaneko, Keizo, Kodama, Shinjiro, Miyazaki, Mariko, Munakata, Yuichiro, Nagasawa, Tasuku, Oe, Yuji, Sugawara, Hiroto, Takahashi, Kei, Hirata, Kazushige, Inomata, Keiko, Otomo, Shoko, Uchida, Taeko, Yamashita, Chigusa, Kiyosue, Arihiro, Tamura, Ryota, Dube, Francoi, Bolduc, Marilene, Talbot, Marie-Christine, Cham, Leslie, Lai, Vesta, Tse, Josephine, Jolly, Shivinder, Duck, Tabbatha, Lyle, Scott, Epp, Rachel, Galloway, Camille, Haskett, Susan, Matvienko, Elizabeta, Paulsen, Liam, Moist, Louise, Lozon, Zabrina, Ramsey, Tina, Whitmore, Brittany, Al-Zeer, Bader, Macleod, Paula, O'Sullivan, Aoife, Sheriff, Zainab, Tholl, Sam, Pandey, Amritanshu, Armstrong, Samantha, Gebeyehu, Bethelihem, Toth, Patrick, Goldenberg, Ronald, Jahangiriesmaili, Mahsa, Sanguila, Shariff, Suresh, Neethi, Talsania, Tanvi, Zalunardo, Nadia, Agharazii, Mohsen, Roussel, Marie-Pier, Saillant, Annie, Samson, France, Bajaj, Harpreet, Bhavsar, Miken, Dhall, Parul, Dhillon, Gagandeep, Grewal, Bhupinder, Nimbkar, Taniya, Madore, Francoi, Marcotte, Guylaine, Steen, Oren, Bullen, Mathura, Raguwaran, Shayani, Valleteau, Andre, Langlois, Marie-France, Brown, Christine, Steele, Andrew, Garrity, Melissa, Ghate, Taneera, Robinson, Holly, Tolibas, Michael, Tailor, Chetna, Elliott, Lauren, McClary-Wright, Christine, Boreky, Fadia, Fikry, Sameh, Ali, Ayesha, Barot, Chintankumar, Basily, Wagdy, Saram, Thisun, Varad, Vinay, Khandwala, Hasnain, Aguilera, Alex, Alvarez, Patricia, Gill, Balwinder, Huda, Nazihah, Navivala, Aamir, Pinto, Daniel, Bevilacqua, Micheli, Fung, Elaine, Hernandez, Geraldine, Mann, Puneet, Saini, Jaskiran, Rabasa-Lhoret, Remi, Bovan, Danijela, Devaux, Marie, Barnini, Cecilia, Leoncini, Giovanna, Manco, Luca, Nobili, Giulia, Piemontese, Matteo, Aucella, Filippo, Grifa, Rachele, Totaro, Francesco, La Manna, Gaetano, Capelli, Irene, Cianciolo, Giuseppe, Lerario, Sarah, Zappulo, Fulvia, Rosati, Alberto, Fani, Filippo, Spatoliatore, Giuseppe, Gesualdo, Loreto, Pesce, Francesco, Russo, Maria, Zippo, Maria, Cafiero, Cesira, Motta, Daria, Bianco, Simona, Bilucaglia, Donatella, Messa, Piergiorgio, Pavone, Laura, Tripodi, Federica, Vettoretti, Simone, Fioretto, Paola, Carraro, Gianni, Farnia, Filippo, Postal, Anna, D'Amelio, Alessandro, Cardone, Antonio, Piccinni, Giovanni, Aloisi, Annalisa, Scolari, Francesco, Alberici, Federico, Guerini, Alice, Saccà, Chiara, Salviani, Chiara, Zani, Roberta, DE NICOLA, Luca, Garofalo, Carlo, Elena Liberti, Maria, Minutolo, Roberto, Pennino, Luigi, Polese, Lucio, Mené, Paolo, Barberi, Simona, Falcone, Clorinda, Russo, Francesco, Caroppo, Maurizio, Santorelli, Gennaro, Rivera, Rodolfo, Santoro, Domenico, Giuffrida, Alfio, Zirino, Fortunata, Calvi, Cristina, Estienne, Luca, Gambaro, Giovanni, Gangemi, Concetta, Ortalda, Vittorio, Pessolano, Giuseppina, Grandaliano, Giuseppe, Baccaro, Rocco, Ferraro, Pietro, Mangiacapra, Roberto, Melandri, Marco, Foligno, Nadia, Quartagno, Rita, Vezzoli, Giuseppe, Brioni, Elena, and Group, EMPA-KIDNEY Collaborative

Subjects
chronic renal disease, empagliflozin, empa-kidney, General Medicine
Abstract

Background The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients. Methods We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m2 of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m2 with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to Results A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; PConclusions Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo. (Funded by Boehringer Ingelheim and others; EMPA-KIDNEY ClinicalTrials.gov number, NCT03594110. opens in new tab; EudraCT number, 2017-002971-24. opens in new tab.)

Published
2023

16. Unveiling the Machinery behind Chromosome Folding by Polymer Physics Modeling

Author

Mattia Conte, Andrea Esposito, Francesca Vercellone, Alex Abraham, Simona Bianco, Conte, Mattia, Esposito, Andrea, Vercellone, Francesca, Abraham, Alex, and Bianco, Simona

Subjects
Organic Chemistry, loop-extrusion, General Medicine, polymer physics, phase-separation, Catalysis, Computer Science Applications, Inorganic Chemistry, chromatin architecture, Physical and Theoretical Chemistry, gene regulation, Molecular Biology, Spectroscopy, epigenetic
Abstract

Understanding the mechanisms underlying the complex 3D architecture of mammalian genomes poses, at a more fundamental level, the problem of how two or multiple genomic sites can establish physical contacts in the nucleus of the cells. Beyond stochastic and fleeting encounters related to the polymeric nature of chromatin, experiments have revealed specific, privileged patterns of interactions that suggest the existence of basic organizing principles of folding. In this review, we focus on two major and recently proposed physical processes of chromatin organization: loop-extrusion and polymer phase-separation, both supported by increasing experimental evidence. We discuss their implementation into polymer physics models, which we test against available single-cell super-resolution imaging data, showing that both mechanisms can cooperate to shape chromatin structure at the single-molecule level. Next, by exploiting the comprehension of the underlying molecular mechanisms, we illustrate how such polymer models can be used as powerful tools to make predictions in silico that can complement experiments in understanding genome folding. To this aim, we focus on recent key applications, such as the prediction of chromatin structure rearrangements upon disease-associated mutations and the identification of the putative chromatin organizing factors that orchestrate the specificity of DNA regulatory contacts genome-wide.

Published
2023

18. Controlled Annealing in Adaptive Multicomponent Gels

Author

Paolo Ravarino, Santanu Panja, Simona Bianco, Todor Koev, Matthew Wallace, and Dave J. Adams

Subjects
General Chemistry, General Medicine, Catalysis
Abstract

We use a pH-driven annealing process to convert between co-assembled and self-sorted networks in multicomponent gels. The initially formed gels at low pH are co-assembled, with the two components coexisting within the same self-assembled structures. We use an enzymatic approach to increase the pH, resulting in a gel-to-sol transition, followed by a hydrolysis to lower the pH once again. As the pH decreases, a self-sorted network is formed by a two-stage gelation process determined by the pKa of each component. This approach can be expanded to layered systems to generate many varied systems by changing composition and rates of pH change, adapting their microstructure and so allowing access to a far greater range of morphologies and complexity than can be achieved in single component systems.

Published
2022

19. Polymer models are a versatile tool to study chromatin 3D organization

Author

Andrea Esposito, Andrea M. Chiariello, Alex Abraham, Luca Fiorillo, Francesco Musella, Simona Bianco, Mattia Conte, Antonella Prisco, Mario Nicodemi, Esposito, A., Bianco, S., Fiorillo, L., Conte, M., Abraham, A., Musella, F., Nicodemi, M., Prisco, A., and Chiariello, A. M.

Subjects
Polymers, Computer science, DNA Folding, Inference, Molecular Dynamics Simulation, Models, Biological, Biochemistry, 03 medical and health sciences, 0302 clinical medicine, chromatin architecture, Human–computer interaction, computer simulation, 030304 developmental biology, Structure (mathematical logic), SBS model, 0303 health sciences, Genome, polymer physics, Chromatin, machine learning, Polymer physics, Single-Cell Analysis, phase separation, 030217 neurology & neurosurgery, Genome architecture
Abstract

The development of new experimental technologies is opening the way to a deeper investigation of the three-dimensional organization of chromosomes inside the cell nucleus. Genome architecture is linked to vital functional purposes, yet a full comprehension of the mechanisms behind DNA folding is still far from being accomplished. Theoretical approaches based on polymer physics have been employed to understand the complexity of chromatin architecture data and to unveil the basic mechanisms shaping its structure. Here, we review some recent advances in the field to discuss how Polymer Physics, combined with numerical Molecular Dynamics simulation and Machine Learning based inference, can capture important aspects of genome organization, including the description of tissue-specific structural rearrangements, the detection of novel, regulatory-linked architectural elements and the structural variability of chromatin at the single-cell level.

Published
2021
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20. Macroscopic volume phase transitions in supramolecular gels directed by covalent crosslinking

Author

Bart Dietrich, SANTANU PANJA, Simona Bianco, and Dave Adams

Subjects
Materials Chemistry, General Materials Science
Abstract

Reaction-driven modification of the chemical composition of gels is an interesting approach to synthesize useful materials. Of the different reaction-based systems, crosslinking of the components through the formation of covalent bonds is used to provide mechanical stability to the materials. Here, we show that covalent crosslinking in multicomponent gels can be an effective strategy to synthesize new types of functional materials with spatiotemporal dynamic properties.

Published
2022

21. Physical mechanisms of chromatin spatial organization

Author

Luca Fiorillo, Simona Bianco, Mattia Conte, Francesco Musella, Mario Nicodemi, Alex Abraham, Antonella Prisco, Andrea M. Chiariello, Ehsan Irani, Andrea Esposito, Chiariello, A. M., Bianco, S., Esposito, A., Fiorillo, L., Conte, M., Irani, E., Musella, F., Abraham, A., Prisco, A., and Nicodemi, M.

Subjects
0301 basic medicine, Computational biology, Biology, Models, Biological, Biochemistry, 03 medical and health sciences, Biopolymers, 0302 clinical medicine, chromatin architecture, computer simulation, Molecular Biology, Gene, Spatial organization, Regulation of gene expression, Cell Biology, polymer physics, Chromatin, Folding (chemistry), machine learning, 030104 developmental biology, Gene Expression Regulation, 030220 oncology & carcinogenesis, Mutation, phase separation, active motor
Abstract

In higher eukaryotes, chromosomes have a complex three-dimensional (3D) conformation in the cell nucleus serving vital functional purposes, yet their folding principles remain poorly understood at the single-molecule level. Here, we summarize recent approaches from polymer physics to comprehend the physical mechanisms underlying chromatin architecture. In particular, we focus on two models that have been supported by recent, growing experimental evidence, the Loop Extrusion model and the Strings&Binders phase separation model. We discuss their key ingredients, how they compare to experimental data and some insight they provide on chromatin architecture and gene regulation. Progresses in that research field are opening the possibility to predict how genomic mutations alter the network of contacts between genes and their regulators and how that is linked to genetic diseases, such as congenital disorders and cancer.

Published
2021
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22. Inference of chromosome 3D structures from GAM data by a physics computational approach

Author

Alfonso Corrado, Mattia Conte, Antonella Prisco, Andrea Esposito, Mario Nicodemi, Mariano Barbieri, Andrea M. Chiariello, Ana Pombo, Luca Fiorillo, Carlo Annunziatella, Simona Bianco, Fiorillo, L., Bianco, S., Chiariello, A. M., Barbieri, M., Esposito, A., Annunziatella, C., Conte, M., Corrado, A., Prisco, A., Pombo, A., and Nicodemi, M.

Subjects
Sprite (computer graphics), Polymers, Molecular Conformation, Inference, Whole chromosome, Chromosomes, General Biochemistry, Genetics and Molecular Biology, Mice, 03 medical and health sciences, Chromosome (genetic algorithm), Animals, Statistical Physic, Molecular Biology, 030304 developmental biology, 0303 health sciences, Genome, Physics, 030302 biochemistry & molecular biology, Chromosome Mapping, Experimental data, Mouse Embryonic Stem Cells, SOX9 Transcription Factor, GAM data, Models, Chemical, Genetic Loci, Polymer physics, Algorithm, Genome architecture
Abstract

The combination of modelling and experimental advances can provide deep insights for understanding chromatin 3D organization and ultimately its underlying mechanisms. In particular, models of polymer physics can help comprehend the complexity of genomic contact maps, as those emerging from technologies such as Hi-C, GAM or SPRITE. Here we discuss a method to reconstruct 3D structures from Genome Architecture Mapping (GAM) data, based on PRISMR, a computational approach introduced to find the minimal polymer model best describing Hi-C input data from only polymer physics. After recapitulating the PRISMR procedure, we describe how we extended it for treating GAM data. We successfully test the method on a 6 Mb region around the Sox9 gene and, at a lower resolution, on the whole chromosome 7 in mouse embryonic stem cells. The PRISMR derived 3D structures from GAM co-segregation data are finally validated against independent Hi-C contact maps. The method results to be versatile and robust, hinting that it can be similarly applied to different experimental data, such as SPRITE or microscopy distance data.

Published
2020
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23. Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states

Author

Andrea Esposito, Simona Bianco, Andrea M. Chiariello, Alex Abraham, Luca Fiorillo, Mattia Conte, Raffaele Campanile, Mario Nicodemi, Esposito, A., Bianco, S., Chiariello, A. M., Abraham, A., Fiorillo, L., Conte, M., Campanile, R., and Nicodemi, M.

Subjects
Mammals, Genome, Animal, Polymers, Physics, Chromosome, biophysic, epigenomic, General Biochemistry, Genetics and Molecular Biology, Mammal, Chromatin, Chromosomes, machine learning, chromatin architecture, Cardiovascular and Metabolic Diseases, 3D genome organization, computer simulation, Physic, Animals, CP: Molecular biology, polymer-physic
Abstract

The mammalian genome has a complex, functional 3D organization. However, it remains largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we infer from only Hi-C the cell-type-specific arrangement of DNA binding sites sufficient to recapitulate, through polymer physics, contact patterns genome wide. Our model is validated by its predictions in a set of duplications at Sox9 against available independent data. The binding site types fall in classes that well match chromatin states from segmentation studies, yet they have an overlapping, combinatorial organization along chromosomes necessary to accurately explain contact specificity. The chromatin signatures of the binding site types return a code linking chromatin states to 3D architecture. The code is validated by extensive de novo predictions of Hi-C maps in an independent set of chromosomes. Overall, our results shed light on how 3D information is encrypted in 1D chromatin via the specific combinatorial arrangement of binding sites.

Published
2022

24. Further Delineation of Duplications of ARX Locus Detected in Male Patients with Varying Degrees of Intellectual Disability

Author

Loredana Poeta, Michela Malacarne, Agnese Padula, Denise Drongitis, Lucia Verrillo, Maria Brigida Lioi, Andrea M. Chiariello, Simona Bianco, Mario Nicodemi, Maria Piccione, Emanuela Salzano, Domenico Coviello, Maria Giuseppina Miano, Poeta L., Malacarne M., Padula A., Drongitis D., Verrillo L., Lioi M.B., Chiariello A.M., Bianco S., Nicodemi M., Piccione M., Salzano E., Coviello D., Miano M.G., Poeta, L., Malacarne, M., Padula, A., Drongitis, D., Verrillo, L., Lioi, M. B., Chiariello, A. M., Bianco, S., Nicodemi, M., Piccione, M., Salzano, E., Coviello, D., and Miano, M. G.

Subjects
Male, Transcription Factor, Ultraconserved enhancers, Intellectual disability, 3D structure, Catalysis, Inorganic Chemistry, Mice, Animals, Humans, Physical and Theoretical Chemistry, Child, Molecular Biology, Spectroscopy, Homeodomain Proteins, Animal, KDM5C-SYN1 axi, Organic Chemistry, KDM5C-SYN1 axis, Genes, Homeobox, Homeodomain Protein, General Medicine, Xp21.3 duplication, Computer Science Applications, Ultraconserved enhancer, Settore MED/03 - Genetica Medica, Mutation, ARX, Human, Transcription Factors
Abstract

The X-linked gene encoding aristaless-related homeobox (ARX) is a bi-functional transcription factor capable of activating or repressing gene transcription, whose mutations have been found in a wide spectrum of neurodevelopmental disorders (NDDs); these include cortical malformations, paediatric epilepsy, intellectual disability (ID) and autism. In addition to point mutations, duplications of the ARX locus have been detected in male patients with ID. These rearrangements include telencephalon ultraconserved enhancers, whose structural alterations can interfere with the control of ARX expression in the developing brain. Here, we review the structural features of 15 gain copy-number variants (CNVs) of the ARX locus found in patients presenting wide-ranging phenotypic variations including ID, speech delay, hypotonia and psychiatric abnormalities. We also report on a further novel Xp21.3 duplication detected in a male patient with moderate ID and carrying a fully duplicated copy of the ARX locus and the ultraconserved enhancers. As consequences of this rearrangement, the patient-derived lymphoblastoid cell line shows abnormal activity of the ARX-KDM5C-SYN1 regulatory axis. Moreover, the three-dimensional (3D) structure of the Arx locus, both in mouse embryonic stem cells and cortical neurons, provides new insight for the functional consequences of ARX duplications. Finally, by comparing the clinical features of the 16 CNVs affecting the ARX locus, we conclude that—depending on the involvement of tissue-specific enhancers—the ARX duplications are ID-associated risk CNVs with variable expressivity and penetrance.

Published
2022

25. Further Delineation of Duplications of

Author

Loredana, Poeta, Michela, Malacarne, Agnese, Padula, Denise, Drongitis, Lucia, Verrillo, Maria Brigida, Lioi, Andrea M, Chiariello, Simona, Bianco, Mario, Nicodemi, Maria, Piccione, Emanuela, Salzano, Domenico, Coviello, and Maria Giuseppina, Miano

Subjects
Homeodomain Proteins, Male, Mice, Intellectual Disability, Mutation, Genes, Homeobox, Animals, Humans, Child, Transcription Factors
Abstract

The X-linked gene encoding aristaless-related homeobox (

Published
2022

26. Efficient computational implementation of polymer physics models to explore chromatin structure

Author

Raffaele Campanile, Alfonso Corrado, Luca Fiorillo, Andrea M. Chiariello, Andrea Esposito, Mattia Conte, Maria Gabriella Chiariello, Carlo Annunziatella, Simona Bianco, Conte, M., Esposito, A., Fiorillo, L., Campanile, R., Annunziatella, C., Corrado, A., Chiariello, M. G., Bianco, S., and Chiariello, A. M.

Subjects
Physics, Molecular dynamics, Molecular dynamic, Sprite (lightning), Computer Networks and Communications, Spatial structure, Polymer physics, Biological system, polymer physics, Software, Chromatin, chromatin organization
Abstract

The development of novel experimental technologies able to map genome-wide chromatin contacts, as Hi-C, GAM or SPRITE, allowed to derive detailed information about the spatial structure of chromosomes in the cell nucleus. They revealed that the genome has a complex spatial organisation, which is highly connected with its activity. In the last years, such an abundance of experimental data prompted the development of quantitative models based on Polymer Physics to describe the chromatin architecture, clarifying many aspects about the molecular mechanisms underlying genome folding. Efficient algorithms are thus fundamental to perform massive numerical simulations for testing the accuracy of these models and provide a good description for small genomic regions or for whole chromosomes. Here, we consider the performances of Molecular Dynamics (MD) implementation of commonly used polymer physics models. Such models can be combined with Machine Learning approaches informed with experimental data to produce more accurate descriptions of real genomic regions. However, the execution times increase as a power-law with the size of the input data, which ultimately reflects the complexity of the investigated system. The best strategy is therefore a convenient trade-off between the accuracy in the description and the availability of computational resources. The combination of innovative experimental data and polymer physics theories allow to reconstruct the 3D genome structure. This is achieved by the use of machine learning approaches and massive parallel computing. Efficient algorithms and computational resources are then fundamental to produce models of increasingly high accuracy.

Published
2022

27. A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome

Author

Elena Manara, Luigia Cinque, Orazio Palumbo, Matteo Bertelli, Lucia Micale, Simona Bianco, Mario Nicodemi, Marco Castori, Angelantonio Notarangelo, Maria Grazia Giuffrida, Laura Bernardini, Andrea M. Chiariello, Giulia Guerri, Andrea Esposito, Cinque, L., Micale, L., Manara, E., Esposito, A., Palumbo, O., Chiariello, A. M., Bianco, S., Guerri, G., Bertelli, M., Giuffrida, M. G., Bernardini, L., Notarangelo, A., Nicodemi, M., and Castori, M.

Subjects
Genetics, Chromosome 17 (human), Cardiovascular and Metabolic Diseases, Regulatory sequence, Breakpoint, Locus (genetics), Chromosomal translocation, Biology, Enhancer, Gene, Genetics (clinical), Chromatin
Abstract

Cooks syndrome (CS) is an ultrarare limb malformation due to in tandem microduplications involving KCNJ2 and extending to the 5' regulatory element of SOX9. To date, six CS families were resolved at the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the SOX9-KCNJ2/Sox9-Kcnj2 locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the KCNJ2 locus. On chromosome 17, the breakpoint mapped between KCNJ16 and KCNJ2, and combined with a ~ 5 kb deletion in the 5' of KCNJ2. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated KCNJ2 from a putative enhancer. Gene expression analysis demonstrated downregulation of KCNJ2 in both patient's blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5' of KCNJ2 may mimic the developmental consequences of in tandem duplications affecting the SOX9-KCNJ2/Sox9-Kcnj2 locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.

Published
2022

28. A Polymer Physics Model to Dissect Genome Organization in Healthy and Pathological Phenotypes

Author

Luca Fiorillo, Andrea M. Chiariello, Alex Abraham, Simona Bianco, Francesco Flora, Andrea Esposito, Mattia Conte, Mario Nicodemi, Francesco Musella, Conte, M., Fiorillo, L., Bianco, S., Chiariello, A. M., Esposito, A., Musella, F., Flora, F., Abraham, A., and Nicodemi, M.

Subjects
Pathological phenotype, Computational biology, Biology, Compartmentalization (psychology), Phenotype, Genome organization, Chromatin, Cell nucleus, medicine.anatomical_structure, Architectural pattern, Regulatory sequence, Predictive model, medicine, Polymer physic, Structural variants, Gene, Genomic organization
Abstract

Novel technologies revealed a nontrivial spatial organization of the chromosomes within the cell nucleus, which includes different levels of compartmentalization and architectural patterns. Notably, such complex three-dimensional structure plays a crucial role in vital biological functions and its alterations can produce extensive rewiring of genomic regulatory regions, thus leading to gene misexpression and disease. Here, we show that theoretical and computational approaches, based on polymer physics, can be employed to dissect chromatin contacts in three-dimensional space and to predict the effects of pathogenic structural variants on the genome architecture. In particular, we discuss the folding of the human EPHA4 and the murine Pitx1 loci as case studies.

Published
2022

29. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

Author

Alessa R. Ringel, Quentin Szabo, Andrea M. Chiariello, Konrad Chudzik, Robert Schöpflin, Patricia Rothe, Alexandra L. Mattei, Tobias Zehnder, Dermot Harnett, Verena Laupert, Simona Bianco, Sara Hetzel, Juliane Glaser, Mai H.Q. Phan, Magdalena Schindler, Daniel M. Ibrahim, Christina Paliou, Andrea Esposito, Cesar A. Prada-Medina, Stefan A. Haas, Peter Giere, Martin Vingron, Lars Wittler, Alexander Meissner, Mario Nicodemi, Giacomo Cavalli, Frédéric Bantignies, Stefan Mundlos, Michael I. Robson, Ringel, Alessa R, Szabo, Quentin, Chiariello, Andrea M, Chudzik, Konrad, Schöpflin, Robert, Rothe, Patricia, Mattei, Alexandra L, Zehnder, Tobia, Harnett, Dermot, Laupert, Verena, Bianco, Simona, Hetzel, Sara, Glaser, Juliane, Phan, Mai H Q, Schindler, Magdalena, Ibrahim, Daniel M, Paliou, Christina, Esposito, Andrea, Prada-Medina, Cesar A, Haas, Stefan A, Giere, Peter, Vingron, Martin, Wittler, Lar, Meissner, Alexander, Nicodemi, Mario, Cavalli, Giacomo, Bantignies, Frédéric, Mundlos, Stefan, Robson, Michael I, Centre National de la Recherche Scientifique (France), Université de Montpellier, CINECA, European Research Council, EMBO, Wellcome Trust, and German Research Foundation

Subjects
Cancer Research, CCCTC-Binding Factor, Transcription Factor, Placenta, cohesin, topologically associating domain, General Biochemistry, Genetics and Molecular Biology, Mammal, Evolution, Molecular, Pregnancy, 3D genome organization, evolution, Animals, Promoter Regions, Genetic, Mammals, DNA methylation, loop extrusion, Genome, Topologically associating domains, Animal, CTCF, Chromatin Assembly and Disassembly, Chromatin, enhancer-promoter specificity, Enhancer Elements, Genetic, developmental gene regulation, Cardiovascular and Metabolic Diseases, Lamina-associated domainenhancer-promoter specificityDNA methylationdevelopmental gene regulationevolutionloop extrusioncohesinCTCF3D genome organization, lamina-associated domain, Female, Transcription Factors
Abstract

Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1’s intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42’s unresponsiveness. Rather, Zfp42’s promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes., We thank the Montpellier Ressources Imagerie facility (BioCampus Montpellier, Centre National de la Recherche Scientifique [CNRS], INSERM, University of Montpellier) and for computer resources from CINECA (ISCRA grant thanks to computer resources from INFN and CINECA [ISCRA Grant HP10C8JWU7]). G.C., Q.S., and F.B. were supported by a grant from the European Research Council (Advanced Grant 3DEpi, 788972) and by the CNRS. This work was funded by EMBO and the Wellcome Trust (ALTF1554-2016 and 206475/Z/17/Z; to M.I.R.) as well as the Deutsche Forschungsgemeinschaft (KR3985/7-3 and MU 880/16-1 to S.M.).

Published
2022

30. Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs

Author

Quentin Szabo, M. Phan, Giacomo Cavalli, Cesar Augusto Prada-Medina, Christina Paliou, Sara Hetzel, Michael I. Robson, K. Chudzik, Andrea M. Chiariello, Stephan Haas, Tobias Zehnder, Daniel M. Ibrahim, Alexander Meissner, Andrea Esposito, R. Schoepflin, P. Giere, P. Rothe, Simona Bianco, Martin Vingron, V. Laupert, Dermot Harnett, Stefan Mundlos, Frédéric Bantignies, Alessa R. Ringel, Lars Wittler, Alexandra L. Mattei, Mario Nicodemi, and Magdalena Schindler

Subjects
Regulation of gene expression, History, Polymers and Plastics, Cohesin, Rex1, Promoter, Biology, Industrial and Manufacturing Engineering, Cell biology, Gene expression, DNA methylation, Business and International Management, Enhancer, Psychological repression, Gene
Abstract

SUMMARYCohesin loop extrusion facilitates precise gene expression by continuously driving promoters to sample all enhancers located within the same topologically-associated domain (TAD). However, many TADs contain multiple genes with divergent expression patterns, thereby indicating additional forces further refine how enhancer activities are utilised. Here, we unravel the mechanisms enabling a new gene, Rex1, to emerge with divergent expression within the ancient Fat1 TAD in placental mammals. We show that such divergent expression is not determined by a strict enhancer-promoter compatibility code, intra-TAD position or nuclear envelope-attachment. Instead, TAD-restructuring in embryonic stem cells (ESCs) separates Rex1 and Fat1 with distinct proximal enhancers that independently drive their expression. By contrast, in later embryonic tissues, DNA methylation renders the inactive Rex1 promoter profoundly unresponsive to Fat1 enhancers within the intact TAD. Combined, these features adapted an ancient regulatory landscape during evolution to support two entirely independent Rex1 and Fat1 expression programs. Thus, rather than operating only as rigid blocks of co-regulated genes, TAD-regulatory landscapes can orchestrate complex divergent expression patterns in evolution.HIGHLIGHTSNew genes can emerge in evolution without taking on the expression pattern of their surrounding pre-existing TAD.Compartmentalisation can restructure seemingly evolutionarily stable TADs to control a promoter’s access to enhancers.Lamina-associated domains neither prevent transcriptional activation nor enhancer-promoter communication.Repression rather than promoter-specificity refines when genes respond to promiscuous enhancer activities in specific tissues.

Published
2021
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31. A Polymer Physics Model to Dissect Genome Organization in Healthy and Pathological Phenotypes

Author

Mattia, Conte, Luca, Fiorillo, Simona, Bianco, Andrea M, Chiariello, Andrea, Esposito, Francesco, Musella, Francesco, Flora, Alex, Abraham, and Mario, Nicodemi

Subjects
Mice, Phenotype, Polymers, Physics, Animals, Humans, Chromatin, Chromosomes
Abstract

Novel technologies revealed a nontrivial spatial organization of the chromosomes within the cell nucleus, which includes different levels of compartmentalization and architectural patterns. Notably, such complex three-dimensional structure plays a crucial role in vital biological functions and its alterations can produce extensive rewiring of genomic regulatory regions, thus leading to gene misexpression and disease. Here, we show that theoretical and computational approaches, based on polymer physics, can be employed to dissect chromatin contacts in three-dimensional space and to predict the effects of pathogenic structural variants on the genome architecture. In particular, we discuss the folding of the human EPHA4 and the murine Pitx1 loci as case studies.

Published
2021

32. A novel complex genomic rearrangement affecting the KCNJ2 regulatory region causes a variant of Cooks syndrome

Author

Luigia, Cinque, Lucia, Micale, Elena, Manara, Andrea, Esposito, Orazio, Palumbo, Andrea Maria, Chiariello, Simona, Bianco, Giulia, Guerri, Matteo, Bertelli, Maria Grazia, Giuffrida, Laura, Bernardini, Angelantonio, Notarangelo, Mario, Nicodemi, and Marco, Castori

Subjects
Adult, Gene Rearrangement, Male, Adolescent, Foot Deformities, Congenital, Facies, Regulatory Sequences, Nucleic Acid, Translocation, Genetic, Fingers, Chromosome Breakpoints, Young Adult, Chromosomes, Human, Pair 1, Humans, Female, Potassium Channels, Inwardly Rectifying, Hand Deformities, Congenital, In Situ Hybridization, Fluorescence, Chromosomes, Human, Pair 17, Sequence Deletion
Abstract

Cooks syndrome (CS) is an ultrarare limb malformation due to in tandem microduplications involving KCNJ2 and extending to the 5' regulatory element of SOX9. To date, six CS families were resolved at the molecular level. Subsequent studies explored the evolutionary and pathological complexities of the SOX9-KCNJ2/Sox9-Kcnj2 locus, and suggested a key role for the formation of novel topologically associating domain (TAD) by inter-TAD duplications in causing CS. Here, we report a unique case of CS associated with a de novo 1;17 translocation affecting the KCNJ2 locus. On chromosome 17, the breakpoint mapped between KCNJ16 and KCNJ2, and combined with a ~ 5 kb deletion in the 5' of KCNJ2. Based on available capture Hi-C data, the breakpoint on chromosome 17 separated KCNJ2 from a putative enhancer. Gene expression analysis demonstrated downregulation of KCNJ2 in both patient's blood cells and cultured skin fibroblasts. Our findings suggest that a complex rearrangement falling in the 5' of KCNJ2 may mimic the developmental consequences of in tandem duplications affecting the SOX9-KCNJ2/Sox9-Kcnj2 locus. This finding adds weight to the notion of an intricate role of gene regulatory regions and, presumably, the related three-dimensional chromatin structure in normal and abnormal human morphology.

Published
2021

33. Dynamic and equilibrium properties of finite-size polymer models of chromosome folding

Author

Andrea M. Chiariello, Luca Fiorillo, Francesco Musella, Andrea Esposito, Carlo Annunziatella, Alex Abraham, Mattia Conte, Simona Bianco, Conte, M., Fiorillo, L., Annunziatella, C., Esposito, A., Musella, F., Abraham, A., Bianco, S., and Chiariello, A. M.

Subjects
chemistry.chemical_classification, Physics, Cell Nucleus, Scaling law, Polymers, Polymer, Chromatin, Chromosomes, Folding (chemistry), chemistry, Simple (abstract algebra), Polymer physics, Statistical physics, Scaling
Abstract

Novel technologies are revealing that chromosomes have a complex three-dimensional organization within the cell nucleus that serves functional purposes. Models from polymer physics have been developed to quantitively understand the molecular principles controlling their structure and folding mechanisms. Here, by using massive molecular-dynamics simulations we show that classical scaling laws combined with finite-size effects of a simple polymer model can effectively explain the scaling behavior that chromatin exhibits at the topologically associating domains level, as revealed by experimental observations. Model results are then validated against recently published high-resolution in situ Hi-C data.

Published
2021

34. Polymer physics and machine learning reveal a combinatorial code linking chromatin 3D architecture to 1D epigenetics

Author

Raffaele Campanile, Luca Fiorillo, Andrea M. Chiariello, Andrea Esposito, Alex Abraham, Mario Nicodemi, Mattia Conte, and Simona Bianco

Subjects
business.industry, Machine learning, computer.software_genre, Genome, Chromatin, DNA binding site, Epigenetic Profile, Epigenetics, Artificial intelligence, Binding site, Enhancer, business, Transcription factor, computer
Abstract

The mammalian genome has a complex 3D organization, serving vital functional purposes, yet it remains largely unknown how the multitude of specific DNA contacts, e.g., between transcribed and regulatory regions, is orchestrated by chromatin organizers, such as Transcription Factors. Here, we implement a method combining machine learning and polymer physics to infer from only Hi-C data the genomic 1D arrangement of the minimal set of binding sites sufficient to recapitulate, through only physics, 3D contact patterns genome-wide in human and mouse cells. The inferred binding sites are validated by their predictions on how chromatin refolds in a set of duplications at the Sox9 locus against available independent cHi-C data, showing that their different phenotypes originate from distinct enhancer hijackings in their 3D structure. Albeit derived from only Hi-C, our binding sites fall in epigenetic classes that well match chromatin states from epigenetic segmentation studies, such as active, poised and repressed states. However, the inferred binding domains have an overlapping, combinatorial organization along chromosomes, missing in epigenetic segmentations, which is required to explain Hi-C contact specificity with high accuracy. In a reverse approach, the epigenetic profile of binding domains provides a code to derive from only epigenetic marks the DNA binding sites and, hence, the 3D architecture, as validated by successful predictions of Hi-C matrices in an independent set of chromosomes. Overall, our results shed light on how complex 3D architectural information is encrypted in 1D epigenetics via the related, combinatorial arrangement of specific binding sites along the genome.

Published
2021
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35. CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains

Author

Miao Yu, Bing Ren, Andrea M. Chiariello, Yuanyuan Han, Mattia Conte, Adam Jussila, Yanxiao Zhang, Quan Zhu, Ivan Juric, Xiaowei Zhuang, Hui Huang, Bogdan Bintu, Melodi Tastemel, Ming Hu, Mario Nicodemi, Simona Bianco, Rong Hu, Colin Kern, Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A. M., Yu, M., Hu, R., Tastemel, M., Juric, I., Hu, M., Nicodemi, M., Zhuang, X., and Ren, B.

Subjects
CCCTC-Binding Factor, Transcription, Genetic, Context (language use), Plasma protein binding, Biology, Insulator Element, Article, 03 medical and health sciences, Mice, 0302 clinical medicine, Transcription (biology), Genetics, Animals, Humans, Binding site, Promoter Regions, Genetic, computational data analyses, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Binding Sites, Mouse Embryonic Stem Cells, Mouse Embryonic Stem Cell, Chromatin, Cell biology, Enhancer Elements, Genetic, Gene Expression Regulation, CTCF, Insulator Elements, 030217 neurology & neurosurgery, Function (biology), Human, Protein Binding
Abstract

Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here we explore the sequence requirements of CTCF-mediated transcriptional insulation using a sensitive insulator reporter in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF-binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on upstream flanking sequences at its binding sites. CTCF-binding sites at topologically associating domain boundaries are more likely to function as insulators than those outside topologically associating domain boundaries, independently of binding strength. We demonstrate that insulators form local chromatin domain boundaries and weaken enhancer-promoter contacts. Taken together, our results provide genetic, molecular and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.

Published
2021

36. Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

Author

Andrea M. Chiariello, Mattia Conte, Alexander Kukalev, Simona Bianco, Francesco Musella, Rieke Kempfer, Ana Pombo, Andrea Esposito, Luca Fiorillo, Alex Abraham, Mario Nicodemi, Antonella Prisco, Ibai Irastorza-Azcarate, Fiorillo, L., Musella, F., Conte, M., Kempfer, R., Chiariello, A. M., Bianco, S., Kukalev, A., Irastorza-Azcarate, I., Esposito, A., Abraham, A., Prisco, A., Pombo, A., and Nicodemi, M.

Subjects
Sprite (computer graphics), Computer science, In silico, Computational biology, Biochemistry, Genome, 03 medical and health sciences, Mice, Computer Simulation, Inverse power law, Polymer, Molecular Biology, 030304 developmental biology, 0303 health sciences, Animal, Chromosome Mapping, Cell Biology, Replicate, Chromatin, Single Molecule Imaging, Single-Cell Analysi, Models, Chemical, Cardiovascular and Metabolic Diseases, Benchmark (computing), Genome architecture, Biotechnology, Human
Abstract

Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled, framework against known 3D structures of polymer models of murine and human loci, which can recapitulate Hi-C, GAM and SPRITE experiments and multiplexed fluorescence in situ hybridization (FISH) single-molecule conformations. We find that in silico Hi-C, GAM and SPRITE bulk data are faithful to the reference 3D structures whereas single-cell data reflect strong variability among single molecules. The minimal number of cells required in replicate experiments to return statistically similar contacts is different across the technologies, being lowest in SPRITE and highest in GAM under the same conditions. Noise-to-signal levels follow an inverse power law with detection efficiency and grow with genomic distance differently among the three methods, being lowest in GAM for genomic separations >1 Mb. This Analysis reports a computational approach to implement Hi-C, SPRITE and GAM, which allows researchers to assess the performances of the three technologies to capture DNA contacts in chromatin three-dimensional models.

Published
2021

38. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation

Author

Franz Meitinger, Haruhiko Ishii, Jesse R. Dixon, Simona Bianco, Rong Hu, Bin Li, Huimin Zhao, Xiong Xiong, Mario Nicodemi, Bing Ren, James D. Hocker, Miao Yu, Naoki Kubo, Mattia Conte, David U. Gorkin, Ming Hu, Kubo, N., Ishii, H., Xiong, X., Bianco, S., Meitinger, F., Hu, R., Hocker, J. D., Conte, M., Gorkin, D., Yu, M., Li, B., Dixon, J. R., Hu, M., Nicodemi, M., Zhao, H., and Ren, B.

Subjects
Transcriptional Activation, CCCTC-Binding Factor, Cohesin complex, Article, Cell Line, 03 medical and health sciences, Mice, 0302 clinical medicine, Neural Stem Cells, Structural Biology, Transcription (biology), Animals, Neural Stem Cell, Binding site, Enhancer, Promoter Regions, Genetic, Molecular Biology, computational data analyses, 030304 developmental biology, Regulation of gene expression, 0303 health sciences, Binding Sites, Chemistry, Promoter, Mouse Embryonic Stem Cell, Mouse Embryonic Stem Cells, Chromatin, Cell biology, Enhancer Elements, Genetic, Gene Expression Regulation, CTCF, 030217 neurology & neurosurgery, Protein Binding
Abstract

The CCCTC-binding factor (CTCF) works together with the cohesin complex to drive the formation of chromatin loops and topologically associating domains, but its role in gene regulation has not been fully defined. Here, we investigated the effects of acute CTCF loss on chromatin architecture and transcriptional programs in mouse embryonic stem cells undergoing differentiation to neural precursor cells. We identified CTCF-dependent enhancer-promoter contacts genome-wide and found that they disproportionately affect genes that are bound by CTCF at the promoter and are dependent on long-distance enhancers. Disruption of promoter-proximal CTCF binding reduced both long-range enhancer-promoter contacts and transcription, which were restored by artificial tethering of CTCF to the promoter. Promoter-proximal CTCF binding is correlated with the transcription of over 2,000 genes across a diverse set of adult tissues. Taken together, the results of our study show that CTCF binding to promoters may promote long-distance enhancer-dependent transcription at specific genes in diverse cell types.

Published
2020

39. CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains

Author

Andrea M. Chiariello, Mario Nicodemi, Ivan Juric, Mattia Conte, Yanxiao Zhang, Rong Hu, Ming Hu, Adam Jussila, Bing Ren, Bogdan Bintu, Colin Kern, Yuanyuan Han, Hui Huang, Miao Yu, Simona Bianco, Quan Zhu, and Xiaowei Zhuang

Subjects
Reporter gene, Spatiotemporal gene expression, Chemistry, CTCF, Mammalian genome, Binding site, Embryonic stem cell, DNA sequencing, Cell biology, Chromatin
Abstract

Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on DNA sequences flanking its core binding motifs, and CTCF binding sites at topologically associating domain(TAD) boundaries are more likely to function as insulators than those outside TAD boundaries, independent of binding strength. Using chromosomal conformation capture assays and high-resolution chromatin imaging techniques, we demonstrate that insulators form local chromatin domain boundaries and reduce enhancer-promoter contacts. Taken together, our results provide strong genetic, molecular, and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.

Published
2020
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40. Chromatin folding variability across single-cells results from state degeneracy in phase-separation

Author

Mario Nicodemi, Mattia Conte, Simona Bianco, Andrea Esposito, Luca Fiorillo, and Andrea M. Chiariello

Subjects
chemistry.chemical_compound, Histone, biology, Cohesin, CTCF, Chemistry, biology.protein, Biophysics, Degeneracy (biology), Binding site, Affinities, DNA, Chromatin
Abstract

Chromosome spatial organization controls functional interactions between genes and regulators, yet the molecular and physical mechanisms underlying folding at the single DNA molecule level remain to be understood. Here we employ models of polymer physics to investigate the conformations of two 2Mb-wide DNA loci in human HCT116 and IMR90 wild-type and cohesin depleted cells. Model predictions on the 3D structure of single-molecules are consistently validated against super-resolution single-cell imaging data, providing evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules. The process is driven by interactions between distinct types of cognate binding sites, correlating each with a different combination of chromatin factors, including CTCF, cohesin and histone marks. The intrinsic thermodynamics degeneracy of conformations results in a broad structural and time variability of single-molecules, reflected in their varying TAD-like contact patterns. Globules breathe in time, inducing stochastic unspecific interactions, yet they produce stable, compact environments where specific contacts become highly favored between regions enriched for cognate binding sites, albeit characterized by weak biochemical affinities. Cohesin depletion tends to reverse globule phase separation into a coil, randomly folded state, resulting in much more variable contacts across single-molecules, hence erasing population-averaged patterns. Overall, globule phase separation appears to be a robust, reversible mechanism of chromatin organization, where stochasticity and specificity coexist.

Published
2020
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41. Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

Author

Mark A. Ungless, Izabela Harabula, Sarah A. Teichmann, Georg Dechant, Leonid Serebreni, Mandy Meijer, Vedran Franke, Luna Zea Redondo, Warren Winick-Ng, Andreas Abentung, Aleksandra A. Kolodziejczyk, Gonçalo Castelo-Branco, Rieke Kempfer, Christoph J. Thieme, Francesco Musella, Mario Nicodemi, Alexander Kukalev, Simona Bianco, Ana Pombo, Elena Torlai Triglia, Galina Apostolova, Luca Fiorillo, Eleanor J. Paul, Dominik Szabo, Ehsan Irani, Ibai Irastorza Azcarate, Andrea M. Chiariello, and Altuna Akalin

Subjects
Regulation of gene expression, 0303 health sciences, Cell type, Cellular differentiation, Biology, Genome, Oligodendrocyte, Chromatin, Cell biology, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, medicine, Compartment (development), Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Neurons and oligodendrocytes are terminally differentiated cells that perform highly specialized functions, which depend on cascades of gene activation and repression to retain homeostatic control over a lifespan. Gene expression is regulated by three-dimensional (3D) genome organisation, from local levels of chromatin compaction to the organisation of topological domains and chromosome compartments. Whereas our understanding of 3D genome architecture has vastly increased in the past decade, it remains difficult to study specialized cells in their native environment without disturbing their activity. To develop the application of Genome Architecture Mapping (GAM) in small numbers of specialized cells in complex tissues, we combined GAM with immunoselection. We applied immunoGAM to map the genome architecture of specific cell populations in the juvenile/adult mouse brain: dopaminergic neurons (DNs) from the midbrain, pyramidal glutamatergic neurons (PGNs) from the hippocampus, and oligodendrocyte lineage cells (OLGs) from the cortex. We integrate 3D genome organisation with single-cell transcriptomics data, and find specific chromatin structures that relate with cell-type specific patterns of gene expression. We discover abundant changes in compartment organisation, especially a strengthening of heterochromatin compartments which establish strong contacts spanning tens of megabases, especially in brain cells. These compartments contain olfactory and taste receptor genes, which are de-repressed in a subpopulation of PGNs with molecular signatures of long-term potentiation (LTP). We also show extensive reorganisation of topological domains where activation of neuronal or oligodendrocyte genes coincides with formation of new TAD borders. Finally, we discover loss of TAD organisation, or ‘TAD melting’, at long (>1Mb) neuronal genes when they are most highly expressed. Our work shows that the 3D organisation of the genome is highly cell-type specific in terminally differentiated cells of the brain, and essential to better understand brain-specific mechanisms of gene regulation.

Published
2020
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42. The Physics of DNA Folding: Polymer Models and Phase-Separation

Author

Andrea Esposito, Alex Abraham, Mattia Conte, Francesca Vercellone, Antonella Prisco, Simona Bianco, and Andrea M. Chiariello

Subjects
Polymers and Plastics, General Chemistry
Abstract

Within cell nuclei, several biophysical processes occur in order to allow the correct activities of the genome such as transcription and gene regulation. To quantitatively investigate such processes, polymer physics models have been developed to unveil the molecular mechanisms underlying genome functions. Among these, phase-separation plays a key role since it controls gene activity and shapes chromatin spatial structure. In this paper, we review some recent experimental and theoretical progress in the field and show that polymer physics in synergy with numerical simulations can be helpful for several purposes, including the study of molecular condensates, gene-enhancer dynamics, and the three-dimensional reconstruction of real genomic regions.

Published
2022
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43. CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

Author

Mario Nicodemi, Bijie Ren, Mattia Conte, Xiong Xiong, Rong Hu, Miao Yu, Bin Li, Franz Meitinger, Huimin Zhao, James D. Hocker, Haruhiko Ishii, Dixon, Ming Hu, Naoki Kubo, Simona Bianco, and David U. Gorkin

Subjects
Regulation of gene expression, CTCF, Gene expression, Promoter, Insulator (genetics), Biology, Enhancer, Gene, Cell biology, Chromatin
Abstract

Topologically associating domains (TAD) and insulated neighborhoods (INs) have been proposed to constrain enhancer-promoter communications to enable cell-type specific transcription programs, but recent studies show that disruption of TADs and INs resulted in relatively mild changes in gene expression profiles. To better understand the role of chromatin architecture in dynamic enhancer-promoter contacts and lineage-specific gene expression, we have utilized the auxin-inducible degron system to acutely deplete CTCF, a key factor involved in TADs and IN formation, in mouse embryonic stem cells (mESCs) and examined chromatin architecture and gene regulation during neural differentiation. We find that while CTCF depletion leads to global weakening of TAD boundaries and loss of INs, only a minor fraction of enhancer-promoter contacts are lost, affecting a small subset of genes. The CTCF-dependent enhancer-promoter contacts tend to be long-range, spanning hundreds of kilobases, and are established directly by CTCF binding to promoters. Disruption of CTCF binding at the promoter reduces enhancer-promoter contacts and transcription, while artificial tethering of CTCF to the promoter restores the enhancer-promoter contacts and gene activation. Genome-wide analysis of CTCF binding and gene expression across multiple mouse tissues suggests that CTCF-dependent promoter-enhancer contacts may regulate expression of additional mouse genes, particularly those expressed in the brain. Our results uncover both CTCF-dependent and independent enhancer-promoter contacts, and highlight a distinct role for CTCF in promoting enhancer-promoter contacts and gene activation in addition to its insulator function.

Published
2020
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44. Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions

Author

Andrea M. Chiariello, Simone Serio, Paolo Kunderfranco, Mario Nicodemi, Mattia Conte, Christina Pagiatakis, Arianna Felicetta, Silvia Crasto, Gianluigi Condorelli, Roberto Papait, Elisa Di Pasquale, Paola Cattaneo, Luca Fiorillo, Simona Bianco, Irene Salamon, Salamon, I., Serio, S., Bianco, S., Pagiatakis, C., Crasto, S., Chiariello, A. M., Conte, M., Cattaneo, P., Fiorillo, L., Felicetta, A., di Pasquale, E., Kunderfranco, P., Nicodemi, M., Papait, R., Condorelli, G., Salamon I., Serio S., Bianco S., Pagiatakis C., Crasto S., Chiariello A.M., Conte M., Cattaneo P., Fiorillo L., Felicetta A., di Pasquale E., Kunderfranco P., Nicodemi M., Papait R., and Condorelli G.

Subjects
0301 basic medicine, Polymer Physic, 02 engineering and technology, Article, Statistical Mechanics, 03 medical and health sciences, Transcription (biology), Molecular Mechanism of Gene Regulation, Computer Simulation, Enhancer, lcsh:Science, Gene, Transcription factor, Molecular Biology, Multidisciplinary, biology, Sirtuin 1, Promoter, Biological Science, Biological Sciences, 021001 nanoscience & nanotechnology, Long non-coding RNA, Cell biology, 030104 developmental biology, biology.protein, lcsh:Q, Histone deacetylase, 0210 nano-technology
Abstract

Summary Enhancer RNAs (eRNAs) are a subset of long noncoding RNA generated from genomic enhancers: they are thought to act as potent promoters of the expression of nearby genes through interaction with the transcriptional and epigenomic machineries. In the present work, we describe two eRNAs transcribed from the enhancer of Nkx2-5—a gene specifying a master cardiomyogenic lineage transcription factor (TF)—which we call Intergenic Regulatory Element Nkx2-5 Enhancers (IRENEs). The IRENEs are encoded, respectively, on the same strand (SS) and in the divergent direction (div) respect to the nearby gene. Of note, these two eRNAs have opposing roles in the regulation of Nkx2-5: IRENE-SS acts as a canonical promoter of transcription, whereas IRENE-div represses the activity of the enhancer through recruitment of the histone deacetylase sirtuin 1. Thus, we have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription., Graphical Abstract, Highlights • Two eRNAs (IRENE-SS, IRENE-div) with opposing functions are found upstream of Nkx2-5 • IRENE-SS works as a classical eRNA, acting as a transcriptional activator • IRENE-div acts unconventionally, functioning as a transcriptional repressor • IRENEs epigenetically control enhancer status and, subsequently, locus architecture, Biological Sciences; Molecular Biology; Molecular Mechanism of Gene Regulation

Published
2020

45. Hybrid Machine Learning and Polymer Physics Approach to Investigate 3D Chromatin Structure

Author

Alfonso Corrado, Andrea Esposito, Renato Sciarretta, Carlo Annunziatella, Andrea M. Chiariello, Mattia Conte, Francesco Musella, Simona Bianco, Luca Fiorillo, Conte, M., Esposito, A., Fiorillo, L., Annunziatella, C., Corrado, A., Musella, F., Sciarretta, R., Chiariello, A. M., and Bianco, S.

Subjects
Polymer Physics, 0303 health sciences, Hybrid machine, Computer science, In silico, Chromosome, Locus (genetics), Computational biology, 01 natural sciences, Genome, Chromatin, Machine Learning, 03 medical and health sciences, Cell nucleus, medicine.anatomical_structure, 0103 physical sciences, Chromatin organization, medicine, Polymer physics, 010306 general physics, Genome architecture, 030304 developmental biology
Abstract

Innovative experimental protocols from Molecular Biology provided in recent years quantitative data about the structure of the cell nucleus. These technologies, such as Hi-C, GAM or SPRITE, revealed that the genome has a non-random three-dimensional (3D) spatial organization, which serves functional purposes. In order to dissect the complexity of chromosome folding, models from Polymer Physics have been employed, highlighting many key aspects of large-scale chromatin organization. A deep understanding of the molecular mechanisms underlying the genome architecture is currently a crucial problem in Biology, since chromatin misfolding or structural variants can reconfigure chromatin domains, thereby resulting in pathogenic phenotypes and disease. Here, we discuss a numerical Polymer-Physics-based approach (PRISMR), able to model 3D chromatin folding by using Machine Learning strategies informed with experimental data. Using as a case study the Pitx1 locus, a genomic region critically involved in hindlimb development, we show that the PRISMR algorithm reproduces in silico with high accuracy the experimental contact data, thus providing a powerful computational tool for analyzing and predicting the 3D chromatin structure.

Published
2020

46. Higher-order Chromosome Structures Investigated by Polymer Physics in Cellular Morphogenesis and Differentiation

Author

Luca Fiorillo, Francesco Musella, Mattia Conte, Simona Bianco, Andrea M. Chiariello, Andrea Esposito, Renato Sciarretta, Esposito, A., Chiariello, A. M., Conte, M., Fiorillo, L., Musella, F., Sciarretta, R., and Bianco, S.

Subjects
Macromolecular Substances, Molecular Conformation, Locus (genetics), Computational biology, Biology, Pitx1, Hierarchical folding, 03 medical and health sciences, Mice, 0302 clinical medicine, Structural Biology, Gene expression, Genome architecture, medicine, Animals, Hierarchical organization, Macromolecular Substance, Molecular Biology, Cell Shape, 030304 developmental biology, Epigenomics, Neurons, Regulation of gene expression, Spatial Analysis, 0303 health sciences, Animal, Cell Differentiation, Neuron, Spatial Analysi, Chromatin, medicine.anatomical_structure, Principled approach, Structural variant, Ectopic expression, Forelimb, 030217 neurology & neurosurgery
Abstract

Experimental advances in Molecular Biology demonstrated that chromatin architecture and gene regulation are deeply related. Hi-C data, for instance, returned a scenario where chromosomes form a complex pattern of interactions, including TADs, metaTADs, and compartments, correlated with genomic and epigenomic features. Here, we discuss the emerging hierarchical organization of chromatin and show how it remains partially conserved during mouse neuronal differentiation with changes highly related to modifications in gene expression. In this scenario, models of polymer physics, such as the Strings & Binders (SBS) model, can be a crucial instrument to understand the molecular mechanisms underlying the formation of such a higher order 3D structure. In particular, we focus on the case study of the murine Pitx1 genomic region. At this locus, two alternative spatial conformations take place in the hindlimb and forelimb tissues, corresponding to two different transcriptional states of Pitx1. We finally show how the structural variants can affect the locus 3D organization leading to ectopic gene expression and limb malformations.

Published
2020

47. Computational approaches from polymer physics to investigate chromatin folding

Author

Mario Nicodemi, Mattia Conte, Luca Fiorillo, Andrea M. Chiariello, Francesco Musella, Andrea Esposito, Simona Bianco, Bianco, S., Chiariello, A. M., Conte, M., Esposito, A., Fiorillo, L., Musella, F., and Nicodemi, M.

Subjects
Loop extrusion model, Polymers, Computational biology, Biology, Pitx1, Models, Biological, Chromosomes, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Molecular level, Chromatin organization, Humans, Statistical Physic, 030304 developmental biology, 0303 health sciences, SBS model, bioinformatic, Physics, Computational Biology, Chromosome, Statistical mechanic, systems biology, Cell Biology, Computer simulation, Key features, Cell function, Chromatin, Folding (chemistry), chemistry, Polymer model, Polymer physics, EPHA4, Structural variants, 030217 neurology & neurosurgery, DNA
Abstract

Microscopy and sequencing-based technologies are providing increasing insights into chromatin architecture. Nevertheless, a full comprehension of chromosome folding and its link with vital cell functions is far from accomplished at the molecular level. Recent theoretical and computational approaches are providing important support to experiments to dissect the three-dimensional structure of chromosomes and its organizational mechanisms. Here, we review, in particular, the String&Binders polymer model of chromatin that describes the textbook scenario where contacts between distal DNA sites are established by cognate binders. It has been shown to recapitulate key features of chromosome folding and to be able at predicting how phenotypes causing structural variants rewire the interactions between genes and regulators.

Published
2020

48. A modern challenge of polymer physics: Novel ways to study, interpret, and reconstruct chromatin structure

Author

Andrea M. Chiariello, Francesco Musella, Simona Bianco, Renato Sciarretta, Luca Fiorillo, Andrea Esposito, Mattia Conte, Fiorillo, L., Bianco, S., Esposito, A., Conte, M., Sciarretta, R., Musella, F., and Chiariello, A. M.

Subjects
Physics, chromatin structure, molecular dynamic, Nanotechnology, polymer physics, Biochemistry, Computer Science Applications, Chromatin, Computational Mathematics, Molecular dynamics, Materials Chemistry, Polymer physics, Physical and Theoretical Chemistry, genetic
Abstract

The constant development of sophisticated technologies is allowing to dissect three-dimensional chromatin structure at high resolution level. The tremendous amount of quantitative experimental data available today requires a conceptual framework able to make sense of them. In this perspective, polymer physics offers a key tool to interpret chromatin architecture data and to unveil the basic mechanisms shaping its structure. In the very last years, several polymer models have been proposed and have allowed to capture complex features emerging from the data. The major peculiarity distinguishing the different models is represented by the more or less complicated physical mechanism used to explain chromatin folding. Here, we review very popular models which have been recently developed and which represent brilliant examples from this interdisciplinary research field. In order to highlight the wide range of practical applications they have, we discuss the cases of the murine Pitx1 and the human EPHA4 loci, showing that polymer physics allows to effectively study chromatin structure in different cell lines and to predict the impact of pathogenic structural variants on the genome three-dimensional architecture. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Theoretical and Physical Chemistry > Statistical Mechanics.

Published
2020

49. Publisher Correction: Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin

Author

Ana Pombo, Mattia Conte, Alex Abraham, Antonella Prisco, Rieke Kempfer, Ibai Irastorza-Azcarate, Luca Fiorillo, Francesco Musella, Alexander Kukalev, Simona Bianco, Mario Nicodemi, Andrea Esposito, and Andrea M. Chiariello

Subjects
Physics, Computational model, Sprite (computer graphics), Computational biophysics, Cell Biology, Computational biology, Molecular Biology, Biochemistry, Biotechnology, Chromatin
Published
2021
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50. The Strings and Binders Switch Model of Chromatin

Author

Carlo Annunziatella, Simona Bianco, Luca Fiorillo, Andrea Esposito, Mario Nicodemi, Andrea M. Chiariello, Bianco, Simona, Chiariello, Andrea M., Annunziatella, Carlo, Esposito, Andrea, Fiorillo, Luca, and Nicodemi, Mario

Subjects
Chemistry, Chromatin, Cell biology
Published
2019
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