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4. Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder

Author

Long, Hannah K, Osterwalder, Marco, Welsh, Ian C, Hansen, Karissa, Davies, James OJ, Liu, Yiran E, Koska, Mervenaz, Adams, Alexander T, Aho, Robert, Arora, Neha, Ikeda, Kazuya, Williams, Ruth M, Sauka-Spengler, Tatjana, Porteus, Matthew H, Mohun, Tim, Dickel, Diane E, Swigut, Tomek, Hughes, Jim R, Higgs, Douglas R, Visel, Axel, Selleri, Licia, and Wysocka, Joanna

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Stem Cell Research - Nonembryonic - Human, Congenital Structural Anomalies, Pediatric, Dental/Oral and Craniofacial Disease, Biotechnology, Stem Cell Research, Stem Cell Research - Embryonic - Human, 1.1 Normal biological development and functioning, Cell Differentiation, Humans, Mutation, Neural Crest, Pierre Robin Syndrome, Regulatory Sequences, Nucleic Acid, SOX9 Transcription Factor, Pierre Robin sequence, SOX9, craniofacial, enhancer, enhanceropathy, gene dosage, long-range regulation, neural crest, non-coding mutation, transcription, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.

Published
2020

6. A genome-wide assessment of the ancestral neural crest gene regulatory network.

Author

Hockman, Dorit, Chong-Morrison, Vanessa, Green, Stephen A, Gavriouchkina, Daria, Candido-Ferreira, Ivan, Ling, Irving TC, Williams, Ruth M, Amemiya, Chris T, Smith, Jeramiah J, Bronner, Marianne E, and Sauka-Spengler, Tatjana

Subjects
Neural Crest, Animals, Petromyzon, Homeodomain Proteins, Cell Adhesion Molecules, Transcription Factors, Gene Expression Profiling, Cell Differentiation, Cell Movement, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Transcription Factor AP-2, Gene Regulatory Networks, SOX Transcription Factors, Epigenesis, Genetic, Gene Expression Regulation, Developmental
Abstract

The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.

Published
2019

7. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Ahern, David J, Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M Azim, Arancibia-Cárcamo, Carolina, Aschenbrenner, Dominik, Attar, Moustafa, Baillie, J Kenneth, Barnes, Eleanor, Bashford-Rogers, Rachael, Bashyal, Archana, Beer, Sally, Berridge, Georgina, Beveridge, Amy, Bibi, Sagida, Bicanic, Tihana, Blackwell, Luke, Bowness, Paul, Brent, Andrew, Brown, Andrew, Broxholme, John, Buck, David, Burnham, Katie, Byrne, Helen, Camara, Susana, Ferreira, Ivan Candido, Charles, Philip, Chen, Wentao, Chen, Yi-Ling, Chong, Amanda, Clutterbuck, Elizabeth, Coles, Mark, Conlon, Christopher, Cornall, Richard, Cribbs, Adam, Curion, Fabiola, Davenport, Emma, Davidson, Neil, Davis, Simon, Dendrou, Calliope, Dequaire, Julie, Dib, Lea, Docker, James, Dold, Christina, Dong, Tao, Downes, Damien, Drakesmith, Hal, Dunachie, Susanna, Duncan, David, Eijsbouts, Chris, Esnouf, Robert, Espinosa, Alexis, Etherington, Rachel, Fairfax, Benjamin, Fairhead, Rory, Fang, Hai, Fassih, Shayan, Felle, Sally, Fernandez Mendoza, Maria, Ferreira, Ricardo, Fischer, Roman, Foord, Thomas, Forrow, Aden, Frater, John, Fries, Anastasia, Gallardo Sanchez, Veronica, Garner, Lucy, Geeves, Clementine, Georgiou, Dominique, Godfrey, Leila, Golubchik, Tanya, Gomez Vazquez, Maria, Green, Angie, Harper, Hong, Harrington, Heather, Heilig, Raphael, Hester, Svenja, Hill, Jennifer, Hinds, Charles, Hird, Clare, Ho, Ling-Pei, Hoekzema, Renee, Hollis, Benjamin, Hughes, Jim, Hutton, Paula, Jackson-Wood, Matthew, Jainarayanan, Ashwin, James-Bott, Anna, Jansen, Kathrin, Jeffery, Katie, Jones, Elizabeth, Jostins, Luke, Kerr, Georgina, Kim, David, Klenerman, Paul, Knight, Julian, Kumar, Vinod, Kumar Sharma, Piyush, Kurupati, Prathiba, Kwok, Andrew, Lee, Angela, Linder, Aline, Lockett, Teresa, Lonie, Lorne, Lopopolo, Maria, Lukoseviciute, Martyna, Luo, Jian, Marinou, Spyridoula, Marsden, Brian, Martinez, Jose, Matthews, Philippa, Mazurczyk, Michalina, McGowan, Simon, McKechnie, Stuart, Mead, Adam, Mentzer, Alexander, Mi, Yuxin, Monaco, Claudia, Montadon, Ruddy, Napolitani, Giorgio, Nassiri, Isar, Novak, Alex, O'Brien, Darragh, O'Connor, Daniel, O'Donnell, Denise, Ogg, Graham, Overend, Lauren, Park, Inhye, Pavord, Ian, Peng, Yanchun, Penkava, Frank, Pereira Pinho, Mariana, Perez, Elena, Pollard, Andrew, Powrie, Fiona, Psaila, Bethan, Quan, T Phuong, Repapi, Emmanouela, Revale, Santiago, Silva-Reyes, Laura, Richard, Jean-Baptiste, Rich-Griffin, Charlotte, Ritter, Thomas, Rollier, Christine, Rowland, Matthew, Ruehle, Fabian, Salio, Mariolina, Sansom, Stephen Nicholas, Sanches Peres, Raphael, Santos Delgado, Alberto, Sauka-Spengler, Tatjana, Schwessinger, Ron, Scozzafava, Giuseppe, Screaton, Gavin, Seigal, Anna, Semple, Malcolm, Sergeant, Martin, Simoglou Karali, Christina, Sims, David, Skelly, Donal, Slawinski, Hubert, Sobrinodiaz, Alberto, Sousos, Nikolaos, Stafford, Lizzie, Stockdale, Lisa, Strickland, Marie, Sumray, Otto, Sun, Bo, Taylor, Chelsea, Taylor, Stephen, Taylor, Adan, Thongjuea, Supat, Thraves, Hannah, Todd, John, Tomic, Adriana, Tong, Orion, Trebes, Amy, Trzupek, Dominik, Tucci, Felicia Anna, Turtle, Lance, Udalova, Irina, Uhlig, Holm, van Grinsven, Erinke, Vendrell, Iolanda, Verheul, Marije, Voda, Alexandru, Wang, Guanlin, Wang, Lihui, Wang, Dapeng, Watkinson, Peter, Watson, Robert, Weinberger, Michael, Whalley, Justin, Witty, Lorna, Wray, Katherine, Xue, Luzheng, Yuen Yeung, Hing, Yin, Zixi, Young, Rebecca, Youngs, Jonathan, Zhang, Ping, Zurke, Yasemin-Xiomara, Banning, Adrian, Antonopoulos, Alexios, Bajaj, Amrita, Kelion, Andrew, Deshpande, Aparna, Kardos, Attila, Hudson, Benjamin, Koo, Bon-Kwon, Shirodaria, Cheerag, Xie, Cheng, Kotanidis, Christos, Mahon, Ciara, Berry, Colin, Adlam, David, Newby, David, Connolly, Derek, Scaletta, Diane, Alexander, Donna, Nicol, Ed, McAlindon, Elisa, Oikonomou, Evangelos, Pugliese, Francesca, Pontone, Gianluca, Benedetti, Giulia, He, Guo-Wei, West, Henry, Kondo, Hidekazu, Benedek, Imre, Das, Intrajeet, Deanfield, John, Graby, John, Greenwood, John, Rodrigues, Jonathan, Ge, Junbo, Channon, Keith, Fabritz, Larissa, Fan, Li-Juan, Kingham, Lucy, Guglielmo, Marco, Lyasheva, Maria, Schmitt, Matthias, Beer, Meinrad, Anderson, Michelle, Desai, Milind, Marwan, Mohamed, Takahashi, Naohiko, Mehta, Nehal, Dai, Neng, Screaton, Nicholas, Sabharwal, Nikant, Maurovich-Horvat, Pál, Rao, Praveen, Kotronias, Rafail, Kharbanda, Rajesh, Preston, Rebecca, Wood, Richard, Blankstein, Ron, Rajani, Ronak, Mirsadraee, Saeed, Munir, Shahzad, Thomas, Sheena, Neubauer, Stefan, Klömpken, Steffen, Petersen, Steffen, Achenbach, Stephan, Anthony, Susan, Mak, Sze, Mittal, Tarun, Benedek, Theodora, Sharma, Vinoda, Lin, Wen-Hua, Kotanidis, Christos P, Rodrigues, Jonathan C L, O’Connor, Daniel, Siddique, Muhammad, Lockstone, Helen, Oikonomou, Evangelos K, Badi, Ileana, Lumley, Sheila F, Constantinides, Bede, Sanderson, Nicholas, Rodger, Gillian, Chau, Kevin K, Lodge, Archie, Tsakok, Maria, Gleeson, Fergus, Indrajeet, Das, Hudson, Benjamin J, Srivastava, Vivek, Farid, Shakil, Krasopoulos, George, Sayeed, Rana, Newby, David E, Channon, Keith M, and Antoniades, Charalambos

Published
2022
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9. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Author

Baranasic, Damir, Hörtenhuber, Matthias, Balwierz, Piotr J., Zehnder, Tobias, Mukarram, Abdul Kadir, Nepal, Chirag, Várnai, Csilla, Hadzhiev, Yavor, Jimenez-Gonzalez, Ada, Li, Nan, Wragg, Joseph, D’Orazio, Fabio M., Relic, Dorde, Pachkov, Mikhail, Díaz, Noelia, Hernández-Rodríguez, Benjamín, Chen, Zelin, Stoiber, Marcus, Dong, Michaël, Stevens, Irene, Ross, Samuel E., Eagle, Anne, Martin, Ryan, Obasaju, Oluwapelumi, Rastegar, Sepand, McGarvey, Alison C., Kopp, Wolfgang, Chambers, Emily, Wang, Dennis, Kim, Hyejeong R., Acemel, Rafael D., Naranjo, Silvia, Łapiński, Maciej, Chong, Vanessa, Mathavan, Sinnakaruppan, Peers, Bernard, Sauka-Spengler, Tatjana, Vingron, Martin, Carninci, Piero, Ohler, Uwe, Lacadie, Scott Allen, Burgess, Shawn M., Winata, Cecilia, van Eeden, Freek, Vaquerizas, Juan M., Gómez-Skarmeta, José Luis, Onichtchouk, Daria, Brown, Ben James, Bogdanovic, Ozren, van Nimwegen, Erik, Westerfield, Monte, Wardle, Fiona C., Daub, Carsten O., Lenhard, Boris, and Müller, Ferenc

Published
2022
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10. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Author

Ahern, David J., Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M. Azim, Arancibia-Cárcamo, Carolina V., Aschenbrenner, Dominik, Attar, Moustafa, Baillie, J. Kenneth, Barnes, Eleanor, Bashford-Rogers, Rachael, Bashyal, Archana, Beer, Sally, Berridge, Georgina, Beveridge, Amy, Bibi, Sagida, Bicanic, Tihana, Blackwell, Luke, Bowness, Paul, Brent, Andrew, Brown, Andrew, Broxholme, John, Buck, David, Burnham, Katie L., Byrne, Helen, Camara, Susana, Candido Ferreira, Ivan, Charles, Philip, Chen, Wentao, Chen, Yi-Ling, Chong, Amanda, Clutterbuck, Elizabeth A., Coles, Mark, Conlon, Christopher P., Cornall, Richard, Cribbs, Adam P., Curion, Fabiola, Davenport, Emma E., Davidson, Neil, Davis, Simon, Dendrou, Calliope A., Dequaire, Julie, Dib, Lea, Docker, James, Dold, Christina, Dong, Tao, Downes, Damien, Drakesmith, Hal, Dunachie, Susanna J., Duncan, David A., Eijsbouts, Chris, Esnouf, Robert, Espinosa, Alexis, Etherington, Rachel, Fairfax, Benjamin, Fairhead, Rory, Fang, Hai, Fassih, Shayan, Felle, Sally, Fernandez Mendoza, Maria, Ferreira, Ricardo, Fischer, Roman, Foord, Thomas, Forrow, Aden, Frater, John, Fries, Anastasia, Gallardo Sanchez, Veronica, Garner, Lucy C., Geeves, Clementine, Georgiou, Dominique, Godfrey, Leila, Golubchik, Tanya, Gomez Vazquez, Maria, Green, Angie, Harper, Hong, Harrington, Heather A., Heilig, Raphael, Hester, Svenja, Hill, Jennifer, Hinds, Charles, Hird, Clare, Ho, Ling-Pei, Hoekzema, Renee, Hollis, Benjamin, Hughes, Jim, Hutton, Paula, Jackson-Wood, Matthew A., Jainarayanan, Ashwin, James-Bott, Anna, Jansen, Kathrin, Jeffery, Katie, Jones, Elizabeth, Jostins, Luke, Kerr, Georgina, Kim, David, Klenerman, Paul, Knight, Julian C., Kumar, Vinod, Kumar Sharma, Piyush, Kurupati, Prathiba, Kwok, Andrew, Lee, Angela, Linder, Aline, Lockett, Teresa, Lonie, Lorne, Lopopolo, Maria, Lukoseviciute, Martyna, Luo, Jian, Marinou, Spyridoula, Marsden, Brian, Martinez, Jose, Matthews, Philippa C., Mazurczyk, Michalina, McGowan, Simon, McKechnie, Stuart, Mead, Adam, Mentzer, Alexander J., Mi, Yuxin, Monaco, Claudia, Montadon, Ruddy, Napolitani, Giorgio, Nassiri, Isar, Novak, Alex, O'Brien, Darragh P., O'Connor, Daniel, O'Donnell, Denise, Ogg, Graham, Overend, Lauren, Park, Inhye, Pavord, Ian, Peng, Yanchun, Penkava, Frank, Pereira Pinho, Mariana, Perez, Elena, Pollard, Andrew J., Powrie, Fiona, Psaila, Bethan, Quan, T. Phuong, Repapi, Emmanouela, Revale, Santiago, Silva-Reyes, Laura, Richard, Jean-Baptiste, Rich-Griffin, Charlotte, Ritter, Thomas, Rollier, Christine S., Rowland, Matthew, Ruehle, Fabian, Salio, Mariolina, Sansom, Stephen Nicholas, Sanches Peres, Raphael, Santos Delgado, Alberto, Sauka-Spengler, Tatjana, Schwessinger, Ron, Scozzafava, Giuseppe, Screaton, Gavin, Seigal, Anna, Semple, Malcolm G., Sergeant, Martin, Simoglou Karali, Christina, Sims, David, Skelly, Donal, Slawinski, Hubert, Sobrinodiaz, Alberto, Sousos, Nikolaos, Stafford, Lizzie, Stockdale, Lisa, Strickland, Marie, Sumray, Otto, Sun, Bo, Taylor, Chelsea, Taylor, Stephen, Taylor, Adan, Thongjuea, Supat, Thraves, Hannah, Todd, John A., Tomic, Adriana, Tong, Orion, Trebes, Amy, Trzupek, Dominik, Tucci, Felicia Anna, Turtle, Lance, Udalova, Irina, Uhlig, Holm, van Grinsven, Erinke, Vendrell, Iolanda, Verheul, Marije, Voda, Alexandru, Wang, Guanlin, Wang, Lihui, Wang, Dapeng, Watkinson, Peter, Watson, Robert, Weinberger, Michael, Whalley, Justin, Witty, Lorna, Wray, Katherine, Xue, Luzheng, Yeung, Hing Yuen, Yin, Zixi, Young, Rebecca K., Youngs, Jonathan, Zhang, Ping, and Zurke, Yasemin-Xiomara

Published
2022
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11. The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

Author

Smith, Jeramiah J, Timoshevskaya, Nataliya, Ye, Chengxi, Holt, Carson, Keinath, Melissa C, Parker, Hugo J, Cook, Malcolm E, Hess, Jon E, Narum, Shawn R, Lamanna, Francesco, Kaessmann, Henrik, Timoshevskiy, Vladimir A, Waterbury, Courtney KM, Saraceno, Cody, Wiedemann, Leanne M, Robb, Sofia MC, Baker, Carl, Eichler, Evan E, Hockman, Dorit, Sauka-Spengler, Tatjana, Yandell, Mark, Krumlauf, Robb, Elgar, Greg, and Amemiya, Chris T

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research - Nonembryonic - Non-Human, Human Genome, Prevention, Stem Cell Research, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Cellular Reprogramming, Chromatin Assembly and Disassembly, Evolution, Molecular, Genome, Germ Cells, Mutagenesis, Petromyzon, Vertebrates, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by polycomb repressive complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys' unique biology and evolutionary/comparative perspective.

Published
2018

12. A blood-based miRNA signature with prognostic value for overall survival in advanced stage non-small cell lung cancer treated with immunotherapy

Author

Rajakumar, Timothy, Horos, Rastislav, Jehn, Julia, Schenz, Judith, Muley, Thomas, Pelea, Oana, Hofmann, Sarah, Kittner, Paul, Kahraman, Mustafa, Heuvelman, Marco, Sikosek, Tobias, Feufel, Jennifer, Skottke, Jasmin, Nötzel, Dennis, Hinkfoth, Franziska, Tikk, Kaja, Daniel-Moreno, Alberto, Ceiler, Jessika, Mercaldo, Nathaniel, Uhle, Florian, Uhle, Sandra, Weigand, Markus A., Elshiaty, Mariam, Lusky, Fabienne, Schindler, Hannah, Ferry, Quentin, Sauka-Spengler, Tatjana, Wu, Qianxin, Rabe, Klaus F., Reck, Martin, Thomas, Michael, Christopoulos, Petros, and Steinkraus, Bruno R.

Published
2022
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15. Chromatin remodeller Chd7 is developmentally regulated in the neural crest by tissue-specific transcription factors.

Author

Williams, Ruth M., Taylor, Guneş, Ling, Irving T. C., Candido-Ferreira, Ivan, Fountain, Daniel M., Mayes, Sarah, Ateş-Kalkan, Perihan Seda, Haug, Julianna O., Price, Andrew J., McKinney, Sean A., Bozhilovh, Yavor K., Tyser, Richard C. V., Srinivas, Shankar, Hughes, Jim R., and Sauka-Spengler, Tatjana

Subjects
DNA-binding proteins, TRANSCRIPTION factors, NEURAL crest, GENE regulatory networks, DNA helicases
Abstract

Neurocristopathies such as CHARGE syndrome result from aberrant neural crest development. A large proportion of CHARGE cases are attributed to pathogenic variants in the gene encoding CHD7, chromodomain helicase DNA binding protein 7, which remodels chromatin. While the role for CHD7 in neural crest development is well documented, how this factor is specifically up-regulated in neural crest cells is not understood. Here, we use epigenomic profiling of chick and human neural crest to identify a cohort of enhancers regulating Chd7 expression in neural crest cells and other tissues. We functionally validate upstream transcription factor binding at candidate enhancers, revealing novel epistatic relationships between neural crest master regulators and Chd7, showing tissue-specific regulation of a globally acting chromatin remodeller. Furthermore, we find conserved enhancer features in human embryonic epigenomic data and validate the activity of the human equivalent CHD7 enhancers in the chick embryo. Our findings embed Chd7 in the neural crest gene regulatory network and offer potentially clinically relevant elements for interpreting CHARGE syndrome cases without causative allocation. CHARGE syndrome results from aberrant neural crest development, affecting eye, heart, and facial structures, and has been attributed to pathogenic variants of the chromatin remodeler CHD7. This study characterizes the enhancers and tissue specific transcription factors that regulate Chd7 expression in the developing chick and human neural crest. [ABSTRACT FROM AUTHOR]

Published
2024
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18. Genetic dissection of the α-globin super-enhancer in vivo

Author

Hay, Deborah, Hughes, Jim R, Babbs, Christian, Davies, James OJ, Graham, Bryony J, Hanssen, Lars LP, Kassouf, Mira T, Oudelaar, A Marieke, Sharpe, Jacqueline A, Suciu, Maria C, Telenius, Jelena, Williams, Ruth, Rode, Christina, Li, Pik-Shan, Pennacchio, Len A, Sloane-Stanley, Jacqueline A, Ayyub, Helena, Butler, Sue, Sauka-Spengler, Tatjana, Gibbons, Richard J, Smith, Andrew JH, Wood, William G, and Higgs, Douglas R

Subjects
Biological Sciences, Genetics, Rare Diseases, 5.2 Cellular and gene therapies, Generic health relevance, Animals, Chromatin, Embryo, Mammalian, Enhancer Elements, Genetic, Erythroid Cells, Gene Expression Regulation, Mice, Mice, Knockout, Transcription Factors, Transcription, Genetic, alpha-Globins, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. These super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.

Published
2016

29. Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies

Author

Hellner, Karin, Miranda, Fabrizio, Fotso Chedom, Donatien, Herrero-Gonzalez, Sandra, Hayden, Daniel M., Tearle, Rick, Artibani, Mara, Carrami, Eli M., Williams, Ruth, Gaitskell, Kezia, Elorbany, Samar, Xu, Ruoyan, Laios, Alex, Buiga, Petronela, Ahmed, Karim, Dhar, Sunanda, Zhang, Rebecca Yu, Campo, Leticia, Myers, Kevin A., Lozano, María, Ruiz-Miró, María, Gatius, Sónia, Mota, Alba, Moreno-Bueno, Gema, Matias-Guiu, Xavier, Benítez, Javier, Witty, Lorna, McVean, Gil, Leedham, Simon, Tomlinson, Ian, Drmanac, Radoje, Cazier, Jean-Baptiste, Klein, Robert, Dunne, Kevin, Bast, Robert C., Jr, Kennedy, Stephen H., Hassan, Bassim, Lise, Stefano, Garcia, María José, Peters, Brock A., Yau, Christopher, Sauka-Spengler, Tatjana, and Ahmed, Ahmed Ashour

Published
2016
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30. Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair

Author

Simões, Filipa C., Cahill, Thomas J., Kenyon, Amy, Gavriouchkina, Daria, Vieira, Joaquim M., Sun, Xin, Pezzolla, Daniela, Ravaud, Christophe, Masmanian, Eva, Weinberger, Michael, Mayes, Sarah, Lemieux, Madeleine E., Barnette, Damien N., Gunadasa-Rohling, Mala, Williams, Ruth M., Greaves, David R., Trinh, Le A., Fraser, Scott E., Dallas, Sarah L., Choudhury, Robin P., Sauka-Spengler, Tatjana, and Riley, Paul R.

Published
2020
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35. The SWI/SNF Complex in Neural Crest Cell Development and Disease.

Author

Fountain, Daniel M. and Sauka-Spengler, Tatjana

Abstract

While the neural crest cell population gives rise to an extraordinary array of derivatives, including elements of the craniofacial skeleton, skin pigmentation, and peripheral nervous system, it is today increasingly recognized that Schwann cell precursors are also multipotent. Two mammalian paralogs of the SWI/SNF (switch/sucrose nonfermentable) chromatin-remodeling complexes, BAF (Brg1-associated factors) and PBAF (polybromo-associated BAF), are critical for neural crest specification during normal mammalian development. There is increasing evidence that pathogenic variants in components of the BAF and PBAF complexes play central roles in the pathogenesis of neural crest–derived tumors. Transgenic mouse models demonstrate a temporal window early in development where pathogenic variants in Smarcb1 result in the formation of aggressive, poorly differentiated tumors, such as rhabdoid tumors. By contrast, later in development, homozygous inactivation of Smarcb1 requires additional pathogenic variants in tumor suppressor genes to drive the development of differentiated adult neoplasms derived from the neural crest, which have a comparatively good prognosis in humans. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Kotanidis, Christos P, primary, Xie, Cheng, additional, Alexander, Donna, additional, Rodrigues, Jonathan C L, additional, Burnham, Katie, additional, Mentzer, Alexander, additional, O’Connor, Daniel, additional, Knight, Julian, additional, Siddique, Muhammad, additional, Lockstone, Helen, additional, Thomas, Sheena, additional, Kotronias, Rafail, additional, Oikonomou, Evangelos K, additional, Badi, Ileana, additional, Lyasheva, Maria, additional, Shirodaria, Cheerag, additional, Lumley, Sheila F, additional, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Chau, Kevin K, additional, Lodge, Archie, additional, Tsakok, Maria, additional, Gleeson, Fergus, additional, Adlam, David, additional, Rao, Praveen, additional, Indrajeet, Das, additional, Deshpande, Aparna, additional, Bajaj, Amrita, additional, Hudson, Benjamin J, additional, Srivastava, Vivek, additional, Farid, Shakil, additional, Krasopoulos, George, additional, Sayeed, Rana, additional, Ho, Ling-Pei, additional, Neubauer, Stefan, additional, Newby, David E, additional, Channon, Keith M, additional, Deanfield, John, additional, Antoniades, Charalambos, additional, Ahern, David J, additional, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M Azim, additional, Arancibia-Cárcamo, Carolina, additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Byrne, Helen, additional, Camara, Susana, additional, Ferreira, Ivan Candido, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth, additional, Coles, Mark, additional, Conlon, Christopher, additional, Cornall, Richard, additional, Cribbs, Adam, additional, Curion, Fabiola, additional, Davenport, Emma, additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope, additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna, additional, Duncan, David, additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy, additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather, additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew, additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa, additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh, additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew, additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine, additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm, additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John, additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yuen Yeung, Hing, additional, Yin, Zixi, additional, Young, Rebecca, additional, Youngs, Jonathan, additional, Zhang, Ping, additional, Zurke, Yasemin-Xiomara, additional, Banning, Adrian, additional, Antonopoulos, Alexios, additional, Kelion, Andrew, additional, Kardos, Attila, additional, Hudson, Benjamin, additional, Koo, Bon-Kwon, additional, Kotanidis, Christos, additional, Mahon, Ciara, additional, Berry, Colin, additional, Newby, David, additional, Connolly, Derek, additional, Scaletta, Diane, additional, Nicol, Ed, additional, McAlindon, Elisa, additional, Oikonomou, Evangelos, additional, Pugliese, Francesca, additional, Pontone, Gianluca, additional, Benedetti, Giulia, additional, He, Guo-Wei, additional, West, Henry, additional, Kondo, Hidekazu, additional, Benedek, Imre, additional, Das, Intrajeet, additional, Graby, John, additional, Greenwood, John, additional, Rodrigues, Jonathan, additional, Ge, Junbo, additional, Channon, Keith, additional, Fabritz, Larissa, additional, Fan, Li-Juan, additional, Kingham, Lucy, additional, Guglielmo, Marco, additional, Schmitt, Matthias, additional, Beer, Meinrad, additional, Anderson, Michelle, additional, Desai, Milind, additional, Marwan, Mohamed, additional, Takahashi, Naohiko, additional, Mehta, Nehal, additional, Dai, Neng, additional, Screaton, Nicholas, additional, Sabharwal, Nikant, additional, Maurovich-Horvat, Pál, additional, Kharbanda, Rajesh, additional, Preston, Rebecca, additional, Wood, Richard, additional, Blankstein, Ron, additional, Rajani, Ronak, additional, Mirsadraee, Saeed, additional, Munir, Shahzad, additional, Klömpken, Steffen, additional, Petersen, Steffen, additional, Achenbach, Stephan, additional, Anthony, Susan, additional, Mak, Sze, additional, Mittal, Tarun, additional, Benedek, Theodora, additional, Sharma, Vinoda, additional, and Lin, Wen-Hua, additional

Published
2022
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41. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Author

European Commission, Agencia Estatal de Investigación (España), Baranasic, Damir, Hörtenhuber, Matthias, Balwierz, Piotr J., Zehnder, Tobias, Mukarram, Abdul Kadir, Nepal, Chirag, Várnai, Csilla, Hadzhiev, Yavor, Jiménez-González, Ada, Li, Nan, Wragg, Joseph, D’Orazio, Fabio M., Relic, Dorde, Pachkov, Mikhail, Díaz, Noelia, Hernández-Rodríguez, Benjamín, Chen, Zelin, Stoiber, Marcus, Dong, Michaël, Stevens, Irene, Ross, Samuel E., Eagle, Anne, Martin, Ryan, Obasaju, Oluwapelumi, Rastegar, Sepand, McGarvey, Alison C., Kopp, Wolfgang, Chambers, Emily, Wang, Dennis, Kim, Hyejeong R., Acemel, Rafael D., Naranjo, Silvia, Łapiński, Maciej, Chong, Vanessa, Mathavan, Sinnakaruppan, Peers, Bernard, Sauka-Spengler, Tatjana, Vingron, Martin, Carninci, Piero, Ohler, Uwe, Lacadie, Scott Allen, Burgess, Shawn M., Winata, Cecilia, Eeden, Freek van, Vaquerizas Erdocia, Juan Manuel, Gómez-Skarmeta, José Luis, Onichtchouk, Daria, Brown, Ben James, Bogdanovic, Ozren, Nimwegen, Erik van, Westerfield, Monte, Wardle, Fiona C., Daub, Carsten O., Lenhard, Boris, Müller, Ferenc, European Commission, Agencia Estatal de Investigación (España), Baranasic, Damir, Hörtenhuber, Matthias, Balwierz, Piotr J., Zehnder, Tobias, Mukarram, Abdul Kadir, Nepal, Chirag, Várnai, Csilla, Hadzhiev, Yavor, Jiménez-González, Ada, Li, Nan, Wragg, Joseph, D’Orazio, Fabio M., Relic, Dorde, Pachkov, Mikhail, Díaz, Noelia, Hernández-Rodríguez, Benjamín, Chen, Zelin, Stoiber, Marcus, Dong, Michaël, Stevens, Irene, Ross, Samuel E., Eagle, Anne, Martin, Ryan, Obasaju, Oluwapelumi, Rastegar, Sepand, McGarvey, Alison C., Kopp, Wolfgang, Chambers, Emily, Wang, Dennis, Kim, Hyejeong R., Acemel, Rafael D., Naranjo, Silvia, Łapiński, Maciej, Chong, Vanessa, Mathavan, Sinnakaruppan, Peers, Bernard, Sauka-Spengler, Tatjana, Vingron, Martin, Carninci, Piero, Ohler, Uwe, Lacadie, Scott Allen, Burgess, Shawn M., Winata, Cecilia, Eeden, Freek van, Vaquerizas Erdocia, Juan Manuel, Gómez-Skarmeta, José Luis, Onichtchouk, Daria, Brown, Ben James, Bogdanovic, Ozren, Nimwegen, Erik van, Westerfield, Monte, Wardle, Fiona C., Daub, Carsten O., Lenhard, Boris, and Müller, Ferenc

Abstract

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals

Published
2022

47. A blood-based miRNA signature predicts immunotherapy efficacy in advanced stage non-small cell lung cancer

Author

Rajakumar, Timothy, primary, Horos, Rastislav, additional, Jehn, Julia, additional, Schenz, Judith, additional, Muley, Thomas, additional, Pelea, Oana, additional, Hofmann, Sarah, additional, Kittneer, Paul, additional, Kahraman, Mustafa, additional, Heuvelman, Marco, additional, Sikosek, Tobias, additional, Feufel, Jennifer, additional, Skottke, Jasmin, additional, Noetzel, Dennis, additional, Hinkfoth, Franziska, additional, Tikk, Kaja, additional, Daniel-Moreno, Alberto, additional, Ceiler, Jessika, additional, Mercaldo, Nathaniel, additional, Uhle, Florian, additional, Uhle, Sandra, additional, Weigand, Markus A, additional, Elshiaty, Mariam, additional, Lusky, Fabienne, additional, Schindler, Hannah, additional, Ferry, Quentin, additional, Sauka-Spengler, Tatjana, additional, Wu, Qianxin, additional, Rabe, Klaus F, additional, Reck, Martin, additional, Thomas, Michael, additional, Christopoulos, Petros, additional, and Steinkraus, Bruno R, additional

Published
2021
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48. Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

Author

Smith, Jeramiah J., Timoshevskaya, Nataliya, Ye, Chengxi, Holt, Carson, Keinath, Melissa C., Parker, Hugo J., Cook, Malcolm E., Hess, Jon E., Narum, Shawn R., Lamanna, Francesco, Kaessmann, Henrik, Timoshevskiy, Vladimir A., Waterbury, Courtney K. M., Saraceno, Cody, Wiedemann, Leanne M., Robb, Sofia M. C., Baker, Carl, Eichler, Evan E., Hockman, Dorit, Sauka-Spengler, Tatjana, Yandell, Mark, Krumlauf, Robb, Elgar, Greg, and Amemiya, Chris T.

Published
2018
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50. Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish

Author

Baranasic, Damir, primary, Hörtenhuber, Matthias, additional, Balwierz, Piotr, additional, Zehnder, Tobias, additional, Mukarram, Abdul Kadir, additional, Nepal, Chirag, additional, Varnai, Csilla, additional, Hadzhiev, Yavor, additional, Jimenez-Gonzalez, Ada, additional, Li, Nan, additional, Wragg, Joseph, additional, D’Orazio, Fabio, additional, Díaz, Noelia, additional, Hernández-Rodríguez, Benjamín, additional, Chen, Zelin, additional, Stoiber, Marcus, additional, Dong, Michaël, additional, Stevens, Irene, additional, Ross, Samuel E., additional, Eagle, Anne, additional, Martin, Ryan, additional, Obasaju, Pelumi, additional, Rastegar, Sepand, additional, McGarvey, Alison C., additional, Kopp, Wolfgang, additional, Chambers, Emily, additional, Wang, Dennis, additional, Kim, Hyejeong R., additional, Acemel, Rafael D., additional, Naranjo, Silvia, additional, Lapinski, Maciej, additional, Chong, Vanessa, additional, Mathavan, Sinnakaruppan, additional, Peers, Bernard, additional, Sauka-Spengler, Tatjana, additional, Vingron, Martin, additional, Carninci, Piero, additional, Ohler, Uwe, additional, Lacadie, Scott Allen, additional, Burgess, Shawn, additional, Winata, Cecilia, additional, van Eeden, Freek, additional, Vaquerizas, Juan M., additional, Gómez-Skarmeta, José Luis, additional, Onichtchouk, Daria, additional, Brown, Ben James, additional, Bogdanovic, Ozren, additional, Westerfield, Monte, additional, Wardle, Fiona C., additional, Daub, Carsten O., additional, Lenhard, Boris, additional, and Müller, Ferenc, additional

Published
2021
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