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222 results on '"Mirny, Leonid A."'

6. The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data

Author

Reiff, Sarah B., Schroeder, Andrew J., Kırlı, Koray, Cosolo, Andrea, Bakker, Clara, Lee, Soohyun, Veit, Alexander D., Balashov, Alexander K., Vitzthum, Carl, Ronchetti, William, Pitman, Kent M., Johnson, Jeremy, Ehmsen, Shannon R., Kerpedjiev, Peter, Abdennur, Nezar, Imakaev, Maxim, Öztürk, Serkan Utku, Çamoğlu, Uğur, Mirny, Leonid A., Gehlenborg, Nils, Alver, Burak H., and Park, Peter J.

Published
2022
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7. Spatial organization of transcribed eukaryotic genes

Author

Leidescher, Susanne, Ribisel, Johannes, Ullrich, Simon, Feodorova, Yana, Hildebrand, Erica, Galitsyna, Alexandra, Bultmann, Sebastian, Link, Stephanie, Thanisch, Katharina, Mulholland, Christopher, Dekker, Job, Leonhardt, Heinrich, Mirny, Leonid, and Solovei, Irina

Published
2022
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12. A pathway for mitotic chromosome formation

Author

Gibcus, Johan H., Samejima, Kumiko, Goloborodko, Anton, Samejima, Itaru, Naumova, Natalia, Nuebler, Johannes, Kanemaki, Masato T., Xie, Linfeng, Paulson, James R., Earnshaw, William C., Mirny, Leonid A., and Dekker, Job

Published
2018

19. Two independent modes of chromatin organization revealed by cohesin removal

Author

Schwarzer, Wibke, Abdennur, Nezar, Goloborodko, Anton, Pekowska, Aleksandra, Fudenberg, Geoffrey, Loe-Mie, Yann, Fonseca, Nuno A, Huber, Wolfgang, H. Haering, Christian, Mirny, Leonid, and Spitz, Francois

Subjects
Epigenetic inheritance -- Observations, Chromatin -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes. By contrast, compartmental segregation is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the three-dimensional organization of the genome results from the interplay of two independent mechanisms: cohesin-independent segregation of the genome into fine-scale compartments, defined by chromatin state; and cohesin-dependent formation of TADs, possibly by loop extrusion, which helps to guide distant enhancers to their target genes., Author(s): Wibke Schwarzer [1]; Nezar Abdennur [2]; Anton Goloborodko [3]; Aleksandra Pekowska [4]; Geoffrey Fudenberg [5]; Yann Loe-Mie [6, 7]; Nuno A Fonseca [8]; Wolfgang Huber [4]; Christian H. Haering [...]

Published
2017
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20. The 4D nucleome project

Author

Dekker, Job, Belmont, Andrew S., Guttman, Mitchell, Leshyk, Victor O., Lis, John T., Lomvardas, Stavros, Mirny, Leonid A., OShea, Clodagh C., Park, Peter J., Ren, Bing, Politz, Joan C. Ritland, Shendure, Jay, and Zhong, Sheng

Subjects
Cell interactions -- Research, Cytological research, Cell nucleus -- Research, Genomes -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells., Author(s): Job Dekker (corresponding author) [1]; Andrew S. Belmont [2]; Mitchell Guttman [3]; Victor O. Leshyk [4]; John T. Lis [5]; Stavros Lomvardas [6]; Leonid A. Mirny [7]; Clodagh C. [...]

Published
2017
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22. Corrigendum: The 4D nucleome project

Author

Dekker, Job, Belmont, Andrew S., Guttman, Mitchell, Leshyk, Victor O., Lis, John T., Lomvardas, Stavros, Mirny, Leonid A., O’Shea, Clodagh C., Park, Peter J., Ren, Bing, Ritland Politz, Joan C., Shendure, Jay, and Zhong, Sheng

Published
2017
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23. Diminished PRRX1 Expression Is Associated With Increased Risk of Atrial Fibrillation and Shortening of the Cardiac Action Potential

Author

Tucker, Nathan R., Dolmatova, Elena V., Lin, Honghuang, Cooper, Rebecca R., Ye, Jiangchuan, Hucker, William J., Jameson, Heather S., Parsons, Victoria A., Weng, Lu-Chen, Mills, Robert W., Sinner, Moritz F., Imakaev, Maxim, Leyton-Mange, Jordan, Vlahakes, Gus, Benjamin, Emelia J., Lunetta, Kathryn L., Lubitz, Steven A., Mirny, Leonid, Milan, David J., and Ellinor, Patrick T.

Published
2017
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27. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Author

Boettiger, Alistair N., Bintu, Bogdan, Moffitt, Jeffrey R., Wang, Siyuan, Beliveau, Brian J., Fudenberg, Geoffrey, Imakaev, Maxim, Mirny, Leonid A., Wu, Chao-ting, and Zhuang, Xiaowei

Subjects
Chromatin -- Research, Genetic research, Epigenetic inheritance -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories (1-5). At the intermediate scale of kilobases to megabases, which encompasses the sizes of genes, gene clusters and regulatory domains, the three-dimensional (3D) organization of DNA is implicated in multiple gene regulatory mechanisms (2-4,6-8), but understanding this organization remains a challenge. At this scale, the genome is partitioned into domains of different epigenetic states that are essential for regulating gene expression (9-11). Here we investigate the 3D organization of chromatin in different epigenetic states using super-resolution imaging. We classified genomic domains in Drosophila cells into transcriptionally active, inactive or Polycomb-repressed states, and observed distinct chromatin organizations for each state. All three types of chromatin domains exhibit power-law scaling between their physical sizes in 3D and their domain lengths, but each type has a distinct scaling exponent. Polycomb-repressed domains show the densest packing and most intriguing chromatin folding behaviour, in which chromatin packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active and inactive chromatin, the Polycomb-repressed domains are characterized by a high degree of chromatin intermixing within the domain. Moreover, compared to inactive domains, Polycomb-repressed domains spatially exclude neighbouring active chromatin to a much stronger degree. Computational modelling and knockdown experiments suggest that reversible chromatin interactions mediated by Polycomb-group proteins play an important role in these unique packaging properties of the repressed chromatin. Taken together, our super-resolution images reveal distinct chromatin packaging for different epigenetic states at the kilobase-to-megabase scale, a length scale that is directly relevant to genome regulation., Multiple lines of evidence suggest that the spatial organization of chromatin at the kilobase-to-megabase scale is important for genomic functions (2-4,6-8,10-12). The sizes of genes, gene clusters and regulatory domains [...]

Published
2016

28. Cells use loop extrusion to weave and tie the genome

Author

Mirny, Leonid A.

Subjects
Gene expression -- Physiological aspects, Cell research, Genomes -- Research, Molecular motors (Biochemistry) -- Genetic aspects, Cells -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

A study reveals that a process called loop extrusion, which is central to the folding and function of chromosomes, also seems to play a key part in the repair of double-strand DNA breaks. A role for loop extrusion in repairing double-strand DNA breaks., Author(s): Leonid A. Mirny Author Affiliations: Cells use loop extrusion to weave and tie the genome One of the challenges that all organisms face is how to compress long DNA [...]

Published
2021
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30. Sequence-dependent sliding kinetics of p53

Author

Leith, Jason S., Tafvizi, Anahita, Huang, Fang, Uspal, William E., Doyle, Patrick S., Fersht, Alan R., Mirny, Leonid A., and van Oijen, Antoine M.

Published
2012

42. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

Author

Flyamer, Ilya M., Gassler, Johanna, Imakaev, Maxim, Brando, Hugo B., Ulianov, Sergey V., Abdennur, Nezar, Razin, Sergey V., Mirny, Leonid A., and Tachibana-Konwalski, Kiku

Subjects
Chromatin -- Physiological aspects, Biological research, Zygote -- Physiological aspects, Fertilization (Biology) -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Ilya M. Flyamer [1, 2, 3]; Johanna Gassler [1]; Maxim Imakaev [4, 5]; Hugo B. Brando [6]; Sergey V. Ulianov [2, 3]; Nezar Abdennur [7]; Sergey V. Razin [2, [...]

Published
2017
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43. Zfx Controls the Self-Renewal of Embryonic and Hematopoietic Stem Cells

Author

Galan-Caridad, Jose M., Harel, Sivan, Arenzana, Teresita L., Hou, Z. Esther, Doetsch, Fiona K., Mirny, Leonid A., and Reizis, Boris

Subjects
Hematopoietic stem cells, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2007.03.014 Byline: Jose M. Galan-Caridad (1), Sivan Harel (1), Teresita L. Arenzana (1), Z. Esther Hou (1), Fiona K. Doetsch (2), Leonid A. Mirny (3), Boris Reizis (1) Abstract: Stem cells (SC) exhibit a unique capacity for self-renewal in an undifferentiated state. It is unclear whether the self-renewal of pluripotent embryonic SC (ESC) and of tissue-specific adult SC such as hematopoietic SC (HSC) is controlled by common mechanisms. The deletion of transcription factor Zfx impaired the self-renewal but not the differentiation capacity of murine ESC; conversely, Zfx overexpression facilitated ESC self-renewal by opposing differentiation. Furthermore, Zfx deletion abolished the maintenance of adult HSC but did not affect erythromyeloid progenitors or fetal HSC. Zfx-deficient ESC and HSC showed increased apoptosis and SC-specific upregulation of stress-inducible genes. Zfx directly activated common target genes in ESC and HSC, as well as ESC-specific target genes including ESC self-renewal regulators Tbx3 and Tcl1. These studies identify Zfx as a shared transcriptional regulator of ESC and HSC, suggesting a common genetic basis of self-renewal in embryonic and adult SC. Author Affiliation: (1) Department of Microbiology, Columbia University Medical Center, New York, NY 10032, USA (2) Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA (3) Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Article History: Received 15 June 2006; Revised 21 October 2006; Accepted 2 March 2007 Article Note: (miscellaneous) Published: April 19, 2007

Published
2007

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