Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells
Jop Kind,Jop Kind,Ludo Pagie,Sandra S. de Vries,Leila Nahidiazar,Siddharth S. Dey,Magda Bienko,Ye Zhan,Bryan R. Lajoie,Carolyn A. de Graaf,Mario Amendola,Geoffrey Fudenberg,Maxim Imakaev,Leonid A. Mirny,Kees Jalink,Job Dekker,Alexander van Oudenaarden,Bas van Steensel +17 more
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TLDR
The consistency of NL contacts is inversely linked to gene activity in single cells and correlates positively with the heterochromatic histone modification H3K9me3, which highlights fundamental principles of single-cell chromatin organization.About:
This article is published in Cell.The article was published on 2015-09-24 and is currently open access. It has received 397 citations till now.read more
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Formation of Chromosomal Domains by Loop Extrusion
Geoffrey Fudenberg,Maxim Imakaev,Carolyn Lu,Anton Goloborodko,Nezar Abdennur,Leonid A. Mirny,Leonid A. Mirny +6 more
TL;DR: This model produces TADs and finer-scale features of Hi-C data because each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops.
Journal ArticleDOI
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.
Elphège P. Nora,Anton Goloborodko,Anne-Laure Valton,Johan H. Gibcus,Alec Uebersohn,Nezar Abdennur,Job Dekker,Leonid A. Mirny,Benoit G. Bruneau +8 more
TL;DR: The data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading, and provides new fundamental insights into the rules governing mammalian genome organization.
Journal ArticleDOI
Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression
TL;DR: The properties of LADs, the molecular mechanisms that determine their association with the nuclear lamina, their dynamic links with other nuclear compartments, and their proposed roles in gene regulation are discussed.
Journal ArticleDOI
Scaling single-cell genomics from phenomenology to mechanism
Amos Tanay,Aviv Regev +1 more
TL;DR: In this article, the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes.
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The 4D nucleome project
Job Dekker,Andrew S. Belmont,Mitchell Guttman,Victor O. Leshyk,John T. Lis,Stavros Lomvardas,Leonid A. Mirny,Clodagh C. O’Shea,Peter J. Park,Bing Ren,Joan C. Ritland Politz,Jay Shendure,Sheng Zhong +12 more
TL;DR: 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.
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An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
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Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman Aiden,Nynke L. van Berkum,Louise Williams,Maxim Imakaev,Tobias Ragoczy,Tobias Ragoczy,Agnes Telling,Agnes Telling,Ido Amit,Bryan R. Lajoie,Peter J. Sabo,Michael O. Dorschner,Richard Sandstrom,Bradley E. Bernstein,Bradley E. Bernstein,Michaël Bender,Mark Groudine,Mark Groudine,Andreas Gnirke,John A. Stamatoyannopoulos,Leonid A. Mirny,Eric S. Lander,Eric S. Lander,Job Dekker +23 more
TL;DR: Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.
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