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
TLDR
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.Abstract:
We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.read more
Citations
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Journal ArticleDOI
Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription
TL;DR: Analysis of chromatin conformation during Drosophila embryogenesis offers insight into when spatial genome organization is first established during development and identifies a key factor that helps trigger this architecture.
Journal ArticleDOI
Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
Brian J. Beliveau,Eric F. Joyce,Nicholas Apostolopoulos,Feyza Yilmaz,Chamith Y. Fonseka,Ruth B. McCole,Yiming Chang,Jin Billy Li,Tharanga Niroshini Senaratne,Benjamin R. Williams,Jean Marie Rouillard,Chao-ting Wu +11 more
TL;DR: This work describes an oligonucleotide- and PCR-based strategy for fluorescence in situ hybridization (FISH) and a bioinformatic platform that enables this technology to be extended to any organism whose genome has been sequenced, anticipating this technology will lead to an enhanced ability to visualize interphase and metaphase chromosomes.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Cohesin‐mediated interactions organize chromosomal domain architecture
Sevil Sofueva,Eitan Yaffe,Wen-Ching Chan,Dimitra Georgopoulou,Matteo Vietri Rudan,Hegias Mira-Bontenbal,Steven M. Pollard,Gary P. Schroth,Amos Tanay,Suzana Hadjur +9 more
TL;DR: It is shown that very specific long‐range interactions are anchored by cohesin/CTCF sites, but not cohes in‐only or CTCF‐only sites, to form a hierarchy of chromosomal loops.
Journal ArticleDOI
Pan-Genome of Wild and Cultivated Soybeans.
Yucheng Liu,Huilong Du,Pengcheng Li,Yanting Shen,Hua Peng,Shu-Lin Liu,Guoan Zhou,Haikuan Zhang,Zhi Liu,Miao Shi,Xuehui Huang,Yan Li,Min Zhang,Zheng Wang,Baoge Zhu,Bin Han,Chengzhi Liang,Zhixi Tian +17 more
TL;DR: The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits.
References
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