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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Measuring the reproducibility and quality of Hi-C data
Galip Gürkan Yardımcı,Hakan Ozadam,Michael E.G. Sauria,Oana Ursu,Koon-Kiu Yan,Tao Yang,Abhijit Chakraborty,Arya Kaul,Bryan R. Lajoie,Fan Song,Ye Zhan,Ferhat Ay,Mark Gerstein,Anshul Kundaje,Qiang Li,James Taylor,Feng Yue,Job Dekker,Job Dekker,William Stafford Noble +19 more
TL;DR: This work assess reproducibility and quality measures by varying sequencing depth, resolution and noise levels in Hi-C data from 13 cell lines, with two biological replicates each, as well as 176 simulated matrices, to identify low-quality experiments.
Journal ArticleDOI
De novo assembly of a Chinese soybean genome
Yanting Shen,Jing Liu,Haiying Geng,Jixiang Zhang,Yucheng Liu,Haikuan Zhang,Shilai Xing,Jianchang Du,Shisong Ma,Zhixi Tian +9 more
TL;DR: The de novo assembly and sequence analysis of a Chinese soybean genome for “Zhonghuang 13” by a combination of SMRT, Hi–C and optical mapping data is reported, finding more than 250,000 structure variations.
Journal ArticleDOI
Models of chromosome structure
Mario Nicodemi,Ana Pombo +1 more
TL;DR: Recent advances in chromosome modeling are reviewed, focusing on a recently proposed framework, the Strings & Binders Switch (SBS) model, which recapitulates key features of chromosome organization in space and time.
Journal ArticleDOI
Accurate and complete genomes from metagenomes
Lin-Xing Chen,Karthik Anantharaman,Alon Shaiber,A. Murat Eren,A. Murat Eren,Jillian F. Banfield,Jillian F. Banfield +6 more
TL;DR: The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them, and methods that could be implemented in bioinformatic approaches for curation are discussed to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
Journal ArticleDOI
Architectural proteins: regulators of 3D genome organization in cell fate.
TL;DR: The regulation of these proteins, their interaction with DNA, and their co-occurrence in the genome, may be responsible for the plasticity of 3D chromatin architecture that dictates cell and time-specific blueprints of gene expression.
References
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Book
The Fractal Geometry of Nature
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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Capturing Chromosome Conformation
TL;DR: Using the yeast Saccharomyces cerevisiae, this work could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis and found that chromatin is highly flexible throughout.
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