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
Evolutionary Insights into RNA trans-Splicing in Vertebrates.
TL;DR: Pre-RNA splicing is an essential step in generating mature mRNA and RNA trans-splicing combines two separate pre-mRNA molecules to form a chimeric non-co-linear RNA, which may exert a function distinct from its original molecules.
Journal ArticleDOI
Transcriptional and epigenetic networks of helper T and innate lymphoid cells.
Han-Yu Shih,Giuseppe Sciumè,Amanda C. Poholek,Golnaz Vahedi,Kiyoshi Hirahara,Kiyoshi Hirahara,Alejandro V. Villarino,Michael Bonelli,Rémy Bosselut,Yuka Kanno,Stefan A. Muljo,John J. O'Shea +11 more
TL;DR: The current status of the flexibility of helper T‐cell responses in relation to their genetic regulatory networks and epigenetic landscapes is reviewed.
Journal ArticleDOI
Modeling chromosomes: beyond pretty pictures
TL;DR: This review proposes that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data‐driven ensembles, and twoclasses of de novo models: structural ensemble and mechanistic ensemble.
Journal ArticleDOI
GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.
Borbala Mifsud,Inigo Martincorena,Elodie Darbo,Robert Sugar,Stefan Schoenfelder,Peter Fraser,Nicholas M. Luscombe,Nicholas M. Luscombe,Nicholas M. Luscombe +8 more
TL;DR: A simple binomial probabilistic model is introduced that resolves complex biases and distinguishes between true and false interactions and provides a statistical framework for further data analysis, such as comparisons of Hi-C interactions between different conditions.
Journal ArticleDOI
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.
Valentina Peona,Mozes P. K. Blom,Mozes P. K. Blom,Luohao Xu,Reto Burri,Shawn Sullivan,Ignas Bunikis,Ivan Liachko,Tri Haryoko,Knud A. Jønsson,Qi Zhou,Qi Zhou,Qi Zhou,Martin Irestedt,Alexander Suh,Alexander Suh +15 more
TL;DR: It is shown that a multiplatform assembly implementing long‐read, linked‐read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC‐rich microchromosomes and the repeat‐rich W chromosome.
References
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