Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
Reads0
Chats0
TLDR
Several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data are described.Abstract:
How DNA is organized in three dimensions inside the cell nucleus and how that affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic, and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C) the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction datasets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyze chromatin interaction data.read more
Citations
More filters
Journal ArticleDOI
Ten years of next-generation sequencing technology.
TL;DR: An overview of the evolution of NGS is provided and the most significant improvements in sequencing technologies and library preparation protocols are discussed and the current landscape of N GS applications is explored to provide a perspective for future developments.
Journal ArticleDOI
Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction.
TL;DR: The 3DEpiLoop algorithm predicts three-dimensional chromatin looping interactions within topologically associating domains (TADs) from one-dimensional epigenomics and transcription factor profiles using the statistical learning.
Journal ArticleDOI
Sequencing depth and coverage: key considerations in genomic analyses
TL;DR: The issue of sequencing depth in the design of next-generation sequencing experiments is discussed and current guidelines and precedents on the issue of coverage are reviewed for four major study designs, including de novo genome sequencing, genome resequencing, transcriptome sequencing and genomic location analyses.
Journal ArticleDOI
A high-resolution map of the three-dimensional chromatin interactome in human cells
Fulai Jin,Yan Li,Jesse R. Dixon,Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Zhen Ye,Ah Young Lee,Chia-An Yen,Anthony D. Schmitt,Anthony D. Schmitt,Celso A. Espinoza,Bing Ren,Bing Ren +13 more
TL;DR: A comprehensive chromatin interaction map generated in human fibroblasts using a genome-wide 3C analysis method (Hi-C) is reported and suggests that the three-dimensional chromatin landscape, once established in a particular cell type, is relatively stable and could influence the selection of target genes by a ubiquitous transcription activator in a cell-specific manner.
Journal ArticleDOI
Two independent modes of chromatin organization revealed by cohesin removal
Wibke Schwarzer,Nezar Abdennur,Anton Goloborodko,Aleksandra Pekowska,Geoffrey Fudenberg,Yann Loe-Mie,Nuno A. Fonseca,Wolfgang Huber,Christian H. Haering,Leonid A. Mirny,François Spitz +10 more
TL;DR: It is shown that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding, and the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape.
References
More filters
Journal ArticleDOI
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.
Journal Article
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.
Journal ArticleDOI
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.
Journal ArticleDOI
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon,Siddarth Selvaraj,Siddarth Selvaraj,Feng Yue,Audrey Kim,Yan-Yan Li,Yin-Zhong Shen,Ming Hu,Jun Liu,Bing Ren,Bing Ren +10 more
TL;DR: It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
Journal ArticleDOI
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.
Related Papers (5)
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
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Elphège P. Nora,Bryan R. Lajoie,Edda G. Schulz,Luca Giorgetti,Luca Giorgetti,Luca Giorgetti,Ikuhiro Okamoto,Ikuhiro Okamoto,Ikuhiro Okamoto,Nicolas Servant,Nicolas Servant,Nicolas Servant,Tristan Piolot,Tristan Piolot,Tristan Piolot,Nynke L. van Berkum,Johannes Meisig,John W. Sedat,Joost Gribnau,Emmanuel Barillot,Emmanuel Barillot,Emmanuel Barillot,Nils Blüthgen,Job Dekker,Edith Heard,Edith Heard,Edith Heard +26 more