Predicting three-dimensional genome organization with chromatin states

We introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin...

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Bibliographic Details
Published inPLoS computational biology Vol. 15; no. 6; p. e1007024
Main Authors Qi, Yifeng, Zhang, Bin
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 01.06.2019
Public Library of Science (PLoS)
Subjects
Artificial intelligence
Binding sites
Biology and Life Sciences
Chromatin
Chromatin - chemistry
Chromatin - genetics
Chromosomes
Computational Biology - methods
Computer applications
Computer simulation
Crosstalk
Deoxyribonucleic acid
DNA
Domains
Experiments
Gene loci
Genetic research
Genome, Human - genetics
Genomes
Genomics
Human genome
Humans
Machine learning
Microscopy
Models, Molecular
Physical Sciences
Polymer industry
Polymers
Predictions
Regulatory sequences
Research and Analysis Methods
Software
Structural analysis
Three dimensional models
United States
United States > US
Massachusetts
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Summary:We introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin structures recapitulate known features of genome organization, including the formation of chromatin loops, topologically associating domains (TADs) and compartments, and are in quantitative agreement with chromosome conformation capture experiments and super-resolution microscopy measurements. Detailed characterization of the predicted structural ensemble reveals the dynamical flexibility of chromatin loops and the presence of cross-talk among neighboring TADs. Analysis of the model's energy function uncovers distinct mechanisms for chromatin folding at various length scales and suggests a need to go beyond simple A/B compartment types to predict specific contacts between regulatory elements using polymer simulations.
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The authors have declared that no competing interests exist.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1007024