Identification of hierarchical chromatin domains

Bioinformatics
Caleb Weinreb, Benjamin J Raphael

Abstract

The three-dimensional structure of the genome is an important regulator of many cellular processes including differentiation and gene regulation. Recently, technologies such as Hi-C that combine proximity ligation with high-throughput sequencing have revealed domains of self-interacting chromatin, called topologically associating domains (TADs), in many organisms. Current methods for identifying TADs using Hi-C data assume that TADs are non-overlapping, despite evidence for a nested structure in which TADs and sub-TADs form a complex hierarchy. We introduce a model for decomposition of contact frequencies into a hierarchy of nested TADs. This model is based on empirical distributions of contact frequencies within TADs, where positions that are far apart have a greater enrichment of contacts than positions that are close together. We find that the increase in contact enrichment with distance is stronger for the inner TAD than for the outer TAD in a TAD/sub-TAD pair. Using this model, we develop the TADtree algorithm for detecting hierarchies of nested TADs. TADtree compares favorably with previous methods, finding TADs with a greater enrichment of chromatin marks such as CTCF at their boundaries. A python implementation of TADtr...Continue Reading

References

Jan 19, 2007·Nature Reviews. Genetics·Christian LanctôtThomas Cremer
Jan 5, 2012·Genes & Development·Elzo de Wit, Wouter de Laat
Feb 19, 2013·Current Opinion in Genetics & Development·Amos Tanay, Giacomo Cavalli
Mar 7, 2013·Nature Structural & Molecular Biology·Giacomo Cavalli, Tom Misteli
May 28, 2013·Cell·Jennifer E Phillips-CreminsVictor G Corces
Dec 18, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jessica ZuinKerstin S Wendt
Jan 9, 2014·Genome Research·Orsolya SymmonsFrançois Spitz
May 29, 2014·Algorithms for Molecular Biology : AMB·Darya FilippovaCarl Kingsford
Aug 28, 2014·Bioinformatics·Celine Lévy-LeducS Robin
Feb 20, 2015·Nature Communications·Roland JägerRichard S Houlston
Jun 9, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Emre SeferCarl Kingsford

❮ Previous
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Citations

Feb 8, 2016·Current Opinion in Cell Biology·M Jordan Rowley, Victor G Corces
Jun 12, 2016·Chromosoma·Sergey V Razin, Yegor S Vassetzky
Sep 27, 2016·Genes·Ill-Min ChungGovindasamy Rajakumar
Jun 13, 2017·Nature Methods·Mattia ForcatoSilvio Bicciato
Dec 19, 2017·Bioinformatics·Bixia TangZhihua Zhang
Apr 9, 2018·Biochemistry. Biokhimii︠a︡·S V Razin, A A Gavrilov
Sep 28, 2018·Journal of Cellular Biochemistry·Artem V LuzhinAlexey A Gavrilov
Dec 21, 2018·Biophysics Reviews·Koustav PalFrancesco Ferrari
Jan 16, 2018·Nature Methods·Heidi K NortonJennifer E Phillips-Cremins
May 3, 2019·Scientific Reports·Sang Hoon LeeLudvig Lizana
Sep 6, 2018·Nucleic Acids Research·Fengling ChenYang Chen
Sep 2, 2017·Cellular & Molecular Biology Letters·Sergey V Razin, Sergey V Ulianov
Sep 1, 2018·Science·Longzhi TanX Sunney Xie
Mar 23, 2019·Genome Biology·Linh Huynh, Fereydoun Hormozdiari
Dec 19, 2019·Nature Reviews. Genetics·Rieke Kempfer, Ana Pombo
Jan 29, 2017·Nucleic Acids Research·Noelle HaddadDaniel Jost
Aug 26, 2018·Genome Biology·Peter KerpedjievNils Gehlenborg
Jul 11, 2020·Nature Communications·Jared V GoodmanAzad Bonni
Jul 2, 2019·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yufang LiLei Liu
Feb 23, 2020·Nucleic Acids Research·Paula Soler-VilaMarc A Marti-Renom
Nov 7, 2019·NAR Genomics and Bioinformatics·Natalie SauerwaldCarl Kingsford
Dec 1, 2019·Molecular Cell·Adam W ClemensHarrison W Gabel
Mar 16, 2021·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Carlos SotoAnuj Srivastava
Mar 17, 2021·PLoS Computational Biology·Ji Hyun BakChangbong Hyeon
Sep 25, 2020·The Annals of Applied Statistics·Y X Rachel WangPeter J Bickel
Apr 19, 2021·Briefings in Bioinformatics·Yunlong WangYaping Fang

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