Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin

Scientific Reports
Asa ThibodeauDuygu Ucar

Abstract

Broad domain promoters and super enhancers are regulatory elements that govern cell-specific functions and harbor disease-associated sequence variants. These elements are characterized by distinct epigenomic profiles, such as expanded deposition of histone marks H3K27ac for super enhancers and H3K4me3 for broad domains, however little is known about how they interact with each other and the rest of the genome in three-dimensional chromatin space. Using network theory methods, we studied chromatin interactions between broad domains and super enhancers in three ENCODE cell lines (K562, MCF7, GM12878) obtained via ChIA-PET, Hi-C, and Hi-CHIP assays. In these networks, broad domains and super enhancers interact more frequently with each other compared to their typical counterparts. Network measures and graphlets revealed distinct connectivity patterns associated with these regulatory elements that are robust across cell types and alternative assays. Machine learning models showed that these connectivity patterns could effectively discriminate broad domains from typical promoters and super enhancers from typical enhancers. Finally, targets of broad domains in these networks were enriched in disease-causing SNPs of cognate cell types...Continue Reading

References

Jan 24, 2007·Bioinformatics·Natasa Przulj
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 6, 2009·Nature·Melissa J FullwoodYijun Ruan
Mar 13, 2010·Bioinformatics·Sheng-Jian XiaoZhi-Liang Ji
Jul 23, 2011·Genes & Cancer·Jinhua XuOlufunmilayo I Olopade
Dec 14, 2011·Bioinformatics·Christopher Whelan, Kemal Sönmez
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Apr 3, 2012·Cell·Chi V Dang
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Oct 15, 2013·Cell·Denes HniszRichard A Young
Oct 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Stephen C J ParkerUNKNOWN NISC Comparative Sequencing Program Authors
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Aug 2, 2014·Cell·Bérénice A BenayounAnne Brunet
Jun 3, 2015·Bioinformatics·Douglas H PhanstielMichael P Snyder
Aug 15, 2015·Genome Biology·Jialiang HuangGuo-Cheng Yuan
Nov 4, 2015·Nucleic Acids Research·Cricket A SloanJ Michael Cherry
Jun 24, 2016·PLoS Computational Biology·Asa ThibodeauDuygu Ucar
Jan 31, 2017·Nature Methods·Vijay RamaniJay Shendure

❮ Previous
Next ❯

Citations

Jan 1, 2019·PLoS Computational Biology·Zhen Wah TanIgor N Berezovsky
Jun 3, 2018·Molecular Systems Biology·Alvaro Rada-IglesiasArgyris Papantonis
Mar 15, 2020·International Journal of Molecular Sciences·Edina Erdős, Bálint László Bálint
May 13, 2020·Epigenomics·Julie Dubois-ChevalierJérôme Eeckhoute
Jul 14, 2020·Bioinformatics·N Malod-DogninN Pržulj
Mar 18, 2020·Nucleic Acids Research·Miguel Madrid-MencíaVera Pancaldi
Dec 29, 2019·BMC Bioinformatics·Juris ViksnaPeteris Rucevskis
Aug 22, 2020·Human Molecular Genetics·Eva Mejia-RamirezM Carolina Florian
Feb 25, 2021·American Journal of Human Genetics·Ilakya SelvarajanMinna U Kaikkonen
Jul 10, 2021·Clinical Epigenetics·Tasnim H BeaconJames R Davie
Aug 8, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Xuezhu WangYang Chen

❮ Previous
Next ❯

Datasets Mentioned

BETA
GM12878
GSE29692

Methods Mentioned

BETA
immunoprecipitation
Hi-C
HiChIP
Hi-ChIP
single-cell Hi-C
RNA-seq

Software Mentioned

ChIP
Hi
HiChIP
learn Python
scikit
QuIN
HiCCUPS
MACS2
GREGOR
GraphletCounter

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.