De Novo Deciphering Three-Dimensional Chromatin Interaction and Topological Domains by Wavelet Transformation of Epigenetic Profiles

dc.contributor.ISNI0000 0001 1707 1372 (Zhang, MQ)en_US
dc.contributor.ORCID0000-0002-4029-8716 (Chen, M)en_US
dc.contributor.authorChen, Yongen_US
dc.contributor.authorWang, Yunfeien_US
dc.contributor.authorXuan, Zhenyuen_US
dc.contributor.authorChen, Minen_US
dc.contributor.authorZhang, Michael Q.en_US
dc.contributor.utdAuthorChen, Yongen_US
dc.contributor.utdAuthorWang, Yunfeien_US
dc.contributor.utdAuthorXuan, Zhenyuen_US
dc.contributor.utdAuthorChen, Minen_US
dc.contributor.utdAuthorZhang, Michael Q.en_US
dc.date.accessioned2017-11-29T22:08:30Z
dc.date.available2017-11-29T22:08:30Z
dc.date.created2016-04-07en_US
dc.date.issued2016-04-07en_US
dc.descriptionIncludes supplementary material.en_US
dc.description.abstractDefining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.en_US
dc.description.sponsorshipNIH [HG001696, MH102616, K25AR063761]; NSFC [91019016, 61273228]; NBRPC [2012CB316503]; NIH [HG001696, MH102616, K25AR063761]; NSFC [91019016, 61273228]; NBRPC [2012CB316503]en_US
dc.identifier.bibliographicCitationChen, Yong, Yunfei Wang, Zhenyu Xuan, Min Chen, et al. 2016. "De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles." Nucleic Acids Research 44(11), doi:10.1093/nar/gkw225en_US
dc.identifier.issn1362-4962en_US
dc.identifier.issue11en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/5594
dc.identifier.volume44en_US
dc.publisherOxford University Pressen_US
dc.relation.urihttp://dx.doi.org/10.1093/nar/gkw225
dc.rightsCC BY 4.0 (Attribution)en_US
dc.rights©2016 The Authors. Published by Oxford University Press on behalf of Nucleic Acids Research.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceNucleic Acids Research
dc.subjectChromatinen_US
dc.subjectHistonesen_US
dc.subjectCell cycleen_US
dc.subjectFibroblastsen_US
dc.subjectEmbryonic stem cellsen_US
dc.subjectEpigenomicsen_US
dc.titleDe Novo Deciphering Three-Dimensional Chromatin Interaction and Topological Domains by Wavelet Transformation of Epigenetic Profilesen_US
dc.type.genrearticleen_US

Files

Original bundle

Now showing 1 - 3 of 3
Loading...
Thumbnail Image
Name:
NSM-3154-6839.70.pdf
Size:
4.52 MB
Format:
Adobe Portable Document Format
Description:
Article
No Thumbnail Available
Name:
nar-03580-met-k-2015-File006.ods
Size:
98.72 KB
Format:
OpenDocument Spreadsheet
Description:
Supplement
Loading...
Thumbnail Image
Name:
nar-03580-met-k-2015-File007.pdf
Size:
678.11 KB
Format:
Adobe Portable Document Format
Description:
Supplement