Integrating Hi-C and FISH Data for Modeling of the 3D Organization of Chromosomes

Simple item page
dc.contributor.authorAbbas, A.
dc.contributor.authorHe, X.
dc.contributor.authorNiu, J.
dc.contributor.authorZhou, B.
dc.contributor.authorZhu, G.
dc.contributor.authorMa, T.
dc.contributor.authorSong, J.
dc.contributor.authorGao, J.
dc.contributor.authorZhang, Michael Q.
dc.contributor.authorZeng, J.
dc.contributor.utdAuthorZhang, Michael Q.
dc.date.accessioned2020-01-29T20:54:17Z
dc.date.available2020-01-29T20:54:17Z
dc.date.issued2019-05-03
dc.description.abstractThe new advances in various experimental techniques that provide complementary information about the spatial conformations of chromosomes have inspired researchers to develop computational methods to fully exploit the merits of individual data sources and combine them to improve the modeling of chromosome structure. Here we propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model. Comprehensive tests on a set of chromosomes, for which both Hi-C and FISH data are available, demonstrate that GEM-FISH can outperform previous chromosome structure modeling methods and accurately capture the higher order spatial features of chromosome conformations. Moreover, our reconstructed 3D models of chromosomes revealed interesting patterns of spatial distributions of super-enhancers which can provide useful insights into understanding the functional roles of these super-enhancers in gene regulation. © 2019, The Author(s).
dc.description.departmentSchool of Natural Sciences and Mathematics
dc.description.departmentCenter for Systems Biology
dc.description.sponsorshipThis work was supported in part by the National Natural Science Foundation of China (61472205 and 81630103), State Key Research Development Program of China (2017YFA0505503), the National Natural Science Foundation of China under Grant (91729301, 31671383, 61475010, 61729501, and 11671005),
dc.identifier.bibliographicCitationAbbas, A., X. He, J. Niu, B. Zhou, et al. 2019. "Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes." Nature Communications 10(1): art. 2049, doi: 10.1038/s41467-019-10005-6
dc.identifier.issn2041-1723
dc.identifier.issue1
dc.identifier.urihttp://dx.doi.org/10.1038/s41467-019-10005-6
dc.identifier.urihttps://hdl.handle.net/10735.1/7214
dc.identifier.volume10
dc.language.isoen
dc.publisherNature Publishing Group
dc.rightsCC BY 4.0 (Attribution)
dc.rights©2019 The Authors
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.source.journalNature Communications
dc.subjectChromosomes
dc.subjectGene expression
dc.subjectPolymers
dc.subjectThree-dimensional modeling
dc.subjectChromatin
dc.subjectFinite element method
dc.subjectFluorescence in situ hybridization
dc.subjectThree dimensional imaging
dc.subjectCell lines
dc.subjectComputer simulation
dc.subjectGenetics
dc.subjectHuman genome
dc.titleIntegrating Hi-C and FISH Data for Modeling of the 3D Organization of Chromosomes
dc.title.alternativeNature Communications
dc.type.genrearticle

Files

Original bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
NSM-3154-260803.54.pdf
Size:
2.94 MB
Format:
Adobe Portable Document Format
Description:
Article
Download

Collections

Zhang, Michael Q.