Chromatin architecture reorganization during stem cell differentiation.

Published

Journal Article

Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.

Full Text

Duke Authors

Cited Authors

  • Dixon, JR; Jung, I; Selvaraj, S; Shen, Y; Antosiewicz-Bourget, JE; Lee, AY; Ye, Z; Kim, A; Rajagopal, N; Xie, W; Diao, Y; Liang, J; Zhao, H; Lobanenkov, VV; Ecker, JR; Thomson, JA; Ren, B

Published Date

  • February 2015

Published In

Volume / Issue

  • 518 / 7539

Start / End Page

  • 331 - 336

PubMed ID

  • 25693564

Pubmed Central ID

  • 25693564

Electronic International Standard Serial Number (EISSN)

  • 1476-4687

International Standard Serial Number (ISSN)

  • 0028-0836

Digital Object Identifier (DOI)

  • 10.1038/nature14222

Language

  • eng