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Chromatin architecture reorganization during stem cell differentiation.

Publication ,  Journal Article
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 ...
Published in: Nature
February 19, 2015

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.

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Published In

Nature

DOI

EISSN

1476-4687

Publication Date

February 19, 2015

Volume

518

Issue

7539

Start / End Page

331 / 336

Location

England

Related Subject Headings

  • Reproducibility of Results
  • Promoter Regions, Genetic
  • Humans
  • General Science & Technology
  • Gene Regulatory Networks
  • Epigenomics
  • Epigenesis, Genetic
  • Enhancer Elements, Genetic
  • Embryonic Stem Cells
  • Chromatin Assembly and Disassembly
 

Citation

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Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., … Ren, B. (2015). Chromatin architecture reorganization during stem cell differentiation. Nature, 518(7539), 331–336. https://doi.org/10.1038/nature14222
Dixon, Jesse R., Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E. Antosiewicz-Bourget, Ah Young Lee, Zhen Ye, et al. “Chromatin architecture reorganization during stem cell differentiation.Nature 518, no. 7539 (February 19, 2015): 331–36. https://doi.org/10.1038/nature14222.
Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, et al. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19;518(7539):331–6.
Dixon, Jesse R., et al. “Chromatin architecture reorganization during stem cell differentiation.Nature, vol. 518, no. 7539, Feb. 2015, pp. 331–36. Pubmed, doi:10.1038/nature14222.
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. Chromatin architecture reorganization during stem cell differentiation. Nature. 2015 Feb 19;518(7539):331–336.

Published In

Nature

DOI

EISSN

1476-4687

Publication Date

February 19, 2015

Volume

518

Issue

7539

Start / End Page

331 / 336

Location

England

Related Subject Headings

  • Reproducibility of Results
  • Promoter Regions, Genetic
  • Humans
  • General Science & Technology
  • Gene Regulatory Networks
  • Epigenomics
  • Epigenesis, Genetic
  • Enhancer Elements, Genetic
  • Embryonic Stem Cells
  • Chromatin Assembly and Disassembly