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Genome-wide chromatin state transitions associated with developmental and environmental cues.

Publication ,  Journal Article
Zhu, J; Adli, M; Zou, JY; Verstappen, G; Coyne, M; Zhang, X; Durham, T; Miri, M; Deshpande, V; De Jager, PL; Bennett, DA; Houmard, JA ...
Published in: Cell
January 31, 2013

Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming.

Duke Scholars

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Published In

Cell

DOI

EISSN

1097-4172

Publication Date

January 31, 2013

Volume

152

Issue

3

Start / End Page

642 / 654

Location

United States

Related Subject Headings

  • Organ Specificity
  • Induced Pluripotent Stem Cells
  • Humans
  • Genome-Wide Association Study
  • Gene-Environment Interaction
  • Gene Expression Regulation
  • Epigenesis, Genetic
  • Embryonic Stem Cells
  • Developmental Biology
  • Chromatin Assembly and Disassembly
 

Citation

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Zhu, J., Adli, M., Zou, J. Y., Verstappen, G., Coyne, M., Zhang, X., … Bernstein, B. E. (2013). Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell, 152(3), 642–654. https://doi.org/10.1016/j.cell.2012.12.033
Zhu, Jiang, Mazhar Adli, James Y. Zou, Griet Verstappen, Michael Coyne, Xiaolan Zhang, Timothy Durham, et al. “Genome-wide chromatin state transitions associated with developmental and environmental cues.Cell 152, no. 3 (January 31, 2013): 642–54. https://doi.org/10.1016/j.cell.2012.12.033.
Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31;152(3):642–54.
Zhu, Jiang, et al. “Genome-wide chromatin state transitions associated with developmental and environmental cues.Cell, vol. 152, no. 3, Jan. 2013, pp. 642–54. Pubmed, doi:10.1016/j.cell.2012.12.033.
Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31;152(3):642–654.
Journal cover image

Published In

Cell

DOI

EISSN

1097-4172

Publication Date

January 31, 2013

Volume

152

Issue

3

Start / End Page

642 / 654

Location

United States

Related Subject Headings

  • Organ Specificity
  • Induced Pluripotent Stem Cells
  • Humans
  • Genome-Wide Association Study
  • Gene-Environment Interaction
  • Gene Expression Regulation
  • Epigenesis, Genetic
  • Embryonic Stem Cells
  • Developmental Biology
  • Chromatin Assembly and Disassembly