Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells

Nat Commun. 2017 Nov 20;8(1):1616. doi: 10.1038/s41467-017-01679-x.


Higher-order chromatin organization controls transcriptional programs that govern cell properties and functions. In order for pluripotent stem cells (PSCs) to appropriately respond to differentiation signals, developmental gene loci should be structurally and spatially regulated to be readily available for immediate transcription, even though these genes are hardly expressed in PSCs. Here, we show that both chromatin interaction profiles and nuclear positions at developmental gene loci differ between human somatic cells and hPSCs, and that changes in the chromatin interactions are closely related to the nuclear repositioning. Moreover, we also demonstrate that developmental gene loci, which have bivalent histone modifications, tend to colocalize in PSCs. Furthermore, this colocalization requires PRC1, PRC2, and TrxG complexes, which are essential regulatory factors for the maintenance of transcriptionally poised developmental genes. Our results indicate that higher-order chromatin regulation may be an integral part of the differentiation capacity that defines pluripotency.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Chromatin / chemistry*
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Gene Expression Regulation, Developmental
  • Genes, Developmental
  • Genetic Loci*
  • Histone Code
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Methylation
  • Pluripotent Stem Cells / chemistry
  • Pluripotent Stem Cells / metabolism*


  • Cell Cycle Proteins
  • Chromatin
  • Histones
  • PRC1 protein, human