Rxivist logo

Epigenomic and 3D genome architecture in naïve and primed human embryonic stem cell states

By Stephanie L. Battle, Naresh Doni Jayavelu, Robert N. Azad, Jennifer Hesson, Faria N. Ahmed, Joseph Alan Zoller, Julie Mathieu, Hannele Ruohola-Baker, Carol B. Ware, R. David Hawkins

Posted 26 Aug 2017
bioRxiv DOI: 10.1101/181123

During mammalian embryogenesis changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the pre-implantation blastocyst (naïve) and post-implantation epiblast (primed), our data demonstrate that a substantial portion of known human enhancers are pre-marked by H3K4me1 in naïve cells, providing an enhanced open chromatin state in naïve pluripotency. The naïve enhancer repertoire occupies nine percent of the genome, three times that of primed cells, and can exist in broad chromatin domains over fifty kilobases. Enhancer chromatin states are largely poised. Seventy-seven percent of naïve enhancers are decommissioned in a stepwise manner as cells become primed. While primed topological associated domains are unaltered upon differentiation, naïve domains expand across primed boundaries, impacting three dimensional genome architecture. Differential topological associated domain edges coincide with naïve H3K4me1 enrichment. Our results suggest that naïve-derived cells have a chromatin landscape reflective of early embryogenesis.

Download data

  • Downloaded 1,445 times
  • Download rankings, all-time:
    • Site-wide: 16,350
    • In developmental biology: 250
  • Year to date:
    • Site-wide: 84,846
  • Since beginning of last month:
    • Site-wide: 112,787

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide