Evolutionarily Conserved Principles Predict 3D Chromatin Organization

M. Jordan Rowley, Michael H. Nichols, Xiaowen Lyu, Masami Ando-Kuri, I. Sarahi M. Rivera, Karen Hermetz, Ping Wang, Yijun Ruan, Victor G. Corces

Research output: Contribution to journalArticle

141 Scopus citations

Abstract

Topologically associating domains (TADs), CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP, we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.

Original languageEnglish (US)
Pages (from-to)837-852.e7
JournalMolecular Cell
Volume67
Issue number5
DOIs
StatePublished - Sep 7 2017

Keywords

  • CTCF
  • Hi-C
  • TAD
  • compartment
  • epigenetics
  • insulator
  • loop
  • transcription

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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  • Cite this

    Rowley, M. J., Nichols, M. H., Lyu, X., Ando-Kuri, M., Rivera, I. S. M., Hermetz, K., Wang, P., Ruan, Y., & Corces, V. G. (2017). Evolutionarily Conserved Principles Predict 3D Chromatin Organization. Molecular Cell, 67(5), 837-852.e7. https://doi.org/10.1016/j.molcel.2017.07.022