Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication

Jiao Sima, Abhijit Chakraborty, Vishnu Dileep, Marco Michalski, Kyle N. Klein, Nicolas P. Holcomb, Jesse L. Turner, Michelle T. Paulsen, Juan Carlos Rivera-Mulia, Claudia Trevilla-Garcia, Daniel A. Bartlett, Peiyao A. Zhao, Brian K. Washburn, Elphège P. Nora, Katerina Kraft, Stefan Mundlos, Benoit G. Bruneau, Mats Ljungman, Peter Fraser, Ferhat AyDavid M. Gilbert

Research output: Contribution to journalArticlepeer-review

107 Scopus citations


The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.

Original languageEnglish (US)
Pages (from-to)816-830.e18
Issue number4
StatePublished - Feb 7 2019

Bibliographical note

Publisher Copyright:
© 2018 Elsevier Inc.


  • CTCF
  • Dppa
  • ERCEs
  • chromatin interactions
  • genome architecture
  • replication timing
  • sub-nuclear compartment
  • super-enhancer
  • topologically associating domain
  • Chromatin
  • Enhancer Elements, Genetic/genetics
  • Mammals/genetics
  • Repressor Proteins/metabolism
  • DNA Replication/genetics
  • DNA/genetics
  • Animals
  • DNA Replication Timing/genetics
  • CCCTC-Binding Factor/genetics
  • Spatio-Temporal Analysis
  • Mice
  • Embryonic Stem Cells

PubMed: MeSH publication types

  • Research Support, Non-U.S. Gov't
  • Journal Article
  • Research Support, N.I.H., Extramural


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