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

45 Scopus citations


cis-regulatory elements control the three-dimensional compartmentalization, architecture of the genome, and replication timing in a CTCF-independent manner.

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

Bibliographical note

Funding Information:
We thank G. Church lab for advice on CRISPRology, S. Schoenfelder for cHi-C, S. Wingett for HiCUP, S. Andrews for cHi-C probe design, F. Krueger for SNPsplit, D. Vera for bioinformatics, R. Didier for FACS, C. Pye and K. Poduch for molecular cloning, C. Huffstetler for figure graphics, R. Tjian for Klf4 enhancer deletion, R. Young and N. Behnam for YY1 samples, B. Chadwick for px458, M. Mechali for SNS origin data, and A. Belmont for helpful discussions. F.A. and A.C. were partially funded by Institute Leadership Funds from La Jolla Institute for Allergy and Immunology and NIH ( R35GM128938 to F.A.). This work was supported by NIH ( R01GM083337 and U54DK107965 to D.M.G.).


  • CTCF
  • Dppa
  • ERCEs
  • chromatin interactions
  • genome architecture
  • replication timing
  • sub-nuclear compartment
  • super-enhancer
  • topologically associating domain

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