Format

Send to

Choose Destination
Cell. 2019 Feb 7;176(4):816-830.e18. doi: 10.1016/j.cell.2018.11.036. Epub 2018 Dec 27.

Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication.

Author information

1
Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
2
La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
3
Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK.
4
Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
5
Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA.
6
Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany.
7
Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.
8
Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK.
9
La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA.
10
Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA. Electronic address: gilbert@bio.fsu.edu.

Abstract

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.

KEYWORDS:

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

PMID:
30595451
DOI:
10.1016/j.cell.2018.11.036

Supplemental Content

Full text links

Icon for Elsevier Science
Loading ...
Support Center