Paper

Identification of cis elements for spatio-temporal control of DNA replication

Washburn, Brian K, Michalski, Marco, Ay, Ferhat, Vera, Daniel, Ljungman, Mats, Jiao Sima, Bartlett, Daniel, Chakraborty, Abhijit, Paulsen, Michelle T, Elph ge P Nora, Fraser, Peter, Bruneau, Benoit G, Vishnu Dileep, Gilbert, David M, Klein, Kyle N, Mundlos, Stefan, Rivera-Mulia, Juan Carlos, Trevilla-Garcia, Claudia, Kraft, Katerina

2018

Overview

The temporal order of DNA replication (replication timing, RT) is highly coupled with genome architecture, but cis-elements regulating spatio-temporal control of replication have remained elusive. We performed an extensive series of CRISPR mediated deletions and inversions and high-resolution capture Hi-C of a pluripotency associated domain (DppA2/4) in mouse embryonic stem cells. Whereas CTCF mediated loops and chromatin domain boundaries were dispensable, deletion of three intra-domain prominent CTCF-independent 3D contact sites caused a domain-wide early to late switch in RT, shift in sub-nuclear chromatin compartment and loss of transcriptional activity, These early replication control elements (ERCEs) display prominent chromatin features resembling enhancers/promoters and individual and pair-wise deletions of the ERCEs confirmed their partial redundancy and interdependency in controlling domain-wide RT and transcription. Our results demonstrate that discrete cis-regulatory elements mediate domain-wide RT, chromatin compartmentalization, and transcription, representing a major advance in dissecting the relationship between genome structure and function.

• Publisher: Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory
• Subject: Chromatin / Clonal deletion / CRISPR / Deoxyribonucleic acid / DNA / DNA biosynthesis / Embryo cells / Enhancers / Genomes / Molecular Biology / Pluripotency / Regulatory sequences / Replication / Stem cell transplantation / Stem cells / Structure-function relationships / Temporal variations / Transcription