PT  - JOURNAL ARTICLE
AU  - Qian Du
AU  - Grady C. Smith
AU  - Phuc Loi Luu
AU  - James M. Ferguson
AU  - Nicola J. Armstrong
AU  - C. Elizabeth Caldon
AU  - Elyssa Campbell
AU  - Shalima S. Nair
AU  - Elena Zotenko
AU  - Cathryn M. Gould
AU  - Michael Buckley
AU  - Dominik Kaczorowski
AU  - Kirston Barton
AU  - Ira W. Deveson
AU  - Martin A. Smith
AU  - Joseph E. Powell
AU  - Ksenia Skvortsova
AU  - Clare Stirzaker
AU  - Joanna Achinger-Kawecka
AU  - Susan J. Clark
TI  - DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity
AID  - 10.1101/2020.10.15.338855
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.10.15.338855
4099  - http://biorxiv.org/content/early/2020/10/16/2020.10.15.338855.short
4100  - http://biorxiv.org/content/early/2020/10/16/2020.10.15.338855.full
AB  - DNA replication timing and three-dimensional (3D) genome organisation occur across large domains associated with distinct epigenome patterns to functionally compartmentalise genome regulation. However, it is still unclear if alternations in the epigenome, in particular cancer-related DNA hypomethylation, can directly result in alterations to cancer higher order genome architecture. Here, we use Hi-C and single cell Repli-Seq, in the colorectal cancer DNMT1 and DNMT3B DNA methyltransferases double knockout model, to determine the impact of DNA hypomethylation on replication timing and 3D genome organisation. First, we find that the hypomethylated cells show a striking loss of replication timing precision with gain of cell-to-cell replication timing heterogeneity and loss of 3D genome compartmentalisation. Second, hypomethylated regions that undergo a large change in replication timing also show loss of allelic replication timing, including at cancer-related genes. Finally, we observe the formation of broad ectopic H3K4me3-H3K9me3 domains across hypomethylated regions where late replication is maintained, that potentially prevent aberrant transcription and loss of genome organisation after DNA demethylation. Together, our results highlight a previously underappreciated role for DNA methylation in maintenance of 3D genome architecture.Competing Interest StatementThe authors have declared no competing interest.