RT Journal Article
SR Electronic
T1 Replication timing maintains the global epigenetic state in human cells
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2019.12.28.890020
DO 10.1101/2019.12.28.890020
A1 Kyle N. Klein
A1 Peiyao A. Zhao
A1 Xiaowen Lyu
A1 Daniel A. Bartlett
A1 Amar Singh
A1 Ipek Tasan
A1 Lotte P. Watts
A1 Shin-ichiro Hiraga
A1 Toyoaki Natsume
A1 Xuemeng Zhou
A1 Danny Leung
A1 Masato T. Kanemaki
A1 Anne D. Donaldson
A1 Huimin Zhao
A1 Stephen Dalton
A1 Victor G. Corces
A1 David M. Gilbert
YR 2019
UL http://biorxiv.org/content/early/2019/12/28/2019.12.28.890020.abstract
AB DNA is replicated in a defined temporal order termed the replication timing (RT) program. RT is spatially segregated in the nucleus with early/late replication corresponding to Hi-C A/B chromatin compartments, respectively. Early replication is also associated with active histone modifications and transcriptional permissiveness. However, the mechanistic interplay between RT, chromatin state, and genome compartmentalization is largely unknown. Here we report that RT is central to epigenome maintenance and compartmentalization in both human embryonic stem cells (hESCs) and cancer cell line HCT116. Knockout (KO) of the conserved RT control factor RIF1, rather than causing discrete RT switches as previously suspected, lead to dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1’s enrichment in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike all prior RIF1 KO cells, including HCT116, which show localized alterations. Regions that retain RT, which are prevalent in HCT116 but rare in hESCs, consist of large H3K9me3 domains revealing two independent mechanisms of RT regulation that are used to different extents in different cell types. RIF1 KO results in a striking genome wide downregulation of H3K27ac peaks and enrichment of H3K9me3 at large domains that remain late replicating, while H3K27me3 and H3K4me3 are re-distributed genome wide in a cell type specific manner. These histone modification changes coincided with global reorganization of genome compartments, transcription changes and a genome wide strengthening of TAD structures. Inducible degradation of RIF1 revealed that disruption of RT is upstream of genome compartmentalization changes. Our findings demonstrate that disruption of RT leads to widespread epigenetic mis-regulation, supporting previously speculative models in which the timing of chromatin assembly at the replication fork plays a key role in maintaining the global epigenetic state, which in turn drives genome architecture.