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Series GSE51334 Query DataSets for GSE51334
Status Public on Nov 20, 2014
Title DNA replication-timing boundaries separate stable chromosome domains with cell-type-specific functions
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale.Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.
 
Overall design Protocols for generating and quality control for replication timing data from microarray hybridization (Repli-chip) or sequencing (Repli-seq) were performed as previously described. CH12, MEL, Gm12878, Gm12801, Gm12812, Gm12813, HeLa-S3, HepG2, HUVEC, IMR90, MCF-7, Sk-N-Sh and NHEK cells were obtained and grown according to standard ENCODE cell culture protocols. Wild-type control and Suz12 knockout naive mESCs were derived from the previously described strain25 and obtained from Anne Laugesen and Kristian Helin and cultured in 2i+LIF medium as previously described. Previously published Repli-chip and Repli-seq3 data sets were also used in this study.
 
Contributor(s) Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Thurman RE, Cheng Y, Gülsoy G, Snyder M, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM
Citation(s) 25409831
Submission date Oct 02, 2013
Last update date Aug 23, 2024
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platforms (25)
GPL5644 NKI/VanSteensel_HSA_390k_1/8_v070724
GPL5646 NKI/VanSteensel_HSA_390k_2/8_v070724
GPL5648 NKI/VanSteensel_HSA_390k_3/8_v070724
Samples (993)
GSM220158 Tig3 human fibroblast cells, LaminB1 DamID, platform 1/8
GSM220159 Tig3 human fibroblast cells, LaminB1 DamID, platform 2/8
GSM220160 Tig3 human fibroblast cells, LaminB1 DamID, platform 3/8
Relations
BioProject PRJNA267243

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Supplementary file Size Download File type/resource
GSE51334_RAW.tar 683.7 Gb (http)(custom) TAR (of BAM, BED, BIGWIG, BROADPEAK, NARROWPEAK, PAIR, TSV, TXT)
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Raw data provided as supplementary file
Processed data provided as supplementary file
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