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Series GSE211570 Query DataSets for GSE211570
Status Public on Jul 11, 2023
Title Replication dynamics identifies the folding principles of the inactive X chromosome [BrdU-IP Repli-seq]
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase upon X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other, and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization on heterochromatin stability and gene regulation.
 
Overall design BrdUIP Repli-seq, RNA-seq, and 4C-seq experiments were performed in wild-type and SmcHD1 mutant female JB4/EI7HZ2 mouse embryonic stem cells, day-9 differentiated cells, and neural stem cells (NSCs). Single-cell Repli-seq (scRepli-seq) was performed in wild-type and SmcHD1 mutant NSCs. We only deposited single-cell data sets which passed our filtering steps.
 
Contributor(s) Poonperm R, Hiratani I
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Submission date Aug 18, 2022
Last update date Jul 11, 2023
Contact name Rawin Poonperm
E-mail(s) rawin.poonperm@riken.jp
Organization name RIKEN BDR
Street address 2-2-3 Minatojima-minamimachi, Chuo-ku
City Kobe-shi
ZIP/Postal code 650-0047
Country Japan
 
Platforms (2)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (50)
GSM6480293 WT JB4/EI7HZ2 mESCs Replicate 1, BrdU-IP Early
GSM6480294 WT JB4/EI7HZ2 mESCs Replicate 1, BrdU-IP Late
GSM6480295 WT JB4/EI7HZ2 mESCs Replicate 2, BrdU-IP Early
This SubSeries is part of SuperSeries:
GSE211574 Replication dynamics identifies the folding principles of the inactive X chromosome
Relations
BioProject PRJNA870924

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE211570_B6JF1_EpiSC_WT_mm9_Rep1_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.noX.qnorm.bedGraph.gz 733.3 Kb (ftp)(http) BEDGRAPH
GSE211570_B6JF1_EpiSC_WT_mm9_Rep2_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.noX.qnorm.bedGraph.gz 752.9 Kb (ftp)(http) BEDGRAPH
GSE211570_B6_MEF_WT_male_mm9_1_IP_Aneu_rmdup_w200ks40k_Percent_q0.05.noX.qnorm.bedGraph.gz 764.8 Kb (ftp)(http) BEDGRAPH
GSE211570_B6_WT_and_KO_bedgraph.tar.gz 1.4 Mb (ftp)(http) TAR
GSE211570_JF1_WT_and_KO_bedgraph.tar.gz 1.4 Mb (ftp)(http) TAR
GSE211570_RPE1_bedgraph.tar.gz 226.5 Kb (ftp)(http) TAR
GSE211570_RTclass_ESCtoNSC_b6_allele.bed.gz 37.1 Kb (ftp)(http) BED
GSE211570_RTclass_ESCtoNSC_jf1_allele.bed.gz 36.9 Kb (ftp)(http) BED
GSE211570_RTclass_SmcHD1-KO_SDSICLCE.bed.gz 2.4 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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