NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE211574 Query DataSets for GSE211574
Status Public on Jul 11, 2023
Title Replication dynamics identifies the folding principles of the inactive X chromosome
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
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.

This SuperSeries is composed of the SubSeries listed below.
 
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.

Refer to individual Series
 
Citation(s) 37563439
Submission date Aug 18, 2022
Last update date Nov 13, 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 (3)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (369)
GSM6480185 WT JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP20Mb
GSM6480186 WT JB4/EI7HZ2 mESCs Replicate 2, 4C-seq, VP20Mb
GSM6480187 SmcHD1-KO JB4/EI7HZ2 mESCs Replicate 1, 4C-seq, VP20Mb
This SuperSeries is composed of the following SubSeries:
GSE211569 Replication dynamics identifies the folding principles of the inactive X chromosome [4C]
GSE211570 Replication dynamics identifies the folding principles of the inactive X chromosome [BrdU-IP Repli-seq]
GSE211571 Replication dynamics identifies the folding principles of the inactive X chromosome [RNA-seq]
Relations
BioProject PRJNA870918

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
GSE211574_RAW.tar 991.6 Mb (http)(custom) TAR (of BEDGRAPH, WIG)
SRA Run SelectorHelp

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap