 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 15, 2023 |
| Title |
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells [RAP-seq_human] |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
X-chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X-chromosome in cis to mediate chromosome-wide gene silencing. In female naïve human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration and XCI does not occur, raising questions about XIST’s function. We found that XIST spreads across the X-chromosome and induces dampening of X-linked gene expression in naïve hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences on autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X-chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.
|
| |
|
| Overall design |
We examined the genomic localization of the XIST lncRNA using RNA Antisense Purification (RAP) in multiple cells: female human naive hESCs (H9, UCLA1, and iPSCs), NHFD (2 replicates), female human primed hESCs (H9 and iPSC), and XIST KO in H9
|
| |
|
| Contributor(s) |
Dror I, Sahakyan A, Chitiashvili T, Tan S, Cano CT, Plath K |
| Citation(s) |
38181737 |
| |
| Submission date |
Aug 22, 2023 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
|
| Street address |
BOX 951737, 36-133 CHS
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095-1737 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (15)
|
| GSM7729016 |
Human Female naive hESC H9 – Input |
| GSM7729017 |
Human Female naive hESC H9 – XIST Pulldown |
| GSM7729018 |
Human Female naive hESC UCLA1 – Input |
| GSM7729019 |
Human Female naive hESC UCLA1 – XIST Pulldown |
| GSM7729020 |
Human Female naive iPSC – Input |
| GSM7729021 |
Human Female naive iPSC – XIST Pulldown |
| GSM7729022 |
Human Female naive hESC H9 with XIST KO – Input |
| GSM7729023 |
Human Female naive hESC H9 with XIST KO – Pulldown |
| GSM7729024 |
Human Female prime hESC H9 – Input |
| GSM7729025 |
Human Female prime hESC H9 – XIST Pulldown |
| GSM7729026 |
Human Female prime iPSC – Input |
| GSM7729027 |
Human Female prime iPSC – XIST Pulldown |
|
| This SubSeries is part of SuperSeries: |
| GSE241444 |
XIST directly regulates X-linked and autosomal genes in naïve human pluripotent cells |
|
| Relations |
| BioProject |
PRJNA1008164 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241439_RAW.tar |
6.8 Mb |
(http)(custom) |
TAR (of BEDGRAPH, BROADPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...