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| Status |
Public on Jun 30, 2018 |
| Title |
Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.
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| Overall design |
n=3 Smchd1del/del vs n=3 Smchd1del/fl female neural stem cell lines analysed by RNA-seq.
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| |
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| Contributor(s) |
Jansz N, Blewitt M |
| Citation(s) |
30127357 |
| Submission date |
Mar 19, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Marnie Blewitt |
| E-mail(s) |
blewitt@wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute
|
| Lab |
Blewitt Lab
|
| Street address |
1G Royal Parade
|
| City |
Parkville |
| State/province |
Victoria |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA439002 |
| SRA |
SRP136027 |
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