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| Status |
Public on Oct 20, 2017 |
| Title |
Ability of SPEN to bind to chromatin in testicular cells |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Since SPEN co-localizes with transcriptionally active chromatin and it is considered as a nuclear matrix platform that organizes and integrates transcriptional responses, we aimed to find out how it is involved in gene expression regulation in spermatogenic cells. We assumed that SPEN could be directly involved in down-regulation of gene expression during recovery from heat shock, when general repression of the transcription was observed. Nascent SPEN (~400 kDa) is processed to several fragments. We tested antibodies to N-terminal, internal, or C-terminal SPEN sequences in ChIP experiments on mouse testicular cells either untreated or heat shocked. Only antibodies against N-terminal or internal SPEN epitopes were effective while C-terminal SPEN did not bind to chromatin. However sequencing of N-terminal or internal SPEN ChIP samples did not reveal any strong SPEN binding to the chromatin and the enrichment was seen primarily in genomic structural variants. This suggests that SPEN could be loosely associated with DNA via other proteins.
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| Overall design |
We sequenced DNA immunoprecipitated from isolated testicular cells using rabbit polyclonal anti-SPEN antibodies raised against N-terminal or internal part of the protein. Cells were either untreated (control) or heat shocked for 15-30 minutes with subsequent recovery. Five to six ChIP replicates were collected per each sequenced sample; negative control sample with rabbit IgG (performed in parralel to SPEN Ab samples, then pooled for sequencing) and input samples were included.
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| Contributor(s) |
Korfanty J, Stokowy T, Widlak W |
| Citation missing |
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| |
| Submission date |
Jun 09, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Tomasz Stokowy |
| E-mail(s) |
tomasz.stokowy@uib.no
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| Organization name |
University of Bergen
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| Department |
IT Division
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| Lab |
Scientific Computing
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| Street address |
Nygardsgaten 5
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| City |
Bergen |
| ZIP/Postal code |
5020 |
| Country |
Norway |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA389788 |
| SRA |
SRP108879 |
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