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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 27, 2018 |
| Title |
Interrogating the functions of PRDM9 domains in meiosis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Homologous recombination is required for proper segregation of homologous chromosomes during meiosis. It predominantly occurs at recombination hotspots that are defined by the DNA binding specificity of the PRDM9 protein. PRDM9 contains three domains which are typically different families of proteins involved in regulation of transcription in other proteins, yet, the role of PRDM9 in gene expression control has not been evaluated. Here we analyze the germline transcriptome of the Prdm9-/- male mice in comparison to Prdm9+/+ males and find no apparent differences in the mRNA and miRNA profiles. We further explore the role of PRDM9 in meiosis by analyzing the activity of PRDM9 lacking effect of the KRAB, SSXRD and post-SET zinc finger domains deletion mutants in a cell expression system and the KRAB domain deletion in mice. We found that although the post-SET zinc finger and the KRAB domains are not essential for the methyltransferase activity of PRDM9 in a cell culture expression systemin vitro, mice lacking the KRAB domain mutant mice domain show only residual PRDM9 methyltransferase activity and undergo meiotic arrest. In aggregate, our data indicate that these domains that are classically involved in gene regulation do not serve that role in PRDM9, but instead are involved in PRDM9 function has likely diverged from the typical function of a transcription factor and adapted the new role in setting the proper chromatin environment for initiation and completion of homologous recombination.
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| Overall design |
Testes mRNA-seq, miRNA-seq, Chip-seq were generated using next generation sequencing.
* The "GSE104850_RAW.tar" archive includes the processed data files for Samples GSM3053281-GSM3053299. *
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| Contributor(s) |
Thibault-Sennett S, Yu Q, Smagulova F, Cloutier J, Brick K, Camerini-Otero D, Petukhova GV |
| Citation(s) |
29674518 |
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| Submission date |
Oct 11, 2017 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Galina Petukhova |
| E-mail(s) |
galina.petukhova@usuhs.edu
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| Organization name |
USUHS
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| Department |
Biochemistry
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| Street address |
4301 Jones Bridge Rd
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (28)
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| GSM3053275 |
mRNA-seq Hop2-/- #2 |
| GSM3053276 |
mRNA-seq WT Adult |
| GSM3053277 |
microRNA-seq Prdm9-/- #1 |
| GSM3053278 |
microRNA-seq Prdm9-/- #2 |
| GSM3053279 |
microRNA-seq Hop2-/- #1 |
| GSM3053280 |
microRNA-seq Hop2-/- #2 |
| GSM3053281 |
H3K4me3 ChIP-seq, GC-1 Pretransfection |
| GSM3053282 |
H3K4me3 ChIP-seq, GC-1 WT #1 |
| GSM3053283 |
H3K4me3 ChIP-seq, GC-1 WT #2 |
| GSM3053284 |
H3K4me3 ChIP-seq, GC-1 WT #3 |
| GSM3053285 |
H3K4me3 ChIP-seq, GC-1 SET #1 |
| GSM3053286 |
H3K4me3 ChIP-seq, GC-1 SET #2 |
| GSM3053287 |
H3K4me3 ChIP-seq, GC-1 KRAB-1 #1 |
| GSM3053288 |
H3K4me3 ChIP-seq, GC-1 KRAB-1 #2 |
| GSM3053289 |
H3K4me3 ChIP-seq, GC-1 KRAB-1 #3 |
| GSM3053290 |
H3K4me3 ChIP-seq, GC-1 KRAB-2 |
| GSM3053291 |
H3K4me3 ChIP-seq, GC-1 SSXRD #1 |
| GSM3053292 |
H3K4me3 ChIP-seq, GC-1 SSXRD #2 |
| GSM3053293 |
H3K4me3 ChIP-seq, GC-1 ZincF #1 |
| GSM3053294 |
H3K4me3 ChIP-seq, GC-1 ZincF #2 |
| GSM3053295 |
input, GC-1 WT |
| GSM3053296 |
H3K4me3 ChIP-seq, Prdm9(K/K) |
| GSM3053297 |
SSDS Prdm9(K/K) |
| GSM3053298 |
H3K4me3 ChIP-seq, WT adult |
| GSM3053299 |
H3K4me3 ChIP-seq, Spo11(-/-) adult |
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| Relations |
| BioProject |
PRJNA413989 |
| SRA |
SRP119794 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104850_RAW.tar |
1.7 Gb |
(http)(custom) |
TAR (of BED, BIGWIG) |
| GSE104850_RNA-seq_TPM_genes.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE104850_RNA-seq_TPM_transcripts.csv.gz |
4.7 Mb |
(ftp)(http) |
CSV |
| GSE104850_RNA-seq_ens_gene_sleuth.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE104850_miRNA_DEseq2_result.csv.gz |
89.0 Kb |
(ftp)(http) |
CSV |
| GSE104850_microRNA-seq_TPM_annotated_miRNA.csv.gz |
24.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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