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Series GSE35498 Query DataSets for GSE35498
Status Public on May 22, 2012
Title Genetic recombination is directed away from functional genetic sites in mice.
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genetic recombination occurs during meiosis, the key developmental program of gametogenesis. Recombination in mammals has been recently linked to the activity of a histone H3 methyl-transferase, PRDM9, the product of the only known speciation gene in mammals. PRDM9 is thought to determine the preferred recombination sites - recombination hotspots - through sequence-specific binding of its highly polymorphic multi-Zn-finger domain. Nevertheless, Prdm9 knockout mice are proficient at initiating recombination. Here we map and analyze the genome-wide distribution of recombination initiation sites in Prdm9 knockout mice and in two mouse strains with different Prdm9 alleles and their F1 hybrid. We show that PRDM9 determines the positions of practically all hotspots in the mouse genome, with the remarkable exception of the pseudoautosomal region – the only area of the genome that undergoes recombination in 100% of cells. Surprisingly, hotspots are still observed in Prdm9 knockout mice and as in wild-type, these hotspots are found at H3K4 trimethylation marks. However, in the absence of PRDM9, the majority of recombination is initiated at promoters and at other sites of PRDM9-independent H3K4 trimethylation. Such sites are rarely targeted in wild-type mice indicating an unexpected role of the PRDM9 protein in sequestering the recombination machinery away from gene promoter regions and other functional genomic elements.
Overall design Detection of meiotic double strand breaks in mouse testis and comparison with H3K4me3 marks.
Contributor(s) Brick K, Smagulova F, Khil P, Camerini-Otero R, Petukhova G
Citation(s) 22660327
Submission date Feb 02, 2012
Last update date Jun 25, 2020
Contact name Kevin Brick
Organization name NIDDK
Department GBB
Street address 5/205 Memorial Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (17)
GSM869781 Anti-DMC1 B6 Sample 1
GSM869782 Anti-DMC1 B6 Sample 2
GSM869783 Anti-DMC1 13R Sample 1
SRA SRP010715
BioProject PRJNA152299

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Supplementary file Size Download File type/resource
GSE35498_13R_DSB_hotspots.bedGraph.gz 161.4 Kb (ftp)(http) BEDGRAPH
GSE35498_13R_H3K4me3_peaks.bedGraph.gz 1007.9 Kb (ftp)(http) BEDGRAPH
GSE35498_9R_DSB_hotspots.bedGraph.gz 155.6 Kb (ftp)(http) BEDGRAPH
GSE35498_9R_H3K4me3_peaks.bedGraph.gz 1.0 Mb (ftp)(http) BEDGRAPH
GSE35498_B6_DSB_hotspots.bedGraph.gz 191.5 Kb (ftp)(http) BEDGRAPH
GSE35498_B6_H3K4me3_peaks.bedGraph.gz 877.9 Kb (ftp)(http) BEDGRAPH
GSE35498_F1_DSB_hotspots.bedGraph.gz 166.0 Kb (ftp)(http) BEDGRAPH
GSE35498_PRDM9_DSB_hotspots.bedGraph.gz 260.2 Kb (ftp)(http) BEDGRAPH
GSE35498_PRDM9_H3K4me3_Liver_peaks.bedGraph.gz 441.0 Kb (ftp)(http) BEDGRAPH
GSE35498_PRDM9_H3K4me3_Testis_peaks.bedGraph.gz 949.6 Kb (ftp)(http) BEDGRAPH
GSE35498_RAW.tar 3.8 Gb (http)(custom) TAR (of BED)
GSE35498_SPO11_H3K4me3_peaks.bedGraph.gz 809.1 Kb (ftp)(http) BEDGRAPH
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