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Genetic recombination is directed away from functional genomic elements in mice.

Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova GV - Nature (2012)

Bottom Line: Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis.Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated gene in mammals.However, in the absence of PRDM9, most recombination is initiated at promoters and at other sites of PRDM9-independent H3K4 trimethylation.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA.

ABSTRACT
Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis. Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated 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 analyse the genome-wide distribution of recombination initiation sites in Prdm9 knockout mice and in two mouse strains with different Prdm9 alleles and their F(1) hybrid. We show that PRDM9 determines the positions of practically all hotspots in the mouse genome, with the exception of the pseudo-autosomal region (PAR)--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 H3 lysine 4 (H3K4) trimethylation marks. However, in the absence of PRDM9, most 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.

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DSB hotspots localize to different loci in 9R and 13R mice. a. DSB hotspots in a representative 0.5 Mb region on chromosome 3. The magenta bar indicates the region shown in the insert. This illustrates two adjacent, yet distinct hotspots in 9R and 13R. Data are smoothed using a 1 Kb sliding window (step 100 bp). Coverage is given as reads per Kb per million (RPKM) b. Overlap between 9R and 13R hotspots. Here and in subsequent panels, only overlaps in the central 400 bp of hotspots are counted. c. Overlap between 9R and C57Bl/6 (B6) hotspots. The excess of B6 hotspots is due to higher ChIP enrichment in this ChIP-Seq sample. B6 hotspots not found in 9R are a weak subset. d. Parental origin of DSB hotspots in the F1 (9R × 13R) mice. e. Stronger 9R and 13R hotspots are active in F1 progeny. The top 14,000 hotspots for each background were binned by strength and the overlap with F1 hotspots assessed for each bin. f. Distribution of hits to the 9R motif (black) and 13R motif (red) around their respective hotspots. Data are plotted in 200 nt steps. g. Alignment of 9R and 13R motifs to the predicted PRDM9 binding sites (see methods). ZNF, Zn finger contact residues; BS, predicted PRDM9 binding site.
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Figure 1: DSB hotspots localize to different loci in 9R and 13R mice. a. DSB hotspots in a representative 0.5 Mb region on chromosome 3. The magenta bar indicates the region shown in the insert. This illustrates two adjacent, yet distinct hotspots in 9R and 13R. Data are smoothed using a 1 Kb sliding window (step 100 bp). Coverage is given as reads per Kb per million (RPKM) b. Overlap between 9R and 13R hotspots. Here and in subsequent panels, only overlaps in the central 400 bp of hotspots are counted. c. Overlap between 9R and C57Bl/6 (B6) hotspots. The excess of B6 hotspots is due to higher ChIP enrichment in this ChIP-Seq sample. B6 hotspots not found in 9R are a weak subset. d. Parental origin of DSB hotspots in the F1 (9R × 13R) mice. e. Stronger 9R and 13R hotspots are active in F1 progeny. The top 14,000 hotspots for each background were binned by strength and the overlap with F1 hotspots assessed for each bin. f. Distribution of hits to the 9R motif (black) and 13R motif (red) around their respective hotspots. Data are plotted in 200 nt steps. g. Alignment of 9R and 13R motifs to the predicted PRDM9 binding sites (see methods). ZNF, Zn finger contact residues; BS, predicted PRDM9 binding site.

Mentions: Homologous recombination is initiated by the introduction of DNA double stranded breaks (DSBs) by the SPO11 protein11, and we have previously shown that recombination sites can be mapped by sequencing the ends of breaks recovered by chromatin immunoprecipitation with antibodies to DMC1 protein bound to these ends (ChIP-Seq, SSDS)12,13. To directly assess the extent to which hotspot location depends on PRDM9 we have employed this approach to generate high-resolution maps of recombination initiation sites in two nearly identical (congenic) mouse strains with different Prdm9 alleles (strains 9R and 13R, Supplementary Fig. 1). We found that although the number of hotspots in 9R and 13R is similar (14,869 and 15,481, respectively) there is practically no overlap in the locations of hotspots (Fig. 1a,b). We next mapped recombination initiation sites in the most commonly used laboratory mouse strain C57Bl/6 (18,313 hotspots), which has the same Prdm9 allele as 9R. We found that more than 98% of 9R hotspots were present in C57Bl/6 (Fig. 1c). Taken together, these data constitute the first direct evidence that practically all recombination hotspots are PRDM9 dependent.


Genetic recombination is directed away from functional genomic elements in mice.

Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova GV - Nature (2012)

DSB hotspots localize to different loci in 9R and 13R mice. a. DSB hotspots in a representative 0.5 Mb region on chromosome 3. The magenta bar indicates the region shown in the insert. This illustrates two adjacent, yet distinct hotspots in 9R and 13R. Data are smoothed using a 1 Kb sliding window (step 100 bp). Coverage is given as reads per Kb per million (RPKM) b. Overlap between 9R and 13R hotspots. Here and in subsequent panels, only overlaps in the central 400 bp of hotspots are counted. c. Overlap between 9R and C57Bl/6 (B6) hotspots. The excess of B6 hotspots is due to higher ChIP enrichment in this ChIP-Seq sample. B6 hotspots not found in 9R are a weak subset. d. Parental origin of DSB hotspots in the F1 (9R × 13R) mice. e. Stronger 9R and 13R hotspots are active in F1 progeny. The top 14,000 hotspots for each background were binned by strength and the overlap with F1 hotspots assessed for each bin. f. Distribution of hits to the 9R motif (black) and 13R motif (red) around their respective hotspots. Data are plotted in 200 nt steps. g. Alignment of 9R and 13R motifs to the predicted PRDM9 binding sites (see methods). ZNF, Zn finger contact residues; BS, predicted PRDM9 binding site.
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Figure 1: DSB hotspots localize to different loci in 9R and 13R mice. a. DSB hotspots in a representative 0.5 Mb region on chromosome 3. The magenta bar indicates the region shown in the insert. This illustrates two adjacent, yet distinct hotspots in 9R and 13R. Data are smoothed using a 1 Kb sliding window (step 100 bp). Coverage is given as reads per Kb per million (RPKM) b. Overlap between 9R and 13R hotspots. Here and in subsequent panels, only overlaps in the central 400 bp of hotspots are counted. c. Overlap between 9R and C57Bl/6 (B6) hotspots. The excess of B6 hotspots is due to higher ChIP enrichment in this ChIP-Seq sample. B6 hotspots not found in 9R are a weak subset. d. Parental origin of DSB hotspots in the F1 (9R × 13R) mice. e. Stronger 9R and 13R hotspots are active in F1 progeny. The top 14,000 hotspots for each background were binned by strength and the overlap with F1 hotspots assessed for each bin. f. Distribution of hits to the 9R motif (black) and 13R motif (red) around their respective hotspots. Data are plotted in 200 nt steps. g. Alignment of 9R and 13R motifs to the predicted PRDM9 binding sites (see methods). ZNF, Zn finger contact residues; BS, predicted PRDM9 binding site.
Mentions: Homologous recombination is initiated by the introduction of DNA double stranded breaks (DSBs) by the SPO11 protein11, and we have previously shown that recombination sites can be mapped by sequencing the ends of breaks recovered by chromatin immunoprecipitation with antibodies to DMC1 protein bound to these ends (ChIP-Seq, SSDS)12,13. To directly assess the extent to which hotspot location depends on PRDM9 we have employed this approach to generate high-resolution maps of recombination initiation sites in two nearly identical (congenic) mouse strains with different Prdm9 alleles (strains 9R and 13R, Supplementary Fig. 1). We found that although the number of hotspots in 9R and 13R is similar (14,869 and 15,481, respectively) there is practically no overlap in the locations of hotspots (Fig. 1a,b). We next mapped recombination initiation sites in the most commonly used laboratory mouse strain C57Bl/6 (18,313 hotspots), which has the same Prdm9 allele as 9R. We found that more than 98% of 9R hotspots were present in C57Bl/6 (Fig. 1c). Taken together, these data constitute the first direct evidence that practically all recombination hotspots are PRDM9 dependent.

Bottom Line: Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis.Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated gene in mammals.However, in the absence of PRDM9, most recombination is initiated at promoters and at other sites of PRDM9-independent H3K4 trimethylation.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA.

ABSTRACT
Genetic recombination occurs during meiosis, the key developmental programme of gametogenesis. Recombination in mammals has been recently linked to the activity of a histone H3 methyltransferase, PR domain containing 9 (PRDM9), the product of the only known speciation-associated 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 analyse the genome-wide distribution of recombination initiation sites in Prdm9 knockout mice and in two mouse strains with different Prdm9 alleles and their F(1) hybrid. We show that PRDM9 determines the positions of practically all hotspots in the mouse genome, with the exception of the pseudo-autosomal region (PAR)--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 H3 lysine 4 (H3K4) trimethylation marks. However, in the absence of PRDM9, most 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.

Show MeSH
Related in: MedlinePlus