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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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Proposed role of the PRDM9 protein. Left: In cells containing a functional copy of PRDM9 (Wild type) the DSB formation machinery (scissors) is directed to preferred DSB sites / PRDM9 binding sites. Right: In the absence of PRDM9, the DSB formation machinery opportunistically makes breaks at PRDM9-independent H3K4me3 marks such as those at promoters and enhancers. This results in inefficient DSB repair and meiotic arrest.
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Figure 4: Proposed role of the PRDM9 protein. Left: In cells containing a functional copy of PRDM9 (Wild type) the DSB formation machinery (scissors) is directed to preferred DSB sites / PRDM9 binding sites. Right: In the absence of PRDM9, the DSB formation machinery opportunistically makes breaks at PRDM9-independent H3K4me3 marks such as those at promoters and enhancers. This results in inefficient DSB repair and meiotic arrest.

Mentions: The sterility of Prdm9−/− mice suggests that the initiation of recombination at H3K4me3-marked functional elements may not be compatible with gametogenesis. Does recombination interfere with the transcription of essential meiotic genes? Since four chromatids are present before the first meiotic division it is unlikely that disruption of transcription on one of them will lead to a significant drop in overall transcription of any particular gene hit by a DSB. On the other hand, it is conceivable that the opposite is true and that transcription interferes with the repair of breaks introduced at promoters. The resulting aberrant recombination would account for the observation that in Prdm9−/− mice persistent DSBs are present and only partial synapsis is seen between homologous chromosomes9 (Supplementary Fig. 10). The Prdm9 gene exhibits complex epistatic interactions culminating in sterility of F1 hybrid males carrying a particular combination of functional Prdm9 alleles7. Unlike in Prdm9−/− mice, repair of meiotic DSBs in such males proceeds normally in a large fraction of cells with 40% of spermatocytes showing complete homologous synapsis7. While this suggests that distinct mechanisms are responsible for meiotic arrest in Prdm9−/− mice and in F1 hybrid males, we cannot exclude the possibility that an alternative role of PRDM9 in meiotic progression accounts for both sterility phenotypes. Although a function of PRDM9 in transcription has not been demonstrated, PRDM9 contains conserved domains implicated in transcription25,26 and could potentially be involved in executing the meiotic transcription program. It is also conceivable that PRDM9 is directly required for efficient progression of recombination. The potential importance of avoiding recombination at functional genomic elements is highlighted in the canid lineage, which has lost Prdm927,28. Though dogs retain recombination hotspots27, preliminary analyses suggest that unlike in Prdm9−/− mice, these hotspots do not appear to be enriched at promoters (Supplementary Information). A trivial explanation would be that dog Prdm9 resides in the unassembled parts of the genome, however, these data may also indicate that alternative mechanisms have evolved to target recombination to specialized genomic regions in species that lack Prdm9. Ultimately, we favour the hypothesis that PRDM9 prevents initiation of recombination in the areas of the genome where successful completion of recombination might be compromised by other nuclear processes (Fig. 4). The re-routing of DSBs from important genomic elements may also play a protective role against potential mutagenic effects of recombination.


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

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

Proposed role of the PRDM9 protein. Left: In cells containing a functional copy of PRDM9 (Wild type) the DSB formation machinery (scissors) is directed to preferred DSB sites / PRDM9 binding sites. Right: In the absence of PRDM9, the DSB formation machinery opportunistically makes breaks at PRDM9-independent H3K4me3 marks such as those at promoters and enhancers. This results in inefficient DSB repair and meiotic arrest.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3367396&req=5

Figure 4: Proposed role of the PRDM9 protein. Left: In cells containing a functional copy of PRDM9 (Wild type) the DSB formation machinery (scissors) is directed to preferred DSB sites / PRDM9 binding sites. Right: In the absence of PRDM9, the DSB formation machinery opportunistically makes breaks at PRDM9-independent H3K4me3 marks such as those at promoters and enhancers. This results in inefficient DSB repair and meiotic arrest.
Mentions: The sterility of Prdm9−/− mice suggests that the initiation of recombination at H3K4me3-marked functional elements may not be compatible with gametogenesis. Does recombination interfere with the transcription of essential meiotic genes? Since four chromatids are present before the first meiotic division it is unlikely that disruption of transcription on one of them will lead to a significant drop in overall transcription of any particular gene hit by a DSB. On the other hand, it is conceivable that the opposite is true and that transcription interferes with the repair of breaks introduced at promoters. The resulting aberrant recombination would account for the observation that in Prdm9−/− mice persistent DSBs are present and only partial synapsis is seen between homologous chromosomes9 (Supplementary Fig. 10). The Prdm9 gene exhibits complex epistatic interactions culminating in sterility of F1 hybrid males carrying a particular combination of functional Prdm9 alleles7. Unlike in Prdm9−/− mice, repair of meiotic DSBs in such males proceeds normally in a large fraction of cells with 40% of spermatocytes showing complete homologous synapsis7. While this suggests that distinct mechanisms are responsible for meiotic arrest in Prdm9−/− mice and in F1 hybrid males, we cannot exclude the possibility that an alternative role of PRDM9 in meiotic progression accounts for both sterility phenotypes. Although a function of PRDM9 in transcription has not been demonstrated, PRDM9 contains conserved domains implicated in transcription25,26 and could potentially be involved in executing the meiotic transcription program. It is also conceivable that PRDM9 is directly required for efficient progression of recombination. The potential importance of avoiding recombination at functional genomic elements is highlighted in the canid lineage, which has lost Prdm927,28. Though dogs retain recombination hotspots27, preliminary analyses suggest that unlike in Prdm9−/− mice, these hotspots do not appear to be enriched at promoters (Supplementary Information). A trivial explanation would be that dog Prdm9 resides in the unassembled parts of the genome, however, these data may also indicate that alternative mechanisms have evolved to target recombination to specialized genomic regions in species that lack Prdm9. Ultimately, we favour the hypothesis that PRDM9 prevents initiation of recombination in the areas of the genome where successful completion of recombination might be compromised by other nuclear processes (Fig. 4). The re-routing of DSBs from important genomic elements may also play a protective role against potential mutagenic effects of recombination.

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