Our paper: Genetic recombination is targeted towards gene promoter regions in dogs

This guest post is by Adam Auton (@adamauton) on his paper (along with coauthors) Genetic recombination is targeted towards gene promoter regions in dogs arXived here.

In this paper, we investigate the age-old question of how meiotic recombination is distributed in the genome of dogs. Before you stop reading, I’d like to spend a couple of paragraphs explaining why this is an interesting topic.

Recombination in mammalian genomes tends to occur in highly localized regions known as recombination hotspots. There are probably about 30,000 or so recombination hotspots in the human genome, each of which are about 2kb wide with recombination rates that can be thousands of times that of the surrounding region. Until a few years ago, the mechanism by which recombination hotspots are localized was largely unknown. This all began to change with the discovery of PRDM9 as the gene responsible for localizing hotspots [1-3]. The role of PRDM9 is to recognize and bind to specific DNA motifs in the genome, which are subsequently epigenetically marked as preferred locations of recombination.

PRDM9 turns out to be quite a fascinating gene. There is extensive variation in PRDM9 both within and across species, which points to strong selective pressures. Importantly, variation in PRDM9 can alter the recognized DNA motifs, thereby altering the locations of recombination hotspots in the genome. The high level of variation in PRDM9 between species appears to explain why recombination hotspots tend to not be shared between even closely related species, such as human and chimpanzees.

We’ve learnt much about the importance of PRDM9 from studies in mice. Knock-out of Prdm9 in mice results in infertility and, most interestingly of all, certain alleles of mouse Prdm9 appear to be incompatible with each other [4,5]. Specifically, Mus m. musculus / Mus m. domesticus hybrid male mice are infertile if they are heterozygotic for specific Prdm9 alleles. As such, Prdm9 has been called a ‘speciation gene’, as it has the potential to restrict gene flow between nascent species, and is the only known such example in mammals.

Given this importance, it was therefore surprising to note that dogs, uniquely amongst mammals, appear to carry a dysfunctional version of PRDM9 [6]. This therefore begs the question of how recombination occurs in dogs, and provides the motivation for our paper.

Estimating recombination rates directly is challenging and costly, as only a few dozen events occur during any given meiosis. Therefore, to characterize large numbers of recombination events on a genome-wide basis, large pedigrees need to be genotyped, which can be both laborious and costly to do in non-model organisms. Luckily, an experiment of this nature has been previously performed in dogs, which revealed a recombination landscape that was reasonably consistent with patterns observed in other mammals [7].

However, without enormous sample sizes, such methods can only investigate patterns at scales far greater than the scale of individual hotspots. In order to investigate fine-scale patterns on a genome-wide basis, one must turn to indirect statistical methods, and it is this approach that we have adopted in our study. First, we whole-genome sequenced a collection of 51 outbred dogs and used this data to call single nucleotide polymorphisms. Having done so, we used the statistical method, LDhat, which infers historical recombination rates via analysis of patterns of linkage disequilibrium. This is a similar approach that adopted by Axelsson et al. [8], who used microarrays to gain strong insights into canine recombination, although our use of sequencing allows us to investigate patterns at a much finer scale.

Our results agree nicely with the broad-scale experimental estimates, but reveal a quite unusual landscape at the fine scale. In particular, we find that canine recombination is strongly enriched in regions with high CpG content. As such, recombination rates are very high around the CpG-rich regions associated with gene promoters, and contrasts with other mammalian species in which recombination hotspots do not show any particularly strong affinity for gene promoter regions. However, it is also reminiscent of patterns seen in Prdm9 knock-out mice which, although infertile, still produce double-strand breaks that cluster in gene promoter regions [9].

Interestingly, the dog genome is known to have very high CpG content. It has previously been suggested that one potential mechanism by which this may have occurred is biased gene conversion, which can result in the preferential transmission of G-C alleles over A-T alleles in the vicinity of recombination events. To investigate this phenomenon, we also sequenced a related fox species, which allowed us to see if G-C alleles are being gained or lost around recombination hotspots. We see that dog recombination hotspots do indeed appear to be acquiring GC content. This could imply a runaway process, by which CpG-rich regions have become recombinogenic, and hence have started to acquire more GC content, and hence become more recombinogenic.

As such, our results show that recombination in the dog genome appears to have some quite interesting properties. However, questions remain. The loss of PRDM9 in dogs appears to have resulted in some qualitative features that are consistent with knock-out mice, and yet dogs somehow avoid the associated infertility. Perhaps canine meiosis manages to complete without a PRDM9 ortholog, or perhaps an as-yet-unknown gene in the dog genome has adopted the role of PRDM9. In either case, the investigation of recombination in dogs provides a valuable means for building our understanding of how recombination occurs and its importance in shaping the genome.

1. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840.
2. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, et al. (2010) Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327: 876-879.
3. Parvanov ED, Petkov PM, Paigen K (2010) Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835.
4. Flachs P, Mihola O, Simecek P, Gregorova S, Schimenti JC, et al. (2012) Interallelic and intergenic incompatibilities of the Prdm9 (Hst1) gene in mouse hybrid sterility. PLoS Genet 8: e1003044.
5. Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323: 373-375.
6. Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, et al. (2009) Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet 5: e1000753.
7. Wong AK, Ruhe AL, Dumont BL, Robertson KR, Guerrero G, et al. (2010) A comprehensive linkage map of the dog genome. Genetics 184: 595-605.
8. Axelsson E, Webster MT, Ratnakumar A, Ponting CP, Lindblad-Toh K (2012) Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Res 22: 51-63.
9. Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova GV (2012) Genetic recombination is directed away from functional genomic elements in mice. Nature 485: 642-645.

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7 thoughts on “Our paper: Genetic recombination is targeted towards gene promoter regions in dogs

  1. This paper reminds me of a classical result showing that gene conversion in yeast is often localized to promoter regions, e.g.

    An initiation site for meiotic gene conversion in the yeast Saccharomyces cerevisiae.
    Nicolas A, Treco D, Schultes NP, Szostak JW.
    Nature. 1989 Mar 2;338(6210):35-9.
    Abstract: An initiation site for meiotic gene conversion has been identified in the promoter region of the ARG4 gene of Saccharomyces cerevisiae. The chromosome on which initiation occurs is the recipient of genetic information during gene conversion.

    I haven’t folowed this literature closely for a long time, but if I recall correctly there was some controversy about the universality of this trend. It would be interesting to see what the latest is on the genome-wide evidence for this phenomenon in yeast and (if relevant) see how it compares to your results in dogs.

    • Thank you. An earlier draft of this paper actually had a comment along these lines, and I went as far as to speculate that dogs were using a similar mechanism as yeast. However, I received comments from a few people that felt this was overly speculative, and I ultimately removed the comment. The elevated rates around promoters is certainly intriguing, but without additional evidence, the similarity to yeast could be coincidental.

  2. I think I’m missing something–why would biased gene conversion favor GC-rich sequences if they are recombinogenic? Isn’t the standard thing that alleles that are *less* recombinogenic are favored in biased gene conversion? I.e. if there’s an A/G SNP and the G tends to initiate DSBs, then the bias favors the A?

  3. So Adam can probably answer this better, but there are two forms of bias gene conversion. Biased initiation of double stranded breaks and biased repair of heteroduplex DNA.

    1) The former leads to the recombination hotspot paradox, sequence motifs that cause DSB initiation in cis will be undertransmitted in heterozyg. [conversely alleles that disrupt motifs will be undertransmitted].

    2) The latter is due to the idea that the repair of heteroduplex DNA (due to SNPs) may favour repair using GC over AT alleles at a SNP. This is not due to the initiation of the DSB only the repair of it. This is still just a hypothesis in mammals, but getting more established in Yeast, that is consistent with the patterns of mole. evol.

    GC rich regions are generally more recombingenic, perhaps due to the fact that the DNA is more open. This due to (2) leads to further biased gene conversion, making them increasing GC rich.

    At one point in writing about this stuff I wanted to call (1) biased DBS initiation, as the gene conversion itself isn’t biased, to prevent this confusion. But we decided that it was too well established in the literature.

    Graham

    • Just to agree with this, I try and distinguish the two effects. I reserve the term biased gene conversion for effect (2), as I think this is the original meaning of the term. However, the term BGC has also been used to mean (1), so the literatiure can be quite confusing. It would be great if there was a standard term for (1) to distinguish it from BGC. I generally refer to it as something vague like “meiotic drive”, however I don’t really like that term either. Perhaps biased DSB initiation is a good idea. BDSBI is too a long abbreviation tho 🙂

      • Another assumption we’re making is that, whereas mutating the bp of a PRDM9 recognized motif can have a substantial effect on chilling a hotspot, the cooling effect of a single mutation in a dog CpG hotspot is more minor. Thus the repair bias for CG can overcome the initiation bias on AT in dogs. I’m not sure of any good way to test that assumption, but it seems reasonable, and the evidence of runaway CpG islands in dogs offers some support for it.

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