The recombinational anatomy of a mouse chromosome

A new standard genetic map for the laboratory mouse

Genetic maps provide a means to estimate the probability of the co-inheritance of linked loci as they are transmitted across generations in both experimental and natural populations. However, in the age of whole-genome sequences, physical distances measured in base pairs of DNA provide the standard coordinates for navigating the myriad features of genomes. Although genetic and physical maps are colinear, there are well-characterized and sometimes dramatic heterogeneities in the average frequency of meiotic recombination events that occur along the physical extent of chromosomes. There also are documented differences in the recombination landscape between the two sexes. We have revisited high-resolution genetic map data from a large heterogeneous mouse population and have constructed a revised genetic map of the mouse genome, incorporating 10,195 single nucleotide polymorphisms using a set of 47 families comprising 3546 meioses. The revised map provides a different picture of recombination in the mouse from that reported previously. We have further integrated the genetic and physical maps of the genome and incorporated SSLP markers from other genetic maps into this new framework. We demonstrate that utilization of the revised genetic map improves QTL mapping, partially due to the resolution of previously undetected errors in marker ordering along the chromosome.

Variation in genomic recombination rates among heterogeneous stock mice

We used a large panel of pedigreed, genetically admixed house mice to study patterns of recombination rate variation in a leading mammalian model system. We found considerable inter-individual differences in genomic recombination rates and documented a significant heritable component to this variation. These findings point to clear variation in recombination rate among common laboratory strains, a result that carries important implications for genetic analysis in the house mouse.

Relationship between incomplete synapsis and chiasma localization

One of the subjects within the meiotic field that has been actively investigated in the recent years is the temporal and functional relationships between meiotic recombination, cohesin loading and synaptonemal complex (SC) assembly. Although the study of meiotic mutants has shed some light, many questions remain to be answered. Here, we have studied this topic in the orthopteran Paratettix meridionalis, a species with telocentric chromosomes, which shows two unusual cytological features: pairing and synapsis of homologues during prophase I are restricted to the non-centromeric distal regions and extremely distal chiasma localization in metaphase I bivalents. In order to determine whether there is a relationship between both phenomena, we have used: (1) a spreading technique for following the ultrastructure of SC assembly and (2) immunofluorescence for SMC3 and SMC1alpha cohesin subunits, which mark the development of the axial element (a SC component); the histone gamma-H2AX, which mostly labels the sites of double-strand breaks; and the recombinase RAD51. Spermatocytes showed conspicuous polarization of both the maturation of cohesin axes and the initiation of meiotic recombination events. Consequently, it is proposed that maturation of cohesin axes, which begins in very distal regions, could drive the latter loading of recombinases to such regions. This restricted distribution of recombination events along homologues would finally be responsible for the incomplete pairing and synapsis observed in all autosomes of the complement and hence for chiasma localization.

RandoMate: a program for the generation of random mating schemes for small laboratory animals

Advanced intercross lines (AIL) have proven to be a powerful tool in genetic research to map complex genetic traits. The advantage of AIL is the high enrichment of visible recombination events to fine map the position of the target gene. Therefore, AIL are generated under the avoidance of inbreeding. We developed an online software tool, RandoMate, that generates random mating schemes such that only animals from different families are paired. When animals have to be selected randomly for mating, RandoMate optimizes the mating scheme such that all families contribute equally to the next generation. RandoMate uses a divide-and-conquer algorithm to define a mating scheme without brother-sister matings for all animals of a generation. If not all animals can be considered for the next generation, the mating scheme maximizes the randomness of the occurrences of animals from their families to make the family contributions as equal as possible. RandoMate is freely available at http://www2.hu-berlin.de/RandoMate .

Parental origin of chromosomes influences crossover activity within the Kcnq1 transcriptionally imprinted domain of Mus musculus

BACKGROUND

Among the three functions of DNA, mammalian replication and transcription can be subject to epigenetic imprinting specified by the parental origin of chromosomes, and although there is suggestive indication that this is also true for meiotic recombination, no definitive evidence has yet been reported.

RESULTS

We have now obtained such evidence on mouse chromosome 7 by assaying meiotic recombination as it occurs in reciprocal F1 mice. A 166 kb region near the Kcnq1 transcriptionally imprinted domain showed significantly higher recombination activity in the CAST x B6 parental direction (p < 0.03). Characterizing hotspots within this domain revealed a cluster of three hotspots lying within a 100 kb span, among these hotspots, Slc22a18 showed a definitive parent of origin effect on recombination frequency (p < 0.02). Comparing recombination activity in the mouse Kcnq1 and neighboring H19-Igf2 imprinted domains with their human counterparts, we found that elevated recombination activity in these domains is a consequence of their chromosomal position relative to the telomere and not an intrinsic characteristic of transcriptionally imprinted domains as has been previously suggested.

CONCLUSION

Similar to replication and transcription, we demonstrate that meiotic recombination can be subjected to epigenetic imprinting and hotspot activity can be influenced by the parental origin of chromosomes. Furthermore, transcriptionally imprinted regions exhibiting elevated recombination activity are likely a consequence of their chromosomal location rather than their transcriptional characteristic.

Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates

Since Haldane first noticed an excess of paternally derived mutations, it has been considered that most mutations derive from errors during germ line replication. Miyata et al. (1987) proposed that differences in the rate of neutral evolution on X, Y, and autosome can be employed to measure the extent of this male bias. This commonly applied method assumes replication to be the sole source of between-chromosome variation in substitution rates. We propose a simple test of this assumption: If true, estimates of the male bias should be independent of which two chromosomal classes are compared. Prior evidence from rodents suggested that this might not be true, but conclusions were limited by a lack of rat Y-linked sequence. We therefore sequenced two rat Y-linked bacterial artificial chromosomes and determined evolutionary rate by comparison with mouse. For estimation of rates we consider both introns and synonymous rates. Surprisingly, for both data sets the prediction of congruent estimates of alpha is strongly rejected. Indeed, some comparisons suggest a female bias with autosomes evolving faster than Y-linked sequence. We conclude that the method of Miyata et al. (1987) has the potential to provide incorrect estimates. Correcting the method requires understanding of the other causes of substitution that might differ between chromosomal classes. One possible cause is recombination-associated substitution bias for which we find some evidence. We note that if, as some suggest, this association is dominantly owing to male recombination, the high estimates of alpha seen in birds is to be expected as Z chromosomes recombine in males.

Trans-regulation of mouse meiotic recombination hotspots by Rcr1

Meiotic recombination is required for the orderly segregation of chromosomes during meiosis and for providing genetic diversity among offspring. Among mammals, as well as yeast and higher plants, recombination preferentially occurs at highly delimited chromosomal sites 1–2 kb long known as hotspots. Although considerable progress has been made in understanding the roles various proteins play in carrying out the molecular events of the recombination process, relatively little is understood about the factors controlling the location and relative activity of mammalian recombination hotspots. To search for trans-acting factors controlling the positioning of recombination events, we compared the locations of crossovers arising in an 8-Mb segment of a 100-Mb region of mouse Chromosome 1 (Chr 1) when the longer region was heterozygous C57BL/6J (B6) × CAST/EiJ (CAST) and the remainder of the genome was either similarly heterozygous or entirely homozygous B6. The lack of CAST alleles in the remainder of the genome resulted in profound changes in hotspot activity in both females and males. Recombination activity was lost at several hotspots; new, previously undetected hotspots appeared; and still other hotspots remained unaffected, indicating the presence of distant trans-acting gene(s) whose CAST allele(s) activate or suppress the activity of specific hotspots. Testing the activity of three activated hotspots in sperm samples from individual male progeny of two genetic crosses, we identified a single trans-acting regulator of hotspot activity, designated Rcr1, that is located in a 5.30-Mb interval (11.74–17.04 Mb) on Chr 17. Using an Escherichia coli cloning assay to characterize the molecular products of recombination at two of these hotspots, we found that Rcr1 controls the appearance of both crossover and noncrossover gene conversion events, indicating that it likely controls the sites of the double-strand DNA breaks that initiate the recombination process.

Recombination is an essential aspect of meiosis, ensuring proper contact and exchange of genetic material between homologous parental chromosomes, as well as their subsequent segregation to produce haploid gametes. In humans and mice, recombination events are located at preferential sites termed hotspots, whose placement and activity are tightly regulated. We have now identified a hotspot-regulating locus in mammals, Rcr1, that simultaneously controls the locations of multiple hotspots. The discovery of Rcr1 indicates the existence of a newly emerging class of genes important in the recombination processes. Gaining further insights into their function may contribute to a better understanding of genetic factors underlying human fertility and evolution.

Rcr1 is identified as atrans-regulator of meiotic recombination hotspots that appears to act at the initiation of recombination and that maps to a 5.3-megabase region on mouse Chromosome 17.

Genome-wide control of the distribution of meiotic recombination

Meiotic recombination events are not randomly distributed in the genome but occur in specific regions called recombination hotspots. Hotspots are predicted to be preferred sites for the initiation of meiotic recombination and their positions and activities are regulated by yet-unknown controls. The activity of the Psmb9 hotspot on mouse Chromosome 17 (Chr 17) varies according to genetic background. It is active in strains carrying a recombinant Chr 17 where the proximal third is derived from Mus musculus molossinus. We have identified the genetic locus required for Psmb9 activity, named Dsbc1 for Double-strand break control 1, and mapped this locus within a 6.7-Mb region on Chr 17. Based on cytological analysis of meiotic DNA double-strand breaks (DSB) and crossovers (COs), we show that Dsbc1 influences DSB and CO, not only at Psmb9, but in several other regions of Chr 17. We further show that CO distribution is also influenced by Dsbc1 on Chrs 15 and 18. Finally, we provide direct molecular evidence for the regulation in trans mediated by Dsbc1, by showing that it controls the CO activity at the Hlx1 hotspot on Chr 1. We thus propose that Dsbc1 encodes for a trans-acting factor involved in the specification of initiation sites of meiotic recombination genome wide in mice.

In many organisms, an essential feature of meiosis is genetic recombination, which creates diversity in the gametes by mixing the genetic information from each parent into new combinations. Reciprocal recombination, or crossovers, also play a mechanical role during meiosis and are required for the proper segregation of homologous chromosomes to the daughter cells. Crossovers do not occur randomly in the genome but rather are clustered in small regions called hotspots. The factors that determine hotspot locations are poorly understood. We have analyzed a particular recombination hotspot in the mouse genome, called Psmb9, and showed that its activity is induced by a specific allele of a locus that we have mapped and named Dsbc1, for Double-strand break control 1. We have analyzed the properties of Dsbc1 both by the direct detection of recombinant DNA molecules in specific regions and by chromosome-wide cytological detection of proteins involved in recombination. Our results show that Dsbc1 acts genome wide and regulates the distribution of crossovers in several regions on different chromosomes, at least in part by regulating the initiation step of meiotic recombination characterized by the formation of DNA double-strand breaks.

Dsbc1 is a novel locus involved in controlling the localization of meiotic recombination events in the mouse genome.

Detailed recombination studies along chromosome 3B provide new insights on crossover distribution in wheat (Triticum aestivum L.)

In wheat (Triticum aestivum L.), the crossover (CO) frequency increases gradually from the centromeres to the telomeres. However, little is known about the factors affecting both the distribution and the intensity of recombination along this gradient. To investigate this, we studied in detail the pattern of CO along chromosome 3B of bread wheat. A dense reference genetic map comprising 102 markers homogeneously distributed along the chromosome was compared to a physical deletion map. Most of the COs (90%) occurred in the distal subtelomeric regions that represent 40% of the chromosome. About 27% of the proximal regions surrounding the centromere showed a very weak CO frequency with only three COs found in the 752 gametes studied. Moreover, we observed a clear decrease of CO frequency on the distal region of the short arm. Finally, the intensity of interference was assessed for the first time in wheat using a Gamma model. The results showed m values of 1.2 for male recombination and 3.5 for female recombination, suggesting positive interference along wheat chromosome 3B.

Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression

A remarkably diverse set of traits maps to a region on mouse distal chromosome 1 (Chr 1) that corresponds to human Chr 1q21-q23. This region is highly enriched in quantitative trait loci (QTLs) that control neural and behavioral phenotypes, including motor behavior, escape latency, emotionality, seizure susceptibility (Szs1), and responses to ethanol, caffeine, pentobarbital, and haloperidol. This region also controls the expression of a remarkably large number of genes, including genes that are associated with some of the classical traits that map to distal Chr 1 (e.g., seizure susceptibility). Here, we ask whether this QTL-rich region on Chr 1 (Qrr1) consists of a single master locus or a mixture of linked, but functionally unrelated, QTLs. To answer this question and to evaluate candidate genes, we generated and analyzed several gene expression, haplotype, and sequence datasets. We exploited six complementary mouse crosses, and combed through 18 expression datasets to determine class membership of genes modulated by Qrr1. Qrr1 can be broadly divided into a proximal part (Qrr1p) and a distal part (Qrr1d), each associated with the expression of distinct subsets of genes. Qrr1d controls RNA metabolism and protein synthesis, including the expression of approximately 20 aminoacyl-tRNA synthetases. Qrr1d contains a tRNA cluster, and this is a functionally pertinent candidate for the tRNA synthetases. Rgs7 and Fmn2 are other strong candidates in Qrr1d. FMN2 protein has pronounced expression in neurons, including in the dendrites, and deletion of Fmn2 had a strong effect on the expression of few genes modulated by Qrr1d. Our analysis revealed a highly complex gene expression regulatory interval in Qrr1, composed of multiple loci modulating the expression of functionally cognate sets of genes.

Domain-specific regulation of recombination in Caenorhabditis elegans in response to temperature, age and sex

It is generally considered that meiotic recombination rates increase with temperature, decrease with age, and differ between the sexes. We have reexamined the effects of these factors on meiotic recombination in the nematode Caenorhabditis elegans using physical markers that encompass >96% of chromosome III. The only difference in overall crossover frequency between oocytes and male sperm was observed at 16 degrees . In addition, crossover interference (CI) differs between the germ lines, with oocytes displaying higher CI than male sperm. Unexpectedly, our analyses reveal significant changes in crossover distribution in the hermaphrodite oocyte in response to temperature. This feature appears to be a general feature of C. elegans chromosomes as similar changes in response to temperature are seen for the X chromosome. We also find that the distribution of crossovers changes with age in both hermaphrodites and females. Our observations indicate that it is the oocytes from the youngest mothers-and not the oldest-that showed a different pattern of crossovers. Our data enhance the emerging hypothesis that recombination in C. elegans, as in humans, is regulated in large chromosomal domains.

A quantitative assay for crossover and noncrossover molecular events at individual recombination hotspots in both male and female gametes

Meiotic recombination is a fundamental process in all eukaryotes. Among organisms in which recombination initiates prior to synapsis, recombination preferentially occurs in short 1-to 2-kb regions, known as recombination hotspots. Among mammals, genotyping sperm DNA has provided a means of monitoring recombination events at specific hotspots in male meiosis. To complement these current techniques, we developed an assay for amplifying all copies of a hotspot from the DNA of male and female germ cells, cloning the products into Escherichia coli, and SNP genotyping the resulting colonies using fluorescence technology. This approach examines the molecular details of crossover and noncrossover events of individual meioses directly at active hotspots while retaining the simplicity of using pooled DNA. Using this technique, we analyzed recombination events at the Hlx1 hotspot located on mouse chromosome 1, finding that the results agree well with a prior genetic characterization of 3026 male and 3002 female meioses.