Characterization of a Mouse Recombination Hot Spot Locus Encoding a Novel Non-Protein-Coding RNA

Abstract

Our current knowledge of recombination hot spot activity in mammalian systems implicates a role for both the primary DNA sequence and the nature of the chromatin domain around it. In mice, the only recombination hot spots mapped to date have been confined to a cluster within the major histocompatibility complex (MHC) region. We present a high resolution analysis of a new recombination hot spot in the mouse genome which maps to mouse chromosome 8 C-D. Haplotype diversity analysis across 40 different strains of mice has enabled us to map recombination breakpoints to a 1-kb interval. This hot spot has a recombination intensity that is 10-to 100-fold above the genome average and has a mean gene conversion tract length of 371 bp. This meiotically active locus happens to be flanked by a transcribed region encoding a non-protein-coding RNA polymerase II transcript and the previously characterized repair site. Many of the primary DNA sequence features that have been reported for the mouse MHC hot spots are also shared by this hot spot locus and in addition, along with three other MHC hot spot loci, we show a new parallel feature of association of the crossover sites with the nuclear matrix.Most of the advances in our understanding of meiosis and recombination have come from studies of lower eukaryotes, in particular Saccharomyces cerevisiae. Recombination initiates via programmed double-strand breaks at the leptotene interval which are resected and undergo strand exchange and finally give rise to double Holliday junctions by the mid-pachytene interval. Mature crossover products follow around the end of pachytene (14,24). It is generally believed that a similar process operates in higher eukaryotes, including mammals. The rate of recombination is not a uniform function of the physical distance between two markers, leading to the concept of recombination hot spots and cold spots (36). In mice and humans, regions are generally termed as hot spots if their recombination frequency significantly exceeds 1 centimorgan (cM)/ Mb. There are three methods that have been used to map hot spots in mammals. The classical method is to correlate physical distances with genetic distances established by standard pedigree-based linkage analysis. The resolution of this method is limited by the density of markers, the number of individuals examined, and the number of recombination events that occur in a typical pedigree. Methods based on linkage disequilibrium (LD), which refers to the nonrandom association of alleles at linked sites, take into account ancestral recombination events, which would be far greater than those observed from any pedigree-based linkage study, leading to a finer mapping of recombination hot spots. Most measures of LD quantify the degree of association between pairs of markers which decreases as a function of physical distance between them due to increased probability of recombination between the markers. However, both of these techniques do not have the resolution to characterize crossovers at a molecular level. The ...

Estimating Meiotic Gene Conversion Rates From Population Genetic Data

“…These results will vary depending on the SNP spacing and the actual gene conversion rate. Fortunately, estimates of the gene conversion tract length are available for several organisms (e.g., Palmer et al 2003;Jeffreys and May 2004;Nishant et al 2004) although little is yet known about whether there is heterogeneity in this length between different genomic regions.…”

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

“…Given that RUF6 gene clusters are in close proximity to these loci, it is tempting to speculate that RUF6 transcripts may play a role in expression or maintenance of these malarial antigens. Interestingly, in vertebrates, the 59 end of the crossover domain of a hotspot locus is known to transcribe a novel RNA transcript (Nishant et al 2004). …”

mrhl RNA, a Long Noncoding RNA, Negatively Regulates Wnt Signaling through Its Protein Partner Ddx5/p68 in Mouse Spermatogonial Cells

“…It is a polyadenylated and unspliced transcript. mrhl RNA is expressed in liver, kidney, spleen, and testes but not in brain, heart, lung, and muscle tissues (26). The 2.4-kb primary transcript is nuclear restricted, localizes to the nucleolus, and gets processed to an 80-nucleotide (nt) intermediate RNA by the Drosha machinery (13).…”

“…During the epithelial-to-mesenchymal transition that is induced by platelet-derived growth factor (PDGF) stimulation, p68, which gets phosphorylated at tyrosine 593, was shown to translocate to the cytoplasm, where it stabilizes beta-catenin; subsequently p68 -beta-catenin translocates back to the nucleus, bringing about downstream transcriptional regulation (43). mrhl is a 2.4-kb noncoding RNA, identified in our laboratory, encoded in the mouse genome embedded within a meiotic recombination hot spot locus on mouse chromosome 8 (26). mrhl RNA is an intronic long noncoding RNA (lncRNA) that is transcribed by RNA polymerase II as an independent transcription unit from the intron of the phkb gene.…”