Male mouse recombination maps for each autosome identified by chromosome painting

Abstract

Linkage maps constructed from genetic analysis of gene order and crossover frequency provide few clues to the basis of genomewide distribution of meiotic recombination, such as chromosome structure, that influences meiotic recombination. To bridge this gap, we have generated the first cytological recombination map that identifies individual autosomes in the male mouse. We prepared meiotic chromosome (synaptonemal complex [SC]) spreads from 110 mouse spermatocytes, identified each autosome by multicolor fluorescence in situ hybridization of chromosome-specific DNA libraries, and mapped >2,000 sites of recombination along individual autosomes, using immunolocalization of MLH1, a mismatch repair protein that marks crossover sites. We show that SC length is strongly correlated with crossover frequency and distribution. Although the length of most SCs corresponds to that predicted from their mitotic chromosome length rank, several SCs are longer or shorter than expected, with corresponding increases and decreases in MLH1 frequency. Although all bivalents share certain general recombination features, such as few crossovers near the centromeres and a high rate of distal recombination, individual bivalents have unique patterns of crossover distribution along their length. In addition to SC length, other, as-yet-unidentified, factors influence crossover distribution leading to hot regions on individual chromosomes, with recombination frequencies as much as six times higher than average, as well as cold spots with no recombination. By reprobing the SC spreads with genetically mapped BACs, we demonstrate a robust strategy for integrating genetic linkage and physical contig maps with mitotic and meiotic chromosome structure.

Figure 1

Immunostaining and FISH signals of the same spermatocyte nucleus in subsequent experiments. The arrowhead identifies SC4 in all images. a, Fluorescent antibody localization of anti-SCP3 antibodies (red) and anti-MLH1-antibodies (green). The chromatin is counterstained with DAPI (blue), with the AT-rich centromeric ends staining more intensely. b, Chromosome painting with pool 1 plus DAPI. c, pool 1 without DAPI. d, pool 2 without DAPI. e, Identification of SCs on the basis of the paint signals with the SC and DAPI signals displayed in an inverted black-and-white image and with the centromeric end of each SC identified by the intense (dark) DAPI staining. f, FISH signals of two BACs: RPCI23 7-J-10, and RPCI23 219-G-3 hybridizing to the chromatin of bivalent 4 (arrow). The inset shows the mapping of the same BACs to a mitotic chromosome 4.

Figure 2

Relationship between average SC length (μm) and the average number of MLH1 foci on mouse SCs.

Figure 3

Distribution of MLH1 foci along individual SCs. The X-axis represents the positions on the SCs from the centromeric end (left) to the distal telomere (right). The Y-axis indicates the frequency of MLH1 foci in each 0.2-μm interval. For each SC, three histograms are presented in a gray box. In order from top to bottom, the histograms show the results for SCs displaying a single MLH1 focus, SCs displaying two MLH1 foci, and the overall frequencies. The histograms of overall frequencies contain a smoothing curve (Lowess line), as well as thresholds indicating significantly increased or decreased recombination frequencies (dotted lines). The graphs are ordered from top to bottom, according to the SC length.

Figure 3

Distribution of MLH1 foci along individual SCs. The X-axis represents the positions on the SCs from the centromeric end (left) to the distal telomere (right). The Y-axis indicates the frequency of MLH1 foci in each 0.2-μm interval. For each SC, three histograms are presented in a gray box. In order from top to bottom, the histograms show the results for SCs displaying a single MLH1 focus, SCs displaying two MLH1 foci, and the overall frequencies. The histograms of overall frequencies contain a smoothing curve (Lowess line), as well as thresholds indicating significantly increased or decreased recombination frequencies (dotted lines). The graphs are ordered from top to bottom, according to the SC length.