Cis- and trans-acting elements regulate the mouse Psmb9 meiotic recombination hotspot

Abstract

In most eukaryotes, the prophase of the first meiotic division is characterized by a high level of homologous recombination between homologous chromosomes. Recombination events are not distributed evenly within the genome, but vary both locally and at large scale. Locally, most recombination events are clustered in short intervals (a few kilobases) called hotspots, separated by large intervening regions with no or very little recombination. Despite the importance of regulating both the frequency and the distribution of recombination events, the genetic factors controlling the activity of the recombination hotspots in mammals are still poorly understood. We previously characterized a recombination hotspot located close to the Psmb9 gene in the mouse major histocompatibility complex by sperm typing, demonstrating that it is a site of recombination initiation. With the goal of uncovering some of the genetic factors controlling the activity of this initiation site, we analyzed this hotspot in both male and female germ lines and compared the level of recombination in different hybrid mice. We show that a haplotype-specific element acts at distance and in trans to activate about 2,000-fold the recombination activity at Psmb9. Another haplotype-specific element acts in cis to repress initiation of recombination, and we propose this control to be due to polymorphisms located within the initiation zone. In addition, we describe subtle variations in the frequency and distribution of recombination events related to strain and sex differences. These findings show that most regulations observed act at the level of initiation and provide the first analysis of the control of the activity of a meiotic recombination hotspot in the mouse genome that reveals the interactions of elements located both in and outside the hotspot.

Figure 1. Maps of the Chromosome 17 and the Psmb9 Hotspot in the Different Strains

(A) Origin of the Chromosome 17 fragments in the different parent lines is presented: black, B10; blue, A (haplotype a); orange, SGR (haplotype wm7). (B) Map of the polymorphisms at the heterozygous state along the Psmb9 hotspot in the various hybrids is shown. The markers −87, 38, 70, 87, StyI, and SphI are 87 bp to the left, and 38, 70, 87, 213, and 474 bp to the right of the BsrFI marker, respectively.

Figure 2. CO Breakpoint Distribution along the Psmb9 Hotspot

CO densities are calculated by dividing the frequency of CO in each interval by its length. CO1 and CO2 represent exchanges in both orientations: black line, CO1 (orientation B10-R209, B10.A-SGR, and R209-SGR, respectively); red line, CO2 (orientation R209-B10, SGR-B10.A, and SGR-R209, respectively); gray area, orientation-averaged CO. Number of events: B10 × R209, female, 112 CO1 and 76 CO2, male, 108 CO1 and 58 CO2; B10.A × SGR, female, 45 CO1 and 69 CO2, male, 62 CO1 and 62 CO2; R209 × SGR, male, 21 CO1 and 73 CO2.

Figure 3. Distribution of Exchange Points at an Initiation Site

(A) A model for meiotic recombination is shown. The region surrounding the initiating DSB, between the breakpoints (arrowheads), is converted. The molecule having suffered the initiating DSB is the recipient of genetic information [2,3]. The CO exchange breakpoints are shifted in opposite directions, depending on which is the initiating chromosome (left panel, Chromosome 1 and right panel, Chromosome 2). (B) The expected distribution of CO exchange breakpoints at an initiation site is shown: blue, Chromosome 1 to Chromosome 2 orientation; red, Chromosome 2 to Chromosome 1 orientation; black, sum of exchanges in both orientations. On the left panel initiation is mainly on Chromosome 1. On the right panel initiation on both chromosomes is with similar frequency.

Figure 4. Cumulative CO Distribution and Transmission Bias in Males and Females

(A) CO distribution in B10.A × SGR is presented: open diamonds, female, orientation B10.A-SGR; open squares, male, orientation B10.A-SGR; gray diamonds, female, orientation SGR-B10.A; gray squares, male, orientation SGR-B10.A; black diamonds, female, both orientations; black squares, male, both orientations. (B) Transmission bias among CO products is presented; transmission frequency of the wm7 allele in B10 × R209 and B10.A × SGR. Gray circles and squares, B10 × R209, female and male, respectively; black circles and squares, B10.A x SGR, female and male, respectively.

Figure 5. Genetic Control in Cis and in Trans of Meiotic Recombination at the Psmb9 Hotspot

1, wm7-specific trans-acting activator; 2, cis-acting repressor specific for SGR chromosome; 3, sex-specific control in trans of the recombination rate.