Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

Key results

1. 01

   ShownAsynapsis depends on PRDM9 binding asymmetry rather than genome-wide divergence. CAST segments, where the B6 allele binds both homologs equally, rescue synapsis in cis. Chromosome silencing inferred from RNA counts works as a validated proxy for asynapsis.

   In PWD/B6 regions the B6-derived PRDM9 allele bound the PWD vs B6 homologs at 80%/20%; in PWD/CAST regions it bound at 51%/49%. RNA-based silencing matched FISH asynapsis rates in PWD x B6 mice (98.7%). A cis exponential-decay model based on CAST length explained ~75% of the variance across chromosomes (r = 0.86, p < 2x10^-15). · PRDM9 binding at recombination hotspots in early…; Chromosome-specific transcriptional silencing in…; PRDM9 binding symmetry and a region containing…

2. 02

   SuggestedA chromosome 15 interval containing Dmc1 and Mei1 acts in trans to set how sensitive each animal is to PRDM9 asymmetry. CAST ancestry in this interval goes with stronger silencing, and likely more asynapsis.

   Relative silencing efficacy across 23 mice was associated with an 18.8 Mb interval (63.5 - 82.4 Mb; r = 0.8, p = 1.9x10^-5; permutation p=0.002). The abstract reports R^2=0.64. The interval holds 309 genes, and Mei1 carries 13 non-synonymous B6/CAST changes. No clear allele-specific expression was seen for the candidate genes. · Abstract; PRDM9 binding symmetry and a region containing…; PRDM9 binding asymmetry predicts downstream…

3. 03

   ShownFertility loss runs through pachytene cell death. Autosomal asynapsis and X-silencing failure jointly predict late-pachytene survival, which alone predicts sperm count; testes weight also tracks a chromosome 11 locus. X-silencing failure follows genome-wide asymmetry, not autosomal competition.

   The joint model predicted 79% of late-pachytene survival. Among upstream factors, only pachytene survival predicted sperm count and testes weight; a 6.5 Mb chromosome 11 locus (r = -0.73, p = 6.5 x 10^-5) added to testes weight prediction. X-silencing failure tracked genome-wide B6 proportion (ρ = 0.61; p = 0.002), not single-cell autosomal silencing (ρ = -0.06). · Similar, dynamic, chromatin alterations occur on…; PRDM9 binding asymmetry predicts downstream…

4. 04

   ShownSome cells escape pachytene arrest and divide while carrying aneuploidies. Autosomal MI errors arise in cis on asymmetric chromosomes, but the cause of MI X/Y missegregation is unclear. MII deletions of autosomes and X/Y appear driven in trans by asynapsis of chromosomes 16 and 19.

   Over 15% of MI cells had sex chromosome abnormalities (vs 1% in B6 x CAST), and 89% of these were inferred to arrest at or before MII. MII cells showed 2% X/Y abnormalities. Asymmetric binding raised complete MI deletions (OR = 2.08; p < 0.001). Asynapsis of chromosomes 16 and 19 predicted MII autosomal deletions (R^2 = 0.92) and X/Y deletions (R^2 = 0.85). · Aneuploidy of the sex chromosomes and of…

5. 05

   ShownPRDM9 binding symmetry reshapes broad-scale crossover maps. On asynapsis-prone chromosomes, crossovers shift into CAST segments rich in symmetric hotspots, which the authors read as evidence that crossover designation begins early, before synapsis is complete.

   245,368 crossovers were mapped in 24 mice. Crossover enrichment in CAST vs B6 segments was >1 on all autosomes except 9 and 14, which carry introgressed domesticus segments. Enrichment correlated with PWD x B6 asynapsis rates (r = 0.91; p = 7.7x10^-7) and reached ~2-fold on chromosomes 18 and 19, vs the 1.26-fold expected from extra DSBs. · (A)symmetric binding by PRDM9 reprograms…