Zinc Finger Domain of the PRDM9 Gene on Chromosome 1 Exhibits High Diversity in Ruminants but Its Paralog PRDM7 Contains Multiple Disruptive Mutations

Abstract

PRDM9 is the sole hybrid sterility gene identified so far in vertebrates. PRDM9 gene encodes a protein with an immensely variable zinc-finger (ZF) domain that determines the site of meiotic recombination hotspots genome-wide. In this study, the terminal ZF domain of PRDM9 on bovine chromosome 1 and its paralog on chromosome 22 were characterized in 225 samples from five ruminant species (cattle, yak, mithun, sheep and goat). We found extraordinary variation in the number of PRDM9 zinc fingers (6 to 12). We sequenced PRDM9 ZF encoding region from 15 individuals (carrying the same ZF number in both copies) and found 43 different ZF domain sequences. Ruminant zinc fingers of PRDM9 were found to be diversifying under positive selection and concerted evolution, specifically at positions involved in defining their DNA-binding specificity, consistent with the reports from other vertebrates such as mice, humans, equids and chimpanzees. ZF-encoding regions of the PRDM7, a paralog of PRDM9 on bovine chromosome 22 and on unknown chromosomes in other studied species were found to contain 84 base repeat units as in PRDM9, but there were multiple disruptive mutations after the first repeat unit. The diversity of the ZFs suggests that PRDM9 may activate recombination hotspots that are largely unique to each ruminant species.

Fig 1. Geographic distribution of ruminant populations analyzed in the present study.

Fig 2. Gel image of PCR product of ZF domain of PRDM9 and PRDM7 genes in ruminants.

M: 100 bp ladder, bright bands correspond to 500 bp, 1000 bp and 1500 bp. 1–4: upper band- A to D alleles of PRDM9 in cattle, lower band- PRDM7 in cattle. 5–6: upper band- A allele of PRDM9 in yak, lower band- PRDM7 in yak. 7–8: upper band- A and B alleles of PRDM9 in mithun, lower band- PRDM7 in mithun. 9–10: upper band- D allele of PRDM9 in sheep, lower band- PRDM7 in sheep. 11–15: upper band- C to G alleles of PRDM9 in goat, lower band- PRDM7 in goat.

Fig 3. Alignment of PRDM7 ZF domains in ruminants.

The stop codons are shown with stars.

Fig 4. Different PRDM9 ZF domains identified in ruminant species.

Different ZF domains have been numerically coded and amino acid variations at different positions have been indicated.

Fig 5. Schematic representation of PRDM9 domains and allelic variation in ruminants.

Different ZF repeats in different alleles and species are coded by letters as already shown in Fig 4. The first finger (shown with green diamond shape) was found to be conserved.

Fig 6. dN/dS estimates of variable amino acid sites in ZF domains of PRDM9 gene in ruminants.

Positive selection was estimated in all species combined as well as for individual species separately. Two asterisks indicate P<0.01 and single asterisk indicates P<0.05.