The case of the fickle fingers: how the PRDM9 zinc finger protein specifies meiotic recombination hotspots in humans

Abstract

During mammalian meiosis, double-strand breaks are deliberately made throughout the genome and then repaired, leading to the exchange of genetic material between copies of chromosomes. How the locations of breaks are specified was largely unknown until a fortuitous confluence of statistical genetics and molecular biology uncovered the role of PRDM9, a DNA binding protein. Many properties of this protein remain mysterious, however, including how it binds to DNA, how it contributes to male infertility-both in humans, and in hybrid mice-and why, in spite of its fundamental function in meiosis, its binding domain varies extensively among humans and across mammals. We present a brief summary of what has recently been learned about PRDM9 in different fields, focusing on the puzzles yet to be resolved.

Figure 1. The three domains of PRDM9, along with the binding prediction for the zinc finger array.

PRDM9 contains a KRAB domain, which is thought to be involved in transcriptional repression, as well as a SET domain that tri-methylates H3K4, an epigenetic mark associated with the initiation of meiotic recombination in yeast and mice ,,. The zinc fingers are color-coded according to the identity of the residues in contact with DNA. The DNA sequence bound by the zinc finger array of the A variant of PRDM9 was predicted using http://zf.princeton.edu/ (under the polynomial support vector machine model) and aligned with the 13-bp motif found to be enriched in historical hotspots .

Figure 2. The effect of PRDM9 zinc finger variants on hotspot activity.

Each column presents males with the same genotype, grouped according to whether they carry two A-type variants (defined as variants predicted to bind the same 13-bp motif as A), two C-type variants (defined as variants predicted to bind the same 17-bp motif as C), or one A-type and one C-type variant. Within a column, each symbol denotes the recombination activity of a given hotspot for a given individual, with circles indicating hotspots that contain a perfect match to the 13-bp motif (for the left panel) or the 17-bp motif (for the right panel) within 1 kb of their center, and triangles indicating hotspots with no perfect matches. The median recombination frequency is shown as a black bar. As can be seen, there is no clear difference between the activity of hotspots with and without a perfect match to the motif. The recombination frequency is reported relative to the median of AA individuals (left panel) or that of C-type/C-type individuals (right panel). The data were obtained by sperm-typing from (left panel) and (right panel). The E and PAR2 hotspots from were excluded from the analysis because they contain polymorphisms disrupting the central 13-bp motif , possibly confounding the effect of variation in PRDM9. The 12B hotspot from was excluded because it was not active in typed C-type/C-type individuals.