Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage.

Authors

Michael Walker, The Jackson LaboratoryFollow
Timothy Billings, The Jackson LaboratoryFollow
Christopher L. Baker, The Jackson LaboratoryFollow
Natalie Powers, The Jackson LaboratoryFollow
Hui Tian, The Jackson LaboratoryFollow
Ruth L. Saxl, The Jackson LaboratoryFollow
Kwangbom Choi, The Jackson LaboratoryFollow
Matthew A. Hibbs, The Jackson LaboratoryFollow
Gregory W. Carter, The Jackson LaboratoryFollow
Mary Ann Handel, The Jackson LaboratoryFollow
Petko M. Petkov, The Jackson LaboratoryFollow

Document Type

Article

Publication Date

9-7-2015

JAX Source

Epigenetics Chromatin 2015 Sep 7; 8:31.

Volume

8

First Page

31

Last Page

31

ISSN

1756-8935

PMID

26351520

Grant

GM078452, GM076468, GM083408, GM099640, GM078643, CA034196

Abstract

BACKGROUND: Genetic recombination plays an important role in evolution, facilitating the creation of new, favorable combinations of alleles and the removal of deleterious mutations by unlinking them from surrounding sequences. In most mammals, the placement of genetic crossovers is determined by the binding of PRDM9, a highly polymorphic protein with a long zinc finger array, to its cognate binding sites. It is one of over 800 genes encoding proteins with zinc finger domains in the human genome.

RESULTS: We report a novel technique, Affinity-seq, that for the first time identifies both the genome-wide binding sites of DNA-binding proteins and quantitates their relative affinities. We have applied this in vitro technique to PRDM9, the zinc-finger protein that activates genetic recombination, obtaining new information on the regulation of hotspots, whose locations and activities determine the recombination landscape. We identified 31,770 binding sites in the mouse genome for the PRDM9(Dom2) variant. Comparing these results with hotspot usage in vivo, we find that less than half of potential PRDM9 binding sites are utilized in vivo. We show that hotspot usage is increased in actively transcribed genes and decreased in genomic regions containing H3K9me2/3 histone marks or bound to the nuclear lamina.

CONCLUSIONS: These results show that a major factor determining whether a binding site will become an active hotspot and what its activity will be are constraints imposed by prior chromatin modifications on the ability of PRDM9 to bind to DNA in vivo. These constraints lead to the presence of long genomic regions depleted of recombination.

Epigenetics Chromatin 2015 Sep 7; 8:31.

Recommended Citation

Walker M, Billings T, Baker CL, Powers N, Tian H, Saxl RL, Choi K, Hibbs MA, Carter GW, Handel M, Petkov PM. Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage. Epigenetics Chromatin 2015 Sep 7; 8:31.