Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage.
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.
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Michael
M
Walker
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Timothy
T
Billings
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Christopher L
CL
Baker
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Natalie
N
Powers
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Hui
H
Tian
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Ruth L
RL
Saxl
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Kwangbom
K
Choi
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Matthew A
MA
Hibbs
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Gregory W
GW
Carter
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Mary Ann
MA
Handel
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Kenneth
K
Paigen
Center for Genome Dynamics, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA.
Petko M
0000-0002-6694-9150
PM
Petkov