A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis.

Nicolas Altemose,Simon R Myers,Nudrat Noor,J Ross Chapman,A Radu Aricescu,Michael Imbeault,Afidalina Tumian,Emmanuelle Bitoun

doi:10.7554/elife.28383

Nicolas Altemose, Simon R Myers + Show 6 more

Open Access

https://doi.org/10.7554/elife.28383

Copy DOI

Journal: eLife	Publication Date: Oct 26, 2017
Citations: 87	License type: CC BY 4.0

Affiliation: University of Oxford, Wellcome Centre for Human Genetics

Abstract

PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.

Highlights

In humans and mice, PRDM9 determines the locations of meiotic recombination hotspots (Baudat et al, 2010; Myers et al, 2010; Parvanov et al, 2010)
Despite cell-type differences between our HEK293T expression system and the chromatin environment of early meiotic cells, our binding peaks capture the majority of biologically relevant recombination hotspots and reveal many additional nonhotspot sites bound by PRDM9 in HEK293T cells
We showed here that PRDM9’s zinc-finger domain can impact its ability to form multimers, its ability to activate gene expression, and its ability to initiate recombination, in particular if it binds near promoters or near targets of other zincfinger proteins

Summary

Introduction

PRDM9 determines the locations of meiotic recombination hotspots (Baudat et al, 2010; Myers et al, 2010; Parvanov et al, 2010). At a subset of PRDM9 binding sites, SPO11 is recruited to form Double Strand Breaks (DSBs) (Neale and Keeney, 2006; Smagulova et al, 2011). These DSBs undergo end resection and the resulting singlestranded DNA ends are decorated with the meiosis-specific protein DMC1 (Neale and Keeney, 2006). To study the DNAbinding properties of mouse PRDM9, one study sequenced genomic DNA fragments bound in vitro

Methods

Results

Conclusion