Chromatin-mediated regulators of meiotic recombination revealed by proteomics of a recombination hotspot

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

Background

Meiotic recombination hotspots control the frequency and distribution of Spo11 (Rec12)-initiated recombination in the genome. Recombination occurs within and is regulated in part by chromatin structure, but relatively few of the many chromatin remodeling factors and histone posttranslational modifications (PTMs) have been interrogated for a role in the process.

Results

We developed a chromatin affinity purification and mass spectrometry-based approach to identify proteins and histone PTMs that regulate recombination hotspots. Small (4.2 kbp) minichromosomes (MiniCs) bearing the fission yeast ade6- M26 hotspot or a basal recombination control were purified approximately 100,000-fold under native conditions from meiosis; then, associated proteins and histone PTMs were identified by mass spectrometry. Proteins and PTMs enriched at the hotspot included known regulators (Atf1, Pcr1, Mst2, Snf22, H3K14ac), validating the approach. The abundance of individual histones varied dynamically during meiotic progression in hotspot versus basal control MiniCs, as did a subset of 34 different histone PTMs, implicating these as potential regulators. Measurements of basal and hotspot recombination in null mutants confirmed that additional, hotspot-enriched proteins are bona fide regulators of hotspot activation within the genome. These chromatin-mediated regulators include histone H2A-H2B and H3-H4 chaperones (Nap1, Hip1/Hir1), subunits of the Ino80 complex (Arp5, Arp8), a DNA helicase/E3 ubiquitin ligase (Rrp2), components of a Swi2/Snf2 family remodeling complex (Swr1, Swc2), and a nucleosome evictor (Fft3/Fun30).

Conclusions

Overall, our findings indicate that a remarkably diverse collection of chromatin remodeling factors and histone PTMs participate in designating where meiotic recombination occurs in the genome, and they provide new insight into molecular mechanisms of the process.

Electronic supplementary material

The online version of this article (10.1186/s13072-018-0233-x) contains supplementary material, which is available to authorized users.

Related collections

Most cited references 71

Record: found
Abstract: found
Article: not found

Basic methods for fission yeast.

Susan Forsburg, Nicholas Rhind (2006)

The fission yeast Schizosaccharomyces pombe is a popular model system, and has been particularly influential in studies of the cell cycle and chromosome dynamics. Despite its differences from Saccharomyces cerevisiae, the tools and methods for fission yeast are conceptually similar to those used in budding yeast. Here, we present basic methods sufficient for a beginner in this system to carry out most required manipulations for genetic analysis or molecular biology. Copyright 2006 John Wiley & Sons, Ltd.

0 comments Cited 215 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

A common sequence motif associated with recombination hot spots and genome instability in humans.

Simon Myers, Colin Freeman, Adam Auton … (2008)

In humans, most meiotic crossover events are clustered into short regions of the genome known as recombination hot spots. We have previously identified DNA motifs that are enriched in hot spots, particularly the 7-mer CCTCCCT. Here we use the increased hot-spot resolution afforded by the Phase 2 HapMap and novel search methods to identify an extended family of motifs based around the degenerate 13-mer CCNCCNTNNCCNC, which is critical in recruiting crossover events to at least 40% of all human hot spots and which operates on diverse genetic backgrounds in both sexes. Furthermore, these motifs are found in hypervariable minisatellites and are clustered in the breakpoint regions of both disease-causing nonallelic homologous recombination hot spots and common mitochondrial deletion hot spots, implicating the motif as a driver of genome instability.

0 comments Cited 163 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

The yeast Fun30 and human SMARCAD1 chromatin remodelers promote DNA end resection

Thomas Costelloe, Raphaël Louge, Nozomi Tomimatsu … (2012)

Several homology-dependent pathways can repair potentially lethal DNA double-strand breaks (DSBs). The first step common to all homologous recombination reactions is the 5′-3′ degradation of DSB ends that yields 3′ single-stranded DNA (ssDNA) required for loading of checkpoint and recombination proteins. The Mre11-Rad50-Xrs2/NBS1 complex and Sae2/CtIP initiate end resection while long-range resection depends on the exonuclease Exo1 or the helicase-topoisomerase complex Sgs1-Top3-Rmi1 with the endonuclease Dna2 1-6 . DSBs occur in the context of chromatin, but how the resection machinery navigates through nucleosomal DNA is a process that is not well understood 7 . Here, we show that the yeast S. cerevisiae Fun30 protein and its human counterpart SMARCAD1 8 , two poorly characterized ATP-dependent chromatin remodelers of the Snf2 ATPase family, are novel factors that are directly involved in the DSB response. Fun30 physically associates with DSB ends and directly promotes both Exo1- and Sgs1-dependent end resection through a mechanism involving its ATPase activity. The function of Fun30 in resection facilitates repair of camptothecin (CPT)-induced DNA lesions, and it becomes dispensable when Exo1 is ectopically overexpressed. Interestingly, SMARCAD1 is also recruited to DSBs and the kinetics of recruitment is similar to that of Exo1. Loss of SMARCAD1 impairs end resection, recombinational DNA repair and renders cells hypersensitive to DNA damage resulting from CPT or PARP inhibitor treatments. These findings unveil an evolutionarily conserved role for the Fun30 and SMARCAD1 chromatin remodelers in controlling end resection, homologous recombination and genome stability in the context of chromatin.

0 comments Cited 98 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Wayne P. Wahls:

ORCID: http://orcid.org/0000-0002-1338-1610

(501) 686-5787 , wahlswaynep@uams.edu

Journal

Journal ID (nlm-ta): Epigenetics Chromatin

Journal ID (iso-abbrev): Epigenetics Chromatin

Title: Epigenetics & Chromatin

Publisher: BioMed Central (London )

ISSN (Electronic): 1756-8935

Publication date (Electronic): 29 October 2018

Publication date PMC-release: 29 October 2018

Publication date Collection: 2018

Volume: 11

Electronic Location Identifier: 64

Affiliations

ISNI 0000 0000 9068 3546, GRID grid.194632.b, Department of Biochemistry and Molecular Biology, , University of Arkansas for Medical Sciencs, ; 4301 West Markham Street (Slot 516), Little Rock, AR 72205-7199 USA

Author information

Wayne P. Wahls http://orcid.org/0000-0002-1338-1610

Article

Publisher ID: 233

DOI: 10.1186/s13072-018-0233-x

PMC ID: 6205778

PubMed ID: 30373637

SO-VID: 6489cbf4-5708-464a-aa37-0cc033740eef

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 14 June 2018

Date accepted : 20 October 2018

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000057, National Institute of General Medical Sciences;

Award ID: GM081766

Award Recipient : Wayne P. Wahls

Custom metadata

ScienceOpen disciplines: Genetics

Keywords: homologous recombination,meiosis,histones,chromatin remodeling,mass spectrometry,proteomics,schizosaccharomyces pombe

Data availability:

ScienceOpen disciplines: Genetics

Keywords: homologous recombination, meiosis, histones, chromatin remodeling, mass spectrometry, proteomics, schizosaccharomyces pombe

Chromatin-mediated regulators of meiotic recombination revealed by proteomics of a recombination hotspot

Read this article at

Abstract

Background

Results

Conclusions

Electronic supplementary material

Related collections

Higher order chromatin architecture

Most cited references 71

Basic methods for fission yeast.

A common sequence motif associated with recombination hot spots and genome instability in humans.

The yeast Fun30 and human SMARCAD1 chromatin remodelers promote DNA end resection

Author and article information

Contributors

Journal

Affiliations

Author information

Article

History

Funding

Categories

Custom metadata

Comments

Comment on this article

Similar content 154

Cited by 12

Most referenced authors 926