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      Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion

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          Abstract

          Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations.

          DOI: http://dx.doi.org/10.7554/eLife.21900.001

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          Most cited references53

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          LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

          To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. We present LAGAN, a system for rapid global alignment of two homologous genomic sequences, and Multi-LAGAN, a system for multiple global alignment of genomic sequences. We tested our systems on a data set consisting of greater than 12 Mb of high-quality sequence from 12 vertebrate species. All the sequence was derived from the genomic region orthologous to an approximately 1.5-Mb region on human chromosome 7q31.3. We found that both LAGAN and Multi-LAGAN compare favorably with other leading alignment methods in correctly aligning protein-coding exons, especially between distant homologs such as human and chicken, or human and fugu. Multi-LAGAN produced the most accurate alignments, while requiring just 75 minutes on a personal computer to obtain the multiple alignment of all 12 sequences. Multi-LAGAN is a practical method for generating multiple alignments of long genomic sequences at any evolutionary distance. Our systems are publicly available at http://lagan.stanford.edu.
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            Endonucleolytic function of MutLalpha in human mismatch repair.

            Half of hereditary nonpolyposis colon cancer kindreds harbor mutations that inactivate MutLalpha (MLH1*PMS2 heterodimer). MutLalpha is required for mismatch repair, but its function in this process is unclear. We show that human MutLalpha is a latent endonuclease that is activated in a mismatch-, MutSalpha-, RFC-, PCNA-, and ATP-dependent manner. Incision of a nicked mismatch-containing DNA heteroduplex by this four-protein system is strongly biased to the nicked strand. A mismatch-containing DNA segment spanned by two strand breaks is removed by the 5'-to-3' activity of MutSalpha-activated exonuclease I. The probable endonuclease active site has been localized to a PMS2 DQHA(X)(2)E(X)(4)E motif. This motif is conserved in eukaryotic PMS2 homologs and in MutL proteins from a number of bacterial species but is lacking in MutL proteins from bacteria that rely on d(GATC) methylation for strand discrimination in mismatch repair. Therefore, the mode of excision initiation may differ in these organisms.
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              The single-end invasion: an asymmetric intermediate at the double-strand break to double-holliday junction transition of meiotic recombination.

              We identify a novel meiotic recombination intermediate, the single-end invasion (SEI), which occurs during the transition from double-strand breaks (DSBs) to double-Holliday junction (dHJs). SEIs are products of strand exchange between one DSB end and its homolog. The structural asymmetry of SEIs indicates that the two ends of a DSB interact with the homolog in temporal succession, via structurally (and thus biochemically) distinct processes. SEIs arise surprisingly late in prophase, concomitant with synaptonemal complex (SC) formation. These and other data imply that SEIs are preceded by nascent DSB-partner intermediates, which then undergo selective differentiation into crossover and noncrossover types, with SC formation and strand exchange as downstream consequences. Late occurrence of strand exchange provides opportunity to reverse recombinational fate even after homologs are coaligned and/or synapsed. This feature can explain crossover suppression between homeologous and structurally heterozygous chromosomes.
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                Author and article information

                Contributors
                Role: Reviewing editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                04 January 2017
                2017
                : 6
                : e21900
                Affiliations
                [1 ]Institut Curie, PSL Research University, CNRS UMR3664 , Paris, France
                [2 ]Université Pierre et Marie Curie , Paris, France
                [3 ]deptInstitute of Molecular Cancer Research , University of Zurich , Zurich, Switzerland
                [4 ]I2BC, iBiTec-S, CEA, CNRS UMR 9198, Université Paris-Sud , Gif-sur-Yvette, France
                [5 ]Université Paris Sud , Orsay, France
                [6 ]CRCM, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, CNRS UMR7258 , Marseille, France
                [7 ]Musée de l'Homme, CNRS UMR 7206 , Paris, France
                [8 ]Institut Curie, Centre de Recherche, PSL Research University, LSMP , Paris, France
                [9]CABIMER, Universidad de Sevilla , Spain
                [10]CABIMER, Universidad de Sevilla , Spain
                Author notes
                [‡]

                Institut Jean-Pierre Bourgin, UMR1318, INRA-AgroParisTech, Paris, France.

                [§]

                Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.

                [†]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-9087-032X
                http://orcid.org/0000-0001-6520-2461
                Article
                21900
                10.7554/eLife.21900
                5215242
                28051769
                d75b29b1-1fa2-49bb-a250-bb7f48c1587c
                © 2017, Duroc et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 27 September 2016
                : 15 December 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-11-LBX-0044
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-12-BSV6-0009
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-13-BSV6-0012-01
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-15-CE11-0011
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001711, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung;
                Award ID: PP00P3 133636
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100002915, Fondation pour la Recherche Médicale;
                Award ID: DEP20131128517
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100004099, Ligue Contre le Cancer;
                Award ID: postdoctoral fellowship
                Award Recipient :
                Funded by: French Infrastructure for Integrated Structural Biology;
                Award ID: ANR-10-INSB-05-01
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Biochemistry
                Genes and Chromosomes
                Custom metadata
                2.5
                Meiotic cells employ a specific pathway to limit the amount of gene conversion occuring at recombination sites.

                Life sciences
                recombination,meiosis,mismatch repair,s. cerevisiae
                Life sciences
                recombination, meiosis, mismatch repair, s. cerevisiae

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