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Spp1 Links Sites of Meiotic DNA Double-Strand Breaks to Chromosome Axes

2013; Elsevier BV; Volume: 49; Issue: 1 Linguagem: Inglês

10.1016/j.molcel.2012.12.011

1097-4164

Bernard de Massy,

DNA and Nucleic Acid Chemistry

Two recent studies (Sommermeyer et al., 2013Sommermeyer V. Béneut C. Chaplais E. Serrentino M.E. Borde V. Mol. Cell. 2013; 49 (this issue): 43-54Abstract Full Text Full Text PDF PubMed Scopus (130) Google Scholar; Acquaviva et al., 2012Acquaviva L. Székvölgyi L. Dichtl B. Dichtl B.S. de La Roche Saint André C. Nicolas A. Géli V. Science. 2012; (Published online November 15, 2012)https://doi.org/10.1126/science.1225739Crossref PubMed Scopus (132) Google Scholar) show that S. cerevisiae Spp1 promotes meiotic DSB formation by interacting with H3K4me3 and Mer2, a protein required for Spo11-catalyzed DSB formation located on chromosome axes. Two recent studies (Sommermeyer et al., 2013Sommermeyer V. Béneut C. Chaplais E. Serrentino M.E. Borde V. Mol. Cell. 2013; 49 (this issue): 43-54Abstract Full Text Full Text PDF PubMed Scopus (130) Google Scholar; Acquaviva et al., 2012Acquaviva L. Székvölgyi L. Dichtl B. Dichtl B.S. de La Roche Saint André C. Nicolas A. Géli V. Science. 2012; (Published online November 15, 2012)https://doi.org/10.1126/science.1225739Crossref PubMed Scopus (132) Google Scholar) show that S. cerevisiae Spp1 promotes meiotic DSB formation by interacting with H3K4me3 and Mer2, a protein required for Spo11-catalyzed DSB formation located on chromosome axes. The programmed induction of meiotic DNA double-strand breaks (DSBs) catalyzed by the Spo11 protein raises one of the major challenges for genome integrity during sexual reproduction. One important issue in the field is to understand what determines the localization of DSB sites and how Spo11 activity is controlled. In S. cerevisiae, Spo11 (which has no sequence specificity) appears to cut where DNA is accessible, in particular at transcription promoters, implying a role for chromatin structure, as described by several studies and recently by the genome-wide mapping of meiotic DSBs (Pan et al., 2011Pan J. Sasaki M. Kniewel R. Murakami H. Blitzblau H.G. Tischfield S.E. Zhu X. Neale M.J. Jasin M. Socci N.D. et al.Cell. 2011; 144: 719-731Abstract Full Text Full Text PDF PubMed Scopus (362) Google Scholar). In addition, several other proteins are known to be essential for DSB formation but are specifically localized to the axes of meiotic chromosomes. Since the DNA sequences undergoing DSBs are in chromatin loops extending from axes, it has been proposed that DSB sites are tethered to chromosome axes to link the various components required for DSB formation and allow DSB repair in the context of chromosome axes (Blat et al., 2002Blat Y. Protacio R.U. Hunter N. Kleckner N. Cell. 2002; 111: 791-802Abstract Full Text Full Text PDF PubMed Scopus (255) Google Scholar). How could such spatial reorganization be achieved? Using different experimental strategies, the groups of Valérie Borde (Sommermeyer et al., 2013Sommermeyer V. Béneut C. Chaplais E. Serrentino M.E. Borde V. Mol. Cell. 2013; 49 (this issue): 43-54Abstract Full Text Full Text PDF PubMed Scopus (130) Google Scholar) and Vincent Géli and Alain Nicolas (Acquaviva et al., 2012Acquaviva L. Székvölgyi L. Dichtl B. Dichtl B.S. de La Roche Saint André C. Nicolas A. Géli V. Science. 2012; (Published online November 15, 2012)https://doi.org/10.1126/science.1225739Crossref PubMed Scopus (132) Google Scholar) have recently identified the missing link in this spatial reorganization in S. cerevisiae, the Spp1 protein. This remarkable discovery provides a major advance in the molecular mechanism of meiotic DSB formation, highlights an amazing combination of actors, and raises questions about the biological significance of this process that may be addressed in the future by understanding the evolutionary conservation and diversity of this mechanism. The high-resolution mapping of Spo11 DSBs, as well as previous studies, has shown that DSBs preferentially occur in NDRs (nucleosome depleted regions), often adjacent to promoters (Pan et al., 2011Pan J. Sasaki M. Kniewel R. Murakami H. Blitzblau H.G. Tischfield S.E. Zhu X. Neale M.J. Jasin M. Socci N.D. et al.Cell. 2011; 144: 719-731Abstract Full Text Full Text PDF PubMed Scopus (362) Google Scholar). DSB levels are not related to transcription activity but can be influenced by transcription factor binding and chromatin accessibility. A well-known histone modification that is enriched near promoters, H3K4me3 is established by the Set1 methyltransferase recruited by RNA polymerase (Pol) II and is detected near DSB sites during meiosis. The challenge for the Borde, Géli, and Nicolas groups was to decipher from this observation which property of transcription promoters could be directly involved in DSB formation. Both studies took the approach of analyzing the roles of various components of the Set1 complex and showed that preventing H3K4 methylation lowers DSB levels. Both groups also identified one subunit of the Set1 complex, Spp1, as a good candidate for a direct role in this DSB activity. Spp1 is a reader of H3K4me2 and H3K4me3 and contains both a PHD (plant homeodomain) finger and a CXXC zinc finger domain. Mutating the Spp1 PHD finger leads to a modest decrease of H3K4me3 but results in a strong decrease in DSB levels, pointing toward the role of H3K4me3 through its interaction with Spp1. This information then raised the question—what is the role of the Spp1/H3K4me3 interaction for DSB formation? The answer came from several approaches: targeting Spp1 to specific genomic sites by virtue of the expression of a Gal4 DNA-binding domain Spp1 (GDBSpp1) fusion protein (Acquaviva et al., 2012Acquaviva L. Székvölgyi L. Dichtl B. Dichtl B.S. de La Roche Saint André C. Nicolas A. Géli V. Science. 2012; (Published online November 15, 2012)https://doi.org/10.1126/science.1225739Crossref PubMed Scopus (132) Google Scholar), looking for partners of Spp1 (in both studies), and analyzing genome-wide Spp1 localization by ChIP-chip (Sommermeyer et al., 2013Sommermeyer V. Béneut C. Chaplais E. Serrentino M.E. Borde V. Mol. Cell. 2013; 49 (this issue): 43-54Abstract Full Text Full Text PDF PubMed Scopus (130) Google Scholar). Remarkably, both studies identified Mer2, a protein essential for DSB formation, as an Spp1 partner. Géli's group detected this interaction through a yeast two-hybrid screen, whereas Borde's group selected this candidate based on its colocalization with Spp1 from ChIP-chip experiments. Two important features of Mer2 are that it forms a complex with Rec114 and Mei4 (the RMM complex) and is localized on axes, defined by the presence of the proteins Red1 and Hop1 and the cohesin Rec8 (Panizza et al., 2011Panizza S. Mendoza M.A. Berlinger M. Huang L. Nicolas A. Shirahige K. Klein F. Cell. 2011; 146: 372-383Abstract Full Text Full Text PDF PubMed Scopus (234) Google Scholar). All three members of the RMM complex are essential for DSB formation, implicating a loop-to-axis tethering of DSB sites as proposed in earlier studies (Blat et al., 2002Blat Y. Protacio R.U. Hunter N. Kleckner N. Cell. 2002; 111: 791-802Abstract Full Text Full Text PDF PubMed Scopus (255) Google Scholar). Although alternative scenarios are possible, this may allow Spo11 to be in contact with the RMM complex and thus proficient for DSB formation. The interaction between Spp1 and Mer2 was also shown by coimmunoprecipitation from meiotic extracts and by chromatin immunoprecipitation. Strikingly, upon expression of GBDSpp1, a strong and specific Mer2 enrichment is detected near Gal4 binding sites (Acquaviva et al., 2012Acquaviva L. Székvölgyi L. Dichtl B. Dichtl B.S. de La Roche Saint André C. Nicolas A. Géli V. Science. 2012; (Published online November 15, 2012)https://doi.org/10.1126/science.1225739Crossref PubMed Scopus (132) Google Scholar). Furthermore, ChIP-chip analysis showed a remarkable property of Spp1, with a change of its localization from promoter regions in vegetative cells to axis sites during meiosis, which are often cohesin binding sites at the 3′ ends of convergent genes. This meiotic localization of Spp1 is highly overlapping with that of Mer2. This binding of Spp1 to axes requires Mer2 but not the Spo11 catalytic activity (Sommermeyer et al., 2013Sommermeyer V. Béneut C. Chaplais E. Serrentino M.E. Borde V. Mol. Cell. 2013; 49 (this issue): 43-54Abstract Full Text Full Text PDF PubMed Scopus (130) Google Scholar). Thus the combination of the two features of Spp1, a PHD finger and a Mer2-interacting domain, lead to the very appealing model in which this protein provides the molecular link between DSB sites and the chromosome axes in the regions where the RMM complex is localized (Figure 1). Interestingly, Spp1 by itself does not specify DSB localization, but it allows Spo11 bound to an accessible region of the chromatin to be active. This is very convincingly shown by a GBDSpp1-targeting experiment in which DSBs are not detected near the Gal4 binding sites, but at a distance in a promoter region where Spo11 may preferentially interact (Acquaviva et al., 2012Acquaviva L. Székvölgyi L. Dichtl B. Dichtl B.S. de La Roche Saint André C. Nicolas A. Géli V. Science. 2012; (Published online November 15, 2012)https://doi.org/10.1126/science.1225739Crossref PubMed Scopus (132) Google Scholar). In the absence of H3K4 methylation (Set1Δ strain), the formation of DSBs is strongly reduced in most regions. However, most DSBs (77%) occur at positions similar to those in the wild-type, demonstrating H3K4me3-independent selection of sites by Spo11 and hinting at alternative pathways for establishing the link between Spo11 and the RMM complex (Borde et al., 2009Borde V. Robine N. Lin W. Bonfils S. Géli V. Nicolas A. EMBO J. 2009; 28: 99-111Crossref PubMed Scopus (276) Google Scholar). The dependency of RMM for DSB formation is still an enigma, however, and whether it influences Spo11 activity, its conformation, or other steps is unknown. The RMM complex is conserved in S. pombe, and recent analysis shows that this complex is interacting with DSB sites through the Mde2 protein, which has no identified ortholog in S. cerevisiae (Miyoshi et al., 2012Miyoshi T. Ito M. Kugou K. Yamada S. Furuichi M. Oda A. Yamada T. Hirota K. Masai H. Ohta K. Mol. Cell. 2012; 47: 722-733Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar). Mde2 may thus have a similar function as S. cerevisiae Spp1 during meiosis and is therefore predicted to interact with some yet unknown feature of regions of DSBs, but not H3K4me3, as S. pombe meiotic DSB sites do not correlate with transcription promoters (Miyoshi et al., 2012Miyoshi T. Ito M. Kugou K. Yamada S. Furuichi M. Oda A. Yamada T. Hirota K. Masai H. Ohta K. Mol. Cell. 2012; 47: 722-733Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar). Altogether, these results provide a remarkable view of the process: Spp1 is recruited to chromosome axes by interaction with Mer2 and promotes Spo11 interaction to axes via binding to H3K4me3 (which is often found next to the NDR where Spo11 has access and binds). The actual order of events, in particular the binding of Spo11 with respect to DSB sites/axis interactions, and whether this binding is promoted and/or stabilized by the Spp1-H3K4me3 interaction, are not known. It is remarkable that a specific protein in mammals, PRDM9, appears to recruit (directly or indirectly) SPO11 to specific genomic sites and promote H3K4me3 (Grey et al., 2011Grey C. Barthès P. Chauveau-Le Friec G. Langa F. Baudat F. de Massy B. PLoS Biol. 2011; 9: e1001176Crossref PubMed Scopus (130) Google Scholar). Since several components of the RMM complex are conserved in mammals and associated with chromosome axes (Kumar et al., 2010Kumar R. Bourbon H.M. de Massy B. Genes Dev. 2010; 24: 1266-1280Crossref PubMed Scopus (132) Google Scholar), one also predicts the requirement for a link between DSB sites and axes. Since, in the absence of PRDM9 in mice, DSB localization is radically altered and DSBs are often detected near transcription start sites (TSSs) (Brick et al., 2012Brick K. Smagulova F. Khil P. Camerini-Otero R.D. Petukhova G.V. Nature. 2012; 485: 642-645Crossref PubMed Scopus (263) Google Scholar), H3K4me3 might be part of the bridging machinery with an unknown PHD finger-containing protein. The significance of these processes relates, on at least two levels, to the requirement for a communication between DSB formation and repair and the chromosome structure. First, DSB formation is regulated by a control in trans between homologous chromatids (Zhang et al., 2011Zhang L. Kim K.P. Kleckner N.E. Storlazzi A. Proc. Natl. Acad. Sci. USA. 2011; 108: 20036-20041Crossref PubMed Scopus (80) Google Scholar). Second, DSB repair can take place through different pathways that should be regulated along chromosomes to establish the proper number of crossovers (CO) required for chromosome segregation. This implies a choice of the interacting chromatid (sister chromatid versus homolog) and a choice of the repair pathway with or without CO. The chromosome axis is one of the components involved in such regulations, likely allowing the transmission of information along chromosomes. It would thus be extremely exciting to be able to follow the dynamics and kinetics of these DNA and chromosomal events live so as to have both a population and a single-cell view of these processes. It would also be important to further understand how signals can be transmitted along chromosomes for both DSB formation and repair controls, as these are still major and challenging questions to be answered.