During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.

Advanced Microscopy Facility VBCF and Department of Chromosome Biology Max Perutz Labs University of Vienna Vienna Biocenter 1030 Vienna Austria

Cancer Research Institute Biomedical Research Center Slovak Academy of Sciences 845 05 Bratislava Slovakia

Comenius University Science Park 841 04 Bratislava Slovakia

Department of Cell Biology Faculty of Science Charles University 128 00 Praha 2 Czechia

Department of Genetics Faculty of Natural Sciences Comenius University in Bratislava 841 04 Bratislava Slovakia

Department of Molecular Biology Faculty of Natural Sciences Comenius University in Bratislava 841 04 Bratislava Slovakia

Department of Molecular Biotechnology and Microbiology Faculty of Science and Technology University of Debrecen H 4010 Debrecen Hungary

Geneton Ltd 841 04 Bratislava Slovakia

Institute of Animal Biochemistry and Genetics Centre of Biosciences Slovak Academy of Sciences 840 05 Bratislava Slovakia

Slovak Centre of Scientific and Technical Information 811 04 Bratislava Slovakia

Zobrazit více v PubMed

Mimitou E.P., Symington L.S.. DNA end resection—unraveling the tail. DNA Repair (Amst.). 2011; 10:344–348. PubMed PMC

Ceccaldi R., Rondinelli B., D’Andrea A.D.. Repair pathway choices and consequences at the double-strand break. Trends Cell Biol. 2016; 26:52–64. PubMed PMC

Krogh B.O., Symington L.S.. Recombination proteins in yeast. Annu. Rev. Genet. 2004; 38:233–271. PubMed

Ranjha L., Howard S.M., Cejka P.. Main steps in DNA double-strand break repair: an introduction to homologous recombination and related processes. Chromosoma. 2018; 127:187–214. PubMed

Grishchuk A.L., Kohli J.. Five RecA-like proteins of Schizosaccharomyces pombe are involved in meiotic recombination. Genetics. 2003; 165:1031–1043. PubMed PMC

Young J.A., Hyppa R.W., Smith G.R.. Conserved and nonconserved proteins for meiotic DNA breakage and repair in yeasts. Genetics. 2004; 167:593–605. PubMed PMC

Ellermeier C., Schmidt H., Smith G.R.. Swi5 acts in meiotic DNA joint molecule formation in Schizosaccharomyces pombe. Genetics. 2004; 168:1891–1898. PubMed PMC

Haruta N., Kurokawa Y., Murayama Y., Akamatsu Y., Unzai S., Tsutsui Y., Iwasaki H.. The Swi5-Sfr1 complex stimulates Rhp51/Rad51- and Dmc1-mediated DNA strand exchange in vitro. Nat. Struct. Mol. Biol. 2006; 13:823–830. PubMed

Bianco P.R., Tracy R.B., Kowalczykowski S.C.. DNA strand exchange proteins: a biochemical and physical comparison. Front. Biosci. 1998; 3:D570–603. PubMed

Morrical S.W. DNA-pairing and annealing processes in homologous recombination and homology-directed repair. Cold Spring Harb. Perspect. Biol. 2015; 7:a016444. PubMed PMC

Krejci L., Macris M., Li Y., Van Komen S., Villemain J., Ellenberger T., Klein H., Sung P.. Role of ATP hydrolysis in the antirecombinase function of Saccharomyces cerevisiae Srs2 protein. J. Biol. Chem. 2004; 279:23193–23199. PubMed

Tsutsui Y., Kurokawa Y., Ito K., Siddique M.S.P., Kawano Y., Yamao F., Iwasaki H. Multiple regulation of Rad51-mediated homologous recombination by fission yeast Fbh1. PLos Genet. 2014; 10:e1004542. PubMed PMC

Osman F., Dixon J., Barr A.R., Whitby M.C.. The F-Box DNA helicase Fbh1 prevents Rhp51-dependent recombination without mediator proteins. Mol. Cell. Biol. 2005; 25:8084–8096. PubMed PMC

Lorenz A., West S.C., Whitby M.C.. The human Holliday junction resolvase GEN1 rescues the meiotic phenotype of a Schizosaccharomyces pombe mus81 mutant. Nucleic. Acids. Res. 2010; 38:1866–1873. PubMed PMC

Polakova S., Molnarova L., Hyppa R.W., Benko Z., Misova I., Schleiffer A., Smith G.R., Gregan J.. Dbl2 regulates Rad51 and DNA joint molecule metabolism to ensure proper meiotic chromosome segregation. PLos Genet. 2016; 12:e1006102. PubMed PMC

Yu Y., Ren J.Y., Zhang J.M., Suo F., Fang X.F., Wu F., Du L.L.. A proteome-wide visual screen identifies fission yeast proteins localizing to DNA double-strand breaks. DNA Repair (Amst.). 2013; 12:433–443. PubMed

Chi P., Kwon Y., Seong C., Epshtein A., Lam I., Sung P., Klein H.L.. Yeast recombination factor Rdh54 functionally interacts with the Rad51 recombinase and catalyzes Rad51 removal from DNA. J. Biol. Chem. 2006; 281:26268–26279. PubMed

Petukhova G., Stratton S., Sung P.. Catalysis of homologous DNA pairing by yeast Rad51 and Rad54 proteins. Nature. 1998; 393:91–94. PubMed

Petukhova G., Sung P., Klein H.. Promotion of Rad51-dependent D-loop formation by yeast recombination factor Rdh54/Tid1. Genes Dev. 2000; 14:2206–2215. PubMed PMC

Van Komen S., Petukhova G., Sigurdsson S., Stratton S., Sung P.. Superhelicity-driven homologous DNA pairing by yeast recombination factors Rad51 and Rad54. Mol. Cell. 2000; 6:563–572. PubMed

Tan T.L., Essers J., Citterio E., Swagemakers S.M., de Wit J., Benson F.E., Hoeijmakers J.H., Kanaar R.. Mouse Rad54 affects DNA conformation and DNA-damage-induced Rad51 foci formation. Curr. Biol. 1999; 9:325–328. PubMed

Jaskelioff M., Van Komen S., Krebs J.E., Sung P., Peterson C.L.. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem. 2003; 278:9212–9218. PubMed

Kwon Y., Chi P., Roh D.H., Klein H., Sung P.. Synergistic action of the Saccharomyces cerevisiae homologous recombination factors Rad54 and Rad51 in chromatin remodeling. DNA Repair (Amst.). 2007; 6:1496–1506. PubMed PMC

Kwon Y., Seong C., Chi P., Greene E.C., Klein H., Sung P.. ATP-dependent chromatin remodeling by the Saccharomyces cerevisiae homologous recombination factor Rdh54. J. Biol. Chem. 2008; 283:10445–10452. PubMed PMC

Bugreev D. V, Mazina O.M., Mazin A.V.. Rad54 protein promotes branch migration of Holliday junctions. Nature. 2006; 442:590–593. PubMed

Solinger J.A., Kiianitsa K., Heyer W.-D.. Rad54, a Swi2/Snf2-like recombinational repair protein, disassembles Rad51:dsDNA filaments. Mol. Cell. 2002; 10:1175–1188. PubMed

Li X., Heyer W.-D.. RAD54 controls access to the invading 3′-OH end after RAD51-mediated DNA strand invasion in homologous recombination in Saccharomyces cerevisiae. Nucleic. Acids. Res. 2009; 37:638–646. PubMed PMC

Szostak J.W., Orr-Weaver T.L., Rothstein R.J., Stahl F.W.. The double-strand-break repair model for recombination. Cell. 1983; 33:25–35. PubMed

Nassif N., Penney J., Pal S., Engels W.R., Gloor G.B.. Efficient copying of nonhomologous sequences from ectopic sites via P-element-induced gap repair. Mol. Cell. Biol. 1994; 14:1613–1625. PubMed PMC

Lorenz A., Osman F., Sun W., Nandi S., Steinacher R., Whitby M.C.. The fission yeast FANCM ortholog directs non-crossover recombination during meiosis. Science. 2012; 336:1585–1588. PubMed PMC

Boddy M.N., Gaillard P.H., McDonald W.H., Shanahan P., Yates J.R., Russell P.. Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell. 2001; 107:537–548. PubMed

Carr A.M., Lambert S.. Replication stress-induced genome instability: the dark side of replication maintenance by homologous recombination. J. Mol. Biol. 2013; 425:4733–4744. PubMed

Petermann E., Orta M.L., Issaeva N., Schultz N., Helleday T.. Hydroxyurea-stalled replication forks become progressively inactivated and require two different RAD51-mediated pathways for restart and repair. Mol. Cell. 2010; 37:492–502. PubMed PMC

Schlacher K., Christ N., Siaud N., Egashira A., Wu H., Jasin M.. Double-strand break repair-independent role for BRCA2 in blocking stalled replication fork degradation by MRE11. Cell. 2011; 145:529–542. PubMed PMC

Hashimoto Y., Ray Chaudhuri A., Lopes M., Costanzo V.. Rad51 protects nascent DNA from Mre11-dependent degradation and promotes continuous DNA synthesis. Nat. Struct. Mol. Biol. 2010; 17:1305–1311. PubMed PMC

Higgs M.R., Reynolds J.J., Winczura A., Blackford A.N., Borel V., Miller E.S., Zlatanou A., Nieminuszczy J., Ryan E.L., Davies N.J.et al. .. BOD1L is required to suppress deleterious resection of stressed replication forks. Mol. Cell. 2015; 59:462–477. PubMed

Hashimoto Y., Puddu F., Costanzo V.. RAD51- and MRE11-dependent reassembly of uncoupled CMG helicase complex at collapsed replication forks. Nat. Struct. Mol. Biol. 2011; 19:17–24. PubMed PMC

Iraqui I., Chekkal Y., Jmari N., Pietrobon V., Fréon K., Costes A., Lambert S.A.E.. Recovery of arrested replication forks by homologous recombination is error-prone. PLos Genet. 2012; 8:e1002976. PubMed PMC

Miyabe I., Mizuno K., Keszthelyi A., Daigaku Y., Skouteri M., Mohebi S., Kunkel T.A., Murray J.M., Carr A.M.. Polymerase δ replicates both strands after homologous recombination–dependent fork restart. Nat. Struct. Mol. Biol. 2015; 22:932–938. PubMed PMC

Mizuno K., Miyabe I., Schalbetter S.A., Carr A.M., Murray J.M.. Recombination-restarted replication makes inverted chromosome fusions at inverted repeats. Nature. 2013; 493:246–249. PubMed PMC

Chen C.-C., Carson J.J., Feser J., Tamburini B., Zabaronick S., Linger J., Tyler J.K.. Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair. Cell. 2008; 134:231–243. PubMed PMC

Tsukuda T., Fleming A.B., Nickoloff J.A., Osley M.A.. Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature. 2005; 438:379–383. PubMed PMC

Paull T.T., Gellert M.. The 3′ to 5′ exonuclease activity of Mre 11 facilitates repair of DNA double-strand breaks. Mol. Cell. 1998; 1:969–979. PubMed

van Attikum H., Fritsch O., Hohn B., Gasser S.M.. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell. 2004; 119:777–788. PubMed

Gospodinov A., Vaissiere T., Krastev D.B., Legube G., Anachkova B., Herceg Z.. Mammalian Ino80 mediates double-strand break repair through its role in DNA end strand resection. Mol. Cell. Biol. 2011; 31:4735–4745. PubMed PMC

Li X., Tyler J.K.. Nucleosome disassembly during human non-homologous end joining followed by concerted HIRA- and CAF-1-dependent reassembly. Elife. 2016; 5:e15129. PubMed PMC

Brachet E., Béneut C., Serrentino M.-E., Borde V.. The CAF-1 and Hir histone chaperones associate with sites of meiotic double-strand breaks in budding yeast. PLoS One. 2015; 10:e0125965. PubMed PMC

Anderson H.E., Wardle J., Korkut S.V., Murton H.E., Lopez-Maury L., Bahler J., Whitehall S.K.. The fission yeast HIRA histone chaperone is required for promoter silencing and the suppression of cryptic antisense transcripts. Mol. Cell. Biol. 2009; 29:5158–5167. PubMed PMC

Chujo M., Tarumoto Y., Miyatake K., Nishida E., Ishikawa F.. HIRA, a conserved histone chaperone, plays an essential role in low-dose stress response via transcriptional stimulation in fission yeast. J. Biol. Chem. 2012; 287:23440–23450. PubMed PMC

Spector M.S., Raff A., DeSilva H., Lee K., Osley M.A.. Hir1p and Hir2p function as transcriptional corepressors to regulate histone gene transcription in the Saccharomyces cerevisiae cell cycle. Mol. Cell. Biol. 1997; 17:545–552. PubMed PMC

Greenall A., Williams E.S., Martin K.A., Palmer J.M., Gray J., Liu C., Whitehall S.K.. Hip3 interacts with the HIRA proteins Hip1 and Slm9 and is required for transcriptional silencing and accurate chromosome segregation. J. Biol. Chem. 2006; 281:8732–8739. PubMed

Cheung V., Chua G., Batada N.N., Landry C.R., Michnick S.W., Hughes T.R., Winston F.. Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol. 2008; 6:e277. PubMed PMC

Nourani A., Robert F., Winston F.. Evidence that Spt2/Sin1, an HMG-like factor, plays roles in transcription elongation, chromatin structure, and genome stability in Saccharomyces cerevisiae. Mol. Cell. Biol. 2006; 26:1496–1509. PubMed PMC

Gregan J., Rabitsch P.K., Rumpf C., Novatchkova M., Schleiffer A., Nasmyth K.. High-throughput knockout screen in fission yeast. Nat. Protoc. 2006; 1:2457–2464. PubMed PMC

Kim D.U., Hayles J., Kim D., Wood V., Park H.O., Won M., Yoo H.S., Duhig T., Nam M., Palmer G.et al. .. Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe. Nat. Biotechnol. 2010; 28:617–623. PubMed PMC

Sabatinos S.A., Forsburg S.L.. Molecular genetics of Schizosaccharomyces pombe. Methods Enzymol. 2010; 470:759–795. PubMed

Guarente L. Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 1983; 101:181–191. PubMed

Bradford M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976; 72:248–254. PubMed

Ekwall K., Cranston G., Allshire R.C.. Fission yeast mutants that alleviate transcriptional silencing in centromeric flanking repeats and disrupt chromosome segregation. Genetics. 1999; 153:1153–1169. PubMed PMC

Lyne R., Burns G., Mata J., Penkett C.J., Rustici G., Chen D., Langford C., Vetrie D., Bähler J.. Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics. 2003; 4:27. PubMed PMC

Bolger A.M., Lohse M., Usadel B.. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30:2114–2120. PubMed PMC

Patro R., Duggal G., Love M.I., Irizarry R.A., Kingsford C.. Salmon provides fast and bias-aware quantification of transcript expression. Nat. Methods. 2017; 14:417–419. PubMed PMC

Robinson M.D., McCarthy D.J., Smyth G.K.. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2009; 26:139–140. PubMed PMC

Kim D., Langmead B., Salzberg S.L.. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods. 2015; 12:357–360. PubMed PMC

Okonechnikov K., Conesa A., García-Alcalde F.. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2015; 32:btv566. PubMed PMC

Ramírez F., Dündar F., Diehl S., Grüning B.A., Manke T.. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 2014; 42:W187–W191. PubMed PMC

Thorvaldsdottir H., Robinson J.T., Mesirov J.P.. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 2013; 14:178–192. PubMed PMC

Koster J., Rahmann S.. Snakemake–a scalable bioinformatics workflow engine. Bioinformatics. 2012; 28:2520–2522. PubMed

Wood V., Harris M.A., McDowall M.D., Rutherford K., Vaughan B.W., Staines D.M., Aslett M., Lock A., Bähler J., Kersey P.J.et al. .. PomBase: A comprehensive online resource for fission yeast. Nucleic Acids Res. 2012; 40:D695–D699. PubMed PMC

Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27:573–580. PubMed PMC

Dhapola P., Chowdhury S.. QuadBase2: web server for multiplexed guanine quadruplex mining and visualization. Nucleic Acids Res. 2016; 44:W277–W283. PubMed PMC

Reimand J., Arak T., Adler P., Kolberg L., Reisberg S., Peterson H., Vilo J.. g:Profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. 2016; 44:W83–W89. PubMed PMC

Reimand J., Kull M., Peterson H., Hansen J., Vilo J.. g:Profiler–a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic. Acids. Res. 2007; 35:W193–W200. PubMed PMC

Gal C., Moore K.M., Paszkiewicz K., Kent N.A., Whitehall S.K.. The impact of the HIRA histone chaperone upon global nucleosome architecture. Cell Cycle. 2015; 14:123–134. PubMed PMC

Převorovský M., Oravcová M., Tvarůžková J., Zach R., Folk P., Půta F., Bähler J.. Fission yeast CSL transcription factors: Mapping their target genes and biological roles. PLoS One. 2015; 10:e0137820. PubMed PMC

Kim D., Langmead B., Salzberg S.L.. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods. 2015; 12:357–360. PubMed PMC

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R.. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25:2078–2079. PubMed PMC

Kizer K.O., Phatnani H.P., Shibata Y., Hall H., Greenleaf A.L., Strahl B.D.. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol. Cell. Biol. 2005; 25:3305–3316. PubMed PMC

Mata J., Lyne R., Burns G., Bähler J.. The transcriptional program of meiosis and sporulation in fission yeast. Nat. Genet. 2002; 32:143–147. PubMed

Chen D., Toone W.M., Mata J., Lyne R., Burns G., Kivinen K., Brazma A., Jones N., Bähler J.. Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell. 2003; 14:214–229. PubMed PMC

Watson A., Mata J., Bähler J., Carr A., Humphrey T.. Global gene expression responses of fission yeast to ionizing radiation. Mol. Biol. Cell. 2004; 15:851–860. PubMed PMC

Cam H.P., Sugiyama T., Chen E.S., Chen X., FitzGerald P.C., Grewal S.I.S.. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 2005; 37:809–819. PubMed

Tashiro S., Nishihara Y., Kugou K., Ohta K., Kanoh J.. Subtelomeres constitute a safeguard for gene expression and chromosome homeostasis. Nucleic Acids Res. 2017; 45:10333–10349. PubMed PMC

Bowen N.J., Jordan I.K., Epstein J.A., Wood V., Levin H.L.. Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res. 2003; 13:1984–1997. PubMed PMC

Rozenzhak S., Mejía-Ramírez E., Williams J.S., Schaffer L., Hammond J.A., Head S.R., Russell P.. Rad3 decorates critical chromosomal domains with gammaH2A to protect genome integrity during S-Phase in fission yeast. PLoS Genet. 2010; 6:e1001032. PubMed PMC

Reinhart B.J., Bartel D.P.. Small RNAs correspond to centromere heterochromatic repeats. Science (80-.). 2002; 297:1831–1831. PubMed

Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I.S., Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 2002; 297:1833–1837. PubMed

Zofall M., Fischer T., Zhang K., Zhou M., Cui B., Veenstra T.D., Grewal S.I.S.. Histone H2A.Z cooperates with RNAi and heterochromatin factors to suppress antisense RNAs. Nature. 2009; 461:419–422. PubMed PMC

Ekwall K., Ruusala T.. Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics. 1994; 136:53–64. PubMed PMC

Grewal S.I., Bonaduce M.J., Klar A.J.. Histone deacetylase homologs regulate epigenetic inheritance of transcriptional silencing and chromosome segregation in fission yeast. Genetics. 1998; 150:563–576. PubMed PMC

Thon G., Bjerling K.P., Nielsen I.S.. Localization and properties of a silencing element near the mat3-M mating-type cassette of Schizosaccharomyces pombe. Genetics. 1999; 151:945–963. PubMed PMC

Hansen K.R., Burns G., Mata J., Volpe T.A., Martienssen R.A., Bahler J., Thon G.. Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol. Cell. Biol. 2005; 25:590–601. PubMed PMC

Nicolas E., Yamada T., Cam H.P., FitzGerald P.C., Kobayashi R., Grewal S.I.S.. Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nat. Struct. Mol. Biol. 2007; 14:372–380. PubMed

Zhang K., Fischer T., Porter R.L., Dhakshnamoorthy J., Zofall M., Zhou M., Veenstra T., Grewal S.I.S.. Clr4/Suv39 and RNA quality control factors cooperate to trigger RNAi and suppress antisense RNA. Science (80-.). 2011; 331:1624–1627. PubMed PMC

Yamane K., Mizuguchi T., Cui B., Zofall M., Noma K., Grewal S.I.S.. Asf1/HIRA facilitate global histone deacetylation and associate with HP1 to promote nucleosome occupancy at heterochromatic loci. Mol. Cell. 2011; 41:56–66. PubMed PMC

Amin A.D., Vishnoi N., Prochasson P.. A global requirement for the HIR complex in the assembly of chromatin. Biochim. Biophys. Acta. 2012; 1819:264–276. PubMed

Green E.M., Antczak A.J., Bailey A.O., Franco A.A., Wu K.J., Yates J.R., Kaufman P.D.. Replication-independent histone deposition by the HIR complex and Asf1. Curr. Biol. 2005; 15:2044–2049. PubMed PMC

Prochasson P., Florens L., Swanson S.K., Washburn M.P., Workman J.L.. The HIR corepressor complex binds to nucleosomes generating a distinct protein/DNA complex resistant to remodeling by SWI/SNF. Genes Dev. 2005; 19:2534–2539. PubMed PMC

Ray-Gallet D., Quivy J.-P., Scamps C., Martini E.M.-D., Lipinski M., Almouzni G.. HIRA is critical for a nucleosome assembly pathway independent of DNA synthesis. Mol. Cell. 2002; 9:1091–1100. PubMed

Tagami H., Ray-Gallet D., Almouzni G., Nakatani Y.. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell. 2004; 116:51–61. PubMed

Blackwell C., Martin K.A., Greenall A., Pidoux A., Allshire R.C., Whitehall S.K.. The Schizosaccharomyces pombe HIRA-like protein Hip1 is required for the periodic expression of histone genes and contributes to the function of complex centromeres. Mol. Cell. Biol. 2004; 24:4309–4320. PubMed PMC

Sharp J.A., Fouts E.T., Krawitz D.C., Kaufman P.D.. Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr. Biol. 2001; 11:463–473. PubMed

Zhang R., Poustovoitov M.V., Ye X., Santos H.A., Chen W., Daganzo S.M., Erzberger J.P., Serebriiskii I.G., Canutescu A.A., Dunbrack R.L.et al. .. Formation of MacroH2A-Containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev. Cell. 2005; 8:19–30. PubMed

Phelps-Durr T.L., Thomas J., Vahab P., Timmermans M.C.P.. Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell. 2005; 17:2886–2898. PubMed PMC

Rea S., Eisenhaber F., O’Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D.et al. .. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature. 2000; 406:593–599. PubMed

Roguev A., Bandyopadhyay S., Zofall M., Zhang K., Fischer T., Collins S.R., Qu H., Shales M., Park H.O., Hayles J.et al. .. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science. 2008; 322:405–410. PubMed PMC

Ryan C.J., Roguev A., Patrick K., Xu J., Jahari H., Tong Z., Beltrao P., Shales M., Qu H., Collins S.R.et al. .. Hierarchical modularity and the evolution of genetic interactomes across species. Mol. Cell. 2012; 46:691–704. PubMed PMC

Barrales R.R., Forn M., Georgescu P.R., Sarkadi Z., Braun S.. Control of heterochromatin localization and silencing by the nuclear membrane protein Lem2. Genes Dev. 2016; 30:133–148. PubMed PMC

Driessen R.P.C., Sitters G., Laurens N., Moolenaar G.F., Wuite G.J.L., Goosen N., Dame R.T. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry. 2014; 53:6430–6438. PubMed PMC

Fischer T., Cui B., Dhakshnamoorthy J., Zhou M., Rubin C., Zofall M., Veenstra T.D., Grewal S.I.S.. Diverse roles of HP1 proteins in heterochromatin assembly and functions in fission yeast. Proc. Natl. Acad. Sci. U.S.A. 2009; 106:8998–9003. PubMed PMC

Bernard P., Allshire R.C.. Centromeres become unstuck without heterochromatin. Trends Cell Biol. 2002; 12:419–424. PubMed

Kent N.A., Adams S., Moorhouse A., Paszkiewicz K.. Chromatin particle spectrum analysis: A method for comparative chromatin structure analysis using paired-end mode next-generation DNA sequencing. Nucleic Acids Res. 2011; 39:e26. PubMed PMC

Jiang C., Pugh B.F.. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 2009; 10:161–172. PubMed PMC

Lantermann A.B., Straub T., Strålfors A., Yuan G.C., Ekwall K., Korber P.. Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae. Nat. Struct. Mol. Biol. 2010; 17:251–257. PubMed

Martin C., Zhang Y.. The diverse functions of histone lysine methylation. Nat. Rev. Mol. Cell Biol. 2005; 6:838–849. PubMed

Cromie G.A., Hyppa R.W., Taylor A.F., Zakharyevich K., Hunter N., Smith G.R.. Single holliday junctions are intermediates of meiotic recombination. Cell. 2006; 127:1167–1178. PubMed PMC

Oh S.D., Lao J.P., Taylor A.F., Smith G.R., Hunter N.. RecQ Helicase, Sgs1, and XPF family endonuclease, Mus81-Mms4, resolve aberrant joint molecules during meiotic recombination. Mol. Cell. 2008; 31:324–336. PubMed PMC

Jessop L., Lichten M.. Mus81/Mms4 endonuclease and Sgs1 helicase collaborate to ensure proper recombination intermediate metabolism during meiosis. Mol. Cell. 2008; 31:313–323. PubMed PMC

Matos J., Blanco M.G., Maslen S., Skehel J.M., West S.C.. Regulatory control of the resolution of DNA recombination intermediates during meiosis and mitosis. Cell. 2011; 147:158–172. PubMed PMC

San Filippo J., Sung P., Klein H.. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 2008; 77:229–257. PubMed

Shim E.Y., Chung W.H., Nicolette M.L., Zhang Y., Davis M., Zhu Z., Paull T.T., Ira G., Lee S.E.. Saccharomyces cerevisiae Mre11/Rad50/Xrs2 and Ku proteins regulate association of Exo1 and Dna2 with DNA breaks. EMBO J. 2010; 29:3370–3380. PubMed PMC

Clerici M., Mantiero D., Guerini I., Lucchini G., Longhese M.P.. The Yku70-Yku80 complex contributes to regulate double-strand break processing and checkpoint activation during the cell cycle. EMBO Rep. 2008; 9:810–818. PubMed PMC

Zheng S., Li D., Lu Z., Liu G., Wang M., Xing P., Wang M., Dong Y., Wang X., Li J.et al. .. Bre1-dependent H2B ubiquitination promotes homologous recombination by stimulating histone eviction at DNA breaks. Nucleic. Acids. Res. 2018; 46:11326–11339. PubMed PMC

Greenstein R.A., Ng H., Barrales R.R., Tan C., Braun S., Al-Sady B.. Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. 2020; bioRxiv doi:31 May 2020, preprint: not peer reviewed10.1101/2020.05.26.117143. PubMed DOI PMC

Jih G., Iglesias N., Currie M.A., Bhanu N.V., Paulo J.A., Gygi S.P., Garcia B.A., Moazed D.. Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature. 2017; 547:463–467. PubMed PMC

Lorenz D.R., Mikheyeva I. V, Johansen P., Meyer L., Berg A., Grewal S.I.S., Cam H.P. CENP-B cooperates with Set1 in bidirectional transcriptional silencing and genome organization of retrotransposons. Mol. Cell. Biol. 2012; 32:4215–4225. PubMed PMC

Sugiyama T., Cam H.P., Sugiyama R., Noma K., Zofall M., Kobayashi R., Grewal S.I.S.. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell. 2007; 128:491–504. PubMed

Cam H.P., Noma K., Ebina H., Levin H.L., Grewal S.I.S.. Host genome surveillance for retrotransposons by transposon-derived proteins. Nature. 2008; 451:431–436. PubMed

Durand-Dubief M., Sinha I., Fagerström-Billai F., Bonilla C., Wright A., Grunstein M., Ekwall K.. Specific functions for the fission yeast Sirtuins Hst2 and Hst4 in gene regulation and retrotransposon silencing. EMBO J. 2007; 26:2477–2488. PubMed PMC

Hansen K.R., Burns G., Mata J., Volpe T.A., Martienssen R.A., Bahler J., Thon G.. Global effects on gene expression in fission yeast by silencing and RNA interference machineries. Mol. Cell. Biol. 2005; 25:590–601. PubMed PMC

Yamanaka S., Mehta S., Reyes-Turcu F.E., Zhuang F., Fuchs R.T., Rong Y., Robb G.B., Grewal S.I.S.. RNAi triggered by specialized machinery silences developmental genes and retrotransposons. Nature. 2013; 493:557–560. PubMed PMC

Zaratiegui M., Vaughn M.W., Irvine D.V., Goto D., Watt S., Bähler J., Arcangioli B., Martienssen R.A.. CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature. 2011; 469:112–115. PubMed PMC

Rai T.S., Glass M., Cole J.J., Rather M.I., Marsden M., Neilson M., Brock C., Humphreys I.R., Everett R.D., Adams P.D.. Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity. Nucleic Acids Res. 2017; 45:11673–11683. PubMed PMC

Pchelintsev N.A., McBryan T., Rai T.S., VanTuyn J., Ray-Gallet D., Almouzni G., Adams P.D.. Placing the HIRA histone chaperone complex in the chromatin landscape. Cell Rep. 2013; 3:1012–1019. PubMed PMC

Peng G., Lin C.C.J., Mo W., Dai H., Park Y.Y., Kim S.M., Peng Y., Mo Q., Siwko S., Hu R.et al. .. Genome-wide transcriptome profiling of homologous recombination DNA repair. Nat. Commun. 2014; 5:3361. PubMed PMC

Durrant W.E., Wang S., Dong X.. Arabidopsis SNI1 and RAD51D regulate both gene transcription and DNA recombination during the defense response. Proc. Natl. Acad. Sci. U.S.A. 2007; 104:4223–4227. PubMed PMC

Wang S., Durrant W.E., Song J., Spivey N.W., Dong X.. Arabidopsis BRCA2 and RAD51 proteins are specifically involved in defense gene transcription during plant immune responses. Proc. Natl. Acad. Sci. U.S.A. 2010; 107:22716–22721. PubMed PMC

Wang Y., Xiao R., Wang H., Cheng Z., Li W., Zhu G., Wang Y., Ma H.. The Arabidopsis RAD51 paralogs RAD51B, RAD51D and XRCC2 play partially redundant roles in somatic DNA repair and gene regulation. New Phytol. 2014; 201:292–304. PubMed

Jeffares D.C., Rallis C., Rieux A., Speed D., Převorovský M., Mourier T., Marsellach F.X., Iqbal Z., Lau W., Cheng T.M.K.et al. .. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat. Genet. 2015; 47:235–241. PubMed PMC

Guo Y., Levin H.L.. High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe. Genome Res. 2010; 20:239–248. PubMed PMC

Zhu Q., Pao G.M., Huynh A.M., Suh H., Tonnu N., Nederlof P.M., Gage F.H., Verma I.M.. BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature. 2011; 477:179–184. PubMed PMC

Padeken J., Zeller P., Towbin B., Katic I., Kalck V., Methot S.P., Gasser S.M.. Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression. Genes Dev. 2019; 33:436–451. PubMed PMC

Szilard R.K., Jacques P.T., Laramée L., Cheng B., Galicia S., Bataille A.R., Yeung M., Mendez M., Bergeron M., Robert F.et al. .. Systematic identification of fragile sites via genome-wide location analysis of γ-H2AX. Nat. Struct. Mol. Biol. 2010; 17:299–305. PubMed PMC

Kaliraman V., Mullen J.R., Fricke W.M., Bastin-Shanower S.A., Brill S.J.. Functional overlap between Sgs1-Top3 and the Mms4-Mus81 endonuclease. Genes Dev. 2001; 15:2730–2740. PubMed PMC

Doe C.L., Osman F., Dixon J., Whitby M.C.. DNA repair by a Rad22-Mus81-dependent pathway that is independent of Rhp51. Nucleic Acids Res. 2004; 32:5570–5581. PubMed PMC

Fricke W.M., Bastin-Shanower S.A., Brill S.J.. Substrate specificity of the Saccharomyces cerevisiae Mus81-Mms4 endonuclease. DNA Repair (Amst.). 2005; 4:243–251. PubMed

Ehmsen K.T., Heyer W.-D.. Saccharomyces cerevisiae Mus81-Mms4 is a catalytic, DNA structure-selective endonuclease. Nucleic Acids Res. 2008; 36:2182–2195. PubMed PMC

Arnaudeau C., Lundin C., Helleday T.. DNA double-strand breaks associated with replication forks are predominantly repaired by homologous recombination involving an exchange mechanism in mammalian cells11Edited by J. Karn. J. Mol. Biol. 2001; 307:1235–1245. PubMed

Clouaire T., Rocher V., Lashgari A., Arnould C., Aguirrebengoa M., Biernacka A., Skrzypczak M., Aymard F., Fongang B., Dojer N.et al. .. Comprehensive mapping of histone modifications at DNA double-strand breaks deciphers repair pathway chromatin signatures. Mol. Cell. 2018; 72:250–262. PubMed PMC

Cohen A., Habib A., Laor D., Yadav S., Kupiec M., Weisman R.. TOR complex 2 in fission yeast is required for chromatin-mediated gene silencing and assembly of heterochromatic domains at subtelomeres. J. Biol. Chem. 2018; 293:8138–8150. PubMed PMC

Wold M.S. REPLICATION PROTEIN A:A heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 1997; 66:61–92. PubMed

Zhang H., Gan H., Wang Z., Lee J.-H., Zhou H., Ordog T., Wold M.S., Ljungman M., Zhang Z.. RPA interacts with HIRA and regulates H3.3 deposition at gene regulatory elements in mammalian cells. Mol. Cell. 2017; 65:272–284. PubMed PMC

Allshire R.C., Ekwall K.. Epigenetic regulation of chromatin states in Schizosaccharomyces pombe. Cold Spring Harb. Perspect. Biol. 2015; 7:a018770. PubMed PMC

Virtanen P., Gommers R., Oliphant T.E., Haberland M., Reddy T., Cournapeau D., Burovski E., Peterson P., Weckesser W., Bright J.et al. .. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods. 2020; 17:261–272. PubMed PMC