Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions

Meiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleotides. DSB hotspots occurred in gene promoters, terminators and introns, driven by AT-sequence richness, which excludes nucleosomes and allows SPO11-1 access. A strong positive relationship was observed between SPO11-1 DSBs and final crossover levels. Euchromatic marks promote recombination in fungi and mammals, and consistently we observe H3K4me3 enrichment in proximity to DSB hotspots at gene 5’-ends. Repetitive transposons are thought to be recombination-silenced during meiosis, in order to prevent non-allelic interactions and genome instability. Unexpectedly, we found strong DSB hotspots in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. Hotspot transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination-enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin on the DSB landscape. Epigenetic activation of transposon meiotic DSBs occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription and H3K4me3. Increased met1 SPO11-1 DSBs occurred most strongly within centromeres and Gypsy and CACTA/EnSpm coldspot transposons. Together, our work reveals complex interactions between chromatin and meiotic DSBs within genes and transposons, with significance for the diversity and evolution of plant genomes.

[1]  M. J. Neale,et al.  Bidirectional resection of DNA double-strand breaks by Mre11 and Exo1 , 2011, Nature.

[2]  A. Tóth,et al.  The PRDM9 KRAB domain is required for meiosis and involved in protein interactions , 2017, Chromosoma.

[3]  M. Gut,et al.  In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites. , 2017, Genome research.

[4]  Julian Lange,et al.  The Landscape of Mouse Meiotic Double-Strand Break Formation, Processing, and Repair , 2016, Cell.

[5]  Stefan R. Henz,et al.  Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions , 2016, Cell.

[6]  Karsten M. Borgwardt,et al.  1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana , 2016, Cell.

[7]  Thomas J. Hardcastle,et al.  Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes , 2016, PLoS genetics.

[8]  G. Mayhew,et al.  The Arabidopsis thaliana mobilome and its impact at the species level , 2016, eLife.

[9]  C. L. Baker,et al.  The Meiotic Recombination Activator PRDM9 Trimethylates Both H3K36 and H3K4 at Recombination Hotspots In Vivo , 2016, PLoS genetics.

[10]  F. Thibaud-Nissen,et al.  Araport11: a complete reannotation of the Arabidopsis thaliana reference genome , 2016, bioRxiv.

[11]  L. Chelysheva,et al.  A DNA topoisomerase VI–like complex initiates meiotic recombination , 2016, Science.

[12]  C. Brun,et al.  The TopoVIB-Like protein family is required for meiotic DNA double-strand break formation , 2016, Science.

[13]  Yuliya V. Karpievitch,et al.  Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation , 2016, bioRxiv.

[14]  M. J. Neale,et al.  Meiotic DSB patterning: A multifaceted process , 2016, Cell cycle.

[15]  S. Keeney,et al.  The kinetochore prevents centromere-proximal crossover recombination during meiosis , 2015, eLife.

[16]  S. Keeney,et al.  Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast , 2015, Science.

[17]  Thomas J. Hardcastle,et al.  DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis , 2015, Genes & development.

[18]  N. Barkai,et al.  DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis[OPEN] , 2015, Plant Cell.

[19]  Gil McVean,et al.  Stable recombination hotspots in birds , 2015, Science.

[20]  I. Henderson,et al.  Meiotic recombination hotspots - a comparative view. , 2015, The Plant journal : for cell and molecular biology.

[21]  N. Servant,et al.  DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination , 2015, Genes & development.

[22]  A. Nicolas,et al.  Initiation of meiotic homologous recombination: flexibility, impact of histone modifications, and chromatin remodeling. , 2015, Cold Spring Harbor perspectives in biology.

[23]  Krystyna A. Kelly,et al.  Juxtaposition of heterozygous and homozygous regions causes reciprocal crossover remodelling via interference during Arabidopsis meiosis , 2015, eLife.

[24]  D. Weigel,et al.  Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping , 2015, G3: Genes, Genomes, Genetics.

[25]  K. Bloom.  Centromeric heterochromatin: the primordial segregation machine. , 2014, Annual review of genetics.

[26]  Hadi Quesneville,et al.  Structural and functional partitioning of bread wheat chromosome 3B , 2014, Science.

[27]  Mariko Sasaki,et al.  Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome , 2014, Genome research.

[28]  C. L. Baker,et al.  PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration , 2014, Genome research.

[29]  B. Massy.  Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. , 2013 .

[30]  S. Wessler,et al.  Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing , 2013, Proceedings of the National Academy of Sciences.

[31]  D. Weigel,et al.  The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana , 2013, eLife.

[32]  I. Henderson,et al.  Contrasted Patterns of Crossover and Non-crossover at Arabidopsis thaliana Meiotic Recombination Hotspots , 2013, PLoS genetics.

[33]  F. Baudat,et al.  Meiotic recombination in mammals: localization and regulation , 2013, Nature Reviews Genetics.

[34]  Krystyna A. Kelly,et al.  High-throughput analysis of meiotic crossover frequency and interference via flow cytometry of fluorescent pollen in Arabidopsis thaliana , 2013, Nature Protocols.

[35]  Scott Keeney,et al.  Meiotic Recombination Initiation in and around Retrotransposable Elements in Saccharomyces cerevisiae , 2013, PLoS genetics.

[36]  S. Jacobsen,et al.  Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome , 2013, Cell.

[37]  A. Nicolas,et al.  The COMPASS Subunit Spp1 Links Histone Methylation to Initiation of Meiotic Recombination , 2013, Science.

[38]  V. Borde,et al.  Spp1, a member of the Set1 Complex, promotes meiotic DSB formation in promoters by tethering histone H3K4 methylation sites to chromosome axes. , 2013, Molecular cell.

[39]  S. Keeney,et al.  Scale matters , 2012, Cell cycle.

[40]  Kevin Brick,et al.  Genetic recombination is directed away from functional genomic elements in mice , 2012, Nature.

[41]  A. Auton,et al.  Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel , 2011, Nature Genetics.

[42]  N. Warthmann,et al.  The recombination landscape in Arabidopsis thaliana F2 populations , 2011, Heredity.

[43]  O. Martin,et al.  Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes , 2011, PLoS genetics.

[44]  C. Grey,et al.  Mouse PRDM9 DNA-Binding Specificity Determines Sites of Histone H3 Lysine 4 Trimethylation for Initiation of Meiotic Recombination , 2011, PLoS biology.

[45]  Xuan Zhu,et al.  A Hierarchical Combination of Factors Shapes the Genome-wide Topography of Yeast Meiotic Recombination Initiation , 2011, Cell.

[46]  A. Gylfason,et al.  Fine-scale recombination rate differences between sexes, populations and individuals , 2010, Nature.

[47]  Mariko Sasaki,et al.  Genome destabilization by homologous recombination in the germ line , 2010, Nature Reviews Molecular Cell Biology.

[48]  G. Presting,et al.  Widespread Gene Conversion in Centromere Cores , 2010, PLoS biology.

[49]  K. Paigen,et al.  Prdm9 Controls Activation of Mammalian Recombination Hotspots , 2010, Science.

[50]  P. Donnelly,et al.  Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination , 2010, Science.

[51]  G. Coop,et al.  PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice , 2010, Science.

[52]  Sanzhen Liu,et al.  Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome , 2009, PLoS genetics.

[53]  S. Henikoff,et al.  Major Evolutionary Transitions in Centromere Complexity , 2009, Cell.

[54]  M. Pellegrini,et al.  Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana , 2009, Genome Biology.

[55]  E. Segal,et al.  Poly(da:dt) Tracts: Major Determinants of Nucleosome Organization This Review Comes from a Themed Issue on Protein-nucleic Acid Interactions Edited , 2022 .

[56]  Alain Nicolas,et al.  Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites , 2009, The EMBO journal.

[57]  Cestmir Vlcek,et al.  A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase , 2009, Science.

[58]  M. Belfort,et al.  The take and give between retrotransposable elements and their hosts. , 2008, Annual review of genetics.

[59]  Céline Loot,et al.  Different Strategies to Persist: The pogo-Like Lemi1 Transposon Produces Miniature Inverted-Repeat Transposable Elements or Typical Defective Elements in Different Plant Genomes , 2008, Genetics.

[60]  Peter Donnelly,et al.  A common sequence motif associated with recombination hot spots and genome instability in humans , 2008, Nature Genetics.

[61]  E. Holub,et al.  WRR4 encodes a TIR-NB-LRR protein that confers broad-spectrum white rust resistance in Arabidopsis thaliana to four physiological races of Albugo candida. , 2008, Molecular plant-microbe interactions : MPMI.

[62]  H. Quesneville,et al.  Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. , 2008, Genomics.

[63]  C. Feschotte,et al.  DNA transposons and the evolution of eukaryotic genomes. , 2007, Annual review of genetics.

[64]  H. Puchta,et al.  The Catalytically Active Tyrosine Residues of Both SPO11-1 and SPO11-2 Are Required for Meiotic Double-Strand Break Induction in Arabidopsis , 2007, The Plant Cell Online.

[65]  O. Mathieu,et al.  Transgenerational Stability of the Arabidopsis Epigenome Is Coordinated by CG Methylation , 2007, Cell.

[66]  E. Sanchez-Moran,et al.  ASY1 mediates AtDMC1-dependent interhomolog recombination during meiosis in Arabidopsis. , 2007, Genes & development.

[67]  R. Martienssen,et al.  Transposable elements and the epigenetic regulation of the genome , 2007, Nature Reviews Genetics.

[68]  Jonathan D. G. Jones,et al.  The plant immune system , 2006, Nature.

[69]  P. Donnelly,et al.  A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome , 2005, Science.

[70]  M. J. Neale,et al.  Endonucleolytic processing of covalent protein-linked DNA double-strand breaks , 2005, Nature.

[71]  K. Silverstein,et al.  Genome Organization of More Than 300 Defensin-Like Genes in Arabidopsis1[w] , 2005, Plant Physiology.

[72]  P. Schnable,et al.  MuDR Transposase Increases the Frequency of Meiotic Crossovers in the Vicinity of a Mu Insertion in the Maize a1 Gene , 2005, Genetics.

[73]  S. Keeney,et al.  Where the crossovers are: recombination distributions in mammals , 2004, Nature Reviews Genetics.

[74]  J. Paszkowski,et al.  Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis , 2003, Nature Genetics.

[75]  S. Jacobsen,et al.  Role of CG and Non-CG Methylation in Immobilization of Transposons in Arabidopsis , 2003, Current Biology.

[76]  J. Jeddeloh,et al.  Arabidopsis MET1 cytosine methyltransferase mutants. , 2003, Genetics.

[77]  F. Franklin,et al.  Asy1, a protein required for meiotic chromosome synapsis, localizes to axis-associated chromatin in Arabidopsis and Brassica , 2002, Journal of Cell Science.

[78]  Jonathan D. G. Jones,et al.  Arabidopsis RPP4 is a member of the RPP5 multigene family of TIR-NB-LRR genes and confers downy mildew resistance through multiple signalling components. , 2002, The Plant journal : for cell and molecular biology.

[79]  H. Fu,et al.  Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[80]  J. Jurka,et al.  Rolling-circle transposons in eukaryotes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[81]  M. Grelon,et al.  AtSPO11‐1 is necessary for efficient meiotic recombination in plants , 2001, The EMBO journal.

[82]  C. Feschotte,et al.  Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. , 2000, Molecular biology and evolution.

[83]  M. Marra,et al.  Genetic definition and sequence analysis of Arabidopsis centromeres. , 1999, Science.

[84]  B. Charlesworth,et al.  Why sex and recombination? , 1998, Science.

[85]  G. Chu.  Double Strand Break Repair* , 1997, The Journal of Biological Chemistry.

[86]  S. Keeney,et al.  Meiosis-Specific DNA Double-Strand Breaks Are Catalyzed by Spo11, a Member of a Widely Conserved Protein Family , 1997, Cell.

[87]  T. Petes,et al.  Relationship between nuclease-hypersensitive sites and meiotic recombination hot spot activity at the HIS4 locus of Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[88]  S. Keeney,et al.  Covalent protein-DNA complexes at the 5' strand termini of meiosis-specific double-strand breaks in yeast. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[89]  M Lichten,et al.  Meiosis-induced double-strand break sites determined by yeast chromatin structure. , 1994, Science.

[90]  A. Nicolas,et al.  An initiation site for meiotic gene conversion in the yeast Saccharomyces cerevisiae , 1989, Nature.

[91]  Jack W. Szostak,et al.  The double-strand-break repair model for recombination , 1983, Cell.

[92]  S. Keeney,et al.  Mechanism and regulation of meiotic recombination initiation. , 2014, Cold Spring Harbor perspectives in biology.

[93]  B. de Massy.  Initiation of meiotic recombination: how and where? Conservation and specificities among eukaryotes. , 2013, Annual review of genetics.

[94]  Gustavo Glusman,et al.  Genome Organization , 2009, Encyclopedia of Complexity and Systems Science.

[95]  M. J. Neale,et al.  End-labeling and analysis of Spo11-oligonucleotide complexes in Saccharomyces cerevisiae. , 2009, Methods in molecular biology.

[96]  Luke E. Berchowitz,et al.  Fluorescent Arabidopsis tetrads: a visual assay for quickly developing large crossover and crossover interference data sets , 2007, Nature Protocols.

[97]  B. Mcclintock,et al.  Controlling elements and the gene. , 1956, Cold Spring Harbor symposia on quantitative biology.

[98]  Thomas J. Hardcastle,et al.  Nature Genetics Advance Online Publication Arabidopsis Meiotic Crossover Hot Spots Overlap with H2a.z Nucleosomes at Gene Promoters , 2022 .