Mapping of Meiotic Single-Stranded DNA Reveals Double-Strand-Break Hotspots near Centromeres and Telomeres

BACKGROUND Every chromosome requires at least one crossover to be faithfully segregated during meiosis. At least two levels of regulation govern crossover distribution: where the initiating DNA double-strand breaks (DSBs) occur and whether those DSBs are repaired as crossovers. RESULTS We mapped meiotic DSBs in budding yeast by identifying sites of DSB-associated single-stranded DNA (ssDNA) accumulation. These analyses revealed substantial DSB activity in pericentrometric regions, in which crossover formation is largely absent. Our data suggest that centromeric suppression of recombination occurs at the level of break repair rather than DSB formation. Additionally, we found an enrichment of DSBs within a approximately 100 kb region near the ends of all chromosomes. Introduction of new telomeres was sufficient for inducing large ectopic regions of increased DSB formation, thereby revealing a remarkable long-range effect of telomeres on DSB formation. The concentration of DSBs close to chromosome ends increases the relative DSB density on small chromosomes, providing an interference-independent mechanism that ensures that all chromosomes receive at least one crossover per homolog pair. CONCLUSIONS Together, our results indicate that selective DSB repair accounts for crossover suppression near centromeres and suggest a simple telomere-guided mechanism that ensures sufficient DSB activity on all chromosomes.

[1]  John A Birdsell,et al.  Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. , 2002, Molecular biology and evolution.

[2]  N. M. Hollingsworth,et al.  Does Chromosome Size Affect Map Distance and Genetic Interference in Budding Yeast? , 2004, Genetics.

[3]  E. Barillot,et al.  Genome-Wide Redistribution of Meiotic Double-Strand Breaks in Saccharomyces cerevisiae , 2006, Molecular and Cellular Biology.

[4]  T. Petes,et al.  Meiotic recombination hot spots and cold spots , 2001, Nature Reviews Genetics.

[5]  D. Gudbjartsson,et al.  A high-resolution recombination map of the human genome , 2002, Nature Genetics.

[6]  N. Kleckner,et al.  DMC1: A meiosis-specific yeast homolog of E. coli recA required for recombination, synaptonemal complex formation, and cell cycle progression , 1992, Cell.

[7]  O. Aparicio,et al.  Components and Dynamics of DNA Replication Complexes in S. cerevisiae: Redistribution of MCM Proteins and Cdc45p during S Phase , 1997, Cell.

[8]  G. Copenhaver,et al.  Does Crossover Interference Count in Saccharomyces cerevisiae? , 2004, Genetics.

[9]  S. Keeney,et al.  Modifying Histones and Initiating Meiotic Recombination New Answers to an Old Question , 2004, Cell.

[10]  P. Pukkila,et al.  Meiotic sister chromatid recombination. , 1995, Advances in genetics.

[11]  J. Huberman,et al.  The in vivo replication origin of the yeast 2 microns plasmid. , 1987, Cell.

[12]  Michael J. Buck,et al.  Global Analysis of the Relationship between the Binding of the Bas1p Transcription Factor and Meiosis-Specific Double-Strand DNA Breaks in Saccharomyces cerevisiae† , 2005 .

[13]  D. MacAlpine,et al.  The high mobility group protein Abf2p influences the level of yeast mitochondrial DNA recombination intermediates in vivo. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[14]  A. Nicolas,et al.  Association of Mre11p with double-strand break sites during yeast meiosis. , 2004, Molecular cell.

[15]  Xuewen Pan,et al.  Heterologous URA3MX cassettes for gene replacement in Saccharomyces cerevisiae , 1999, Yeast.

[16]  G. Roeder,et al.  Tam1, a telomere-associated meiotic protein, functions in chromosome synapsis and crossover interference. , 1997, Genes & development.

[17]  N. Kleckner,et al.  The Single-End Invasion An Asymmetric Intermediate at the Double-Strand Break to Double-Holliday Junction Transition of Meiotic Recombination , 2001, Cell.

[18]  G. Roeder,et al.  Crossover interference is abolished in the absence of a synaptonemal complex protein , 1994, Cell.

[19]  N. Kleckner,et al.  Crossover and noncrossover recombination during meiosis: timing and pathway relationships. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Botstein,et al.  Simple Mendelian inheritance of the reiterated ribosomal DNA of yeast. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Szostak,et al.  Extensive 3′-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site , 1991, Cell.

[22]  A. Nicolas,et al.  An atypical topoisomerase II from archaea with implications for meiotic recombination , 1997, Nature.

[23]  J. Lieb,et al.  Loss of a histone deacetylase dramatically alters the genomic distribution of Spo11p-catalyzed DNA breaks in Saccharomyces cerevisiae , 2007, Proceedings of the National Academy of Sciences.

[24]  N. Kleckner,et al.  Interhomolog Bias during Meiotic Recombination: Meiotic Functions Promote a Highly Differentiated Interhomolog-Only Pathway , 1997, Cell.

[25]  F. Klein,et al.  The control of Spo11's interaction with meiotic recombination hotspots. , 2005, Genes & development.

[26]  Harry Scherthan,et al.  A bouquet makes ends meet , 2001, Nature Reviews Molecular Cell Biology.

[27]  G. Roeder,et al.  Centromere-Proximal Crossovers Are Associated With Precocious Separation of Sister Chromatids During Meiosis in Saccharomyces cerevisiae , 2006, Genetics.

[28]  Megan F. Cole,et al.  Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.

[29]  T. Kitajima,et al.  Distinct Cohesin Complexes Organize Meiotic Chromosome Domains , 2003, Science.

[30]  T. Kodadek,et al.  DMC1 functions in a Saccharomyces cerevisiae meiotic pathway that is largely independent of the RAD51 pathway. , 1997, Genetics.

[31]  Sanjay K. Chhablani,et al.  Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. , 1993, Genes & development.

[32]  David Collingwood,et al.  Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication , 2006, Nature Cell Biology.

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

[34]  J. Haber,et al.  Meiotic and mitotic behavior of dicentric chromosomes in Saccharomyces cerevisiae. , 1984, Genetics.

[35]  M. Lichten,et al.  Direct coupling between meiotic DNA replication and recombination initiation. , 2000, Science.

[36]  D. Kaback,et al.  A function for subtelomeric DNA in Saccharomyces cerevisiae. , 2003, Genetics.

[37]  A. Amon,et al.  The FK506 Binding Protein Fpr3 Counteracts Protein Phosphatase 1 to Maintain Meiotic Recombination Checkpoint Activity , 2005, Cell.

[38]  D. Zickler,et al.  Early Decision Meiotic Crossover Interference prior to Stable Strand Exchange and Synapsis , 2004, Cell.

[39]  J. Huberman,et al.  The in vivo replication origin of the yeast 2μm plasmid , 1987, Cell.

[40]  N. Kleckner,et al.  Physical and Functional Interactions among Basic Chromosome Organizational Features Govern Early Steps of Meiotic Chiasma Formation , 2002, Cell.

[41]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[42]  Ronald W. Davis,et al.  The core meiotic transcriptome in budding yeasts , 2000, Nature Genetics.

[43]  M. Conrad,et al.  Ndj1p, a meiotic telomere protein required for normal chromosome synapsis and segregation in yeast. , 1997, Science.

[44]  T. Allers,et al.  Differential Timing and Control of Noncrossover and Crossover Recombination during Meiosis , 2001, Cell.

[45]  R. Mortimer,et al.  Recombination in yeast. , 1971, Annual review of genetics.

[46]  Harry Scherthan,et al.  Meiotic Telomere Protein Ndj1p Is Required for Meiosis-Specific Telomere Distribution, Bouquet Formation and Efficient Homologue Pairing , 2000, The Journal of cell biology.

[47]  Y. Kaneko,et al.  PCR-mediated repeated chromosome splitting in Saccharomyces cerevisiae. , 2005, BioTechniques.

[48]  G. Roeder,et al.  A yeast centromere acts in cis to inhibit meiotic gene conversion of adjacent sequences. , 1988, Cell.

[49]  V. Guacci,et al.  Chromosome size-dependent control of meiotic recombination. , 1992, Science.

[50]  T. Hassold,et al.  Effect of meiotic recombination on the production of aneuploid gametes in humans , 2005, Cytogenetic and Genome Research.

[51]  D. Kaback,et al.  Decreased meiotic reciprocal recombination in subtelomeric regions in Saccharomyces cerevisiae , 2000, Chromosoma.

[52]  S. Keeney,et al.  Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p. , 2000, Genes & development.

[53]  N. Kleckner,et al.  A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae , 1990, Cell.

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

[55]  G. Roeder,et al.  ZIP1 is a synaptonemal complex protein required for meiotic chromosome synapsis , 1993, Cell.

[56]  T. Petes,et al.  Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[57]  A. Nicolas,et al.  Clustering of meiotic double-strand breaks on yeast chromosome III. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[58]  R. Young,et al.  The core centromere and Sgo1 establish a 50-kb cohesin-protected domain around centromeres during meiosis I. , 2005, Genes & development.

[59]  G. Copenhaver,et al.  Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[60]  M. Lichten,et al.  Mapping Meiotic Single-Strand DNA Reveals a New Landscape of DNA Double-Strand Breaks in Saccharomyces cerevisiae , 2007, PLoS biology.

[61]  K. Nasmyth,et al.  Un Ménage à Quatre The Molecular Biology of Chromosome Segregation in Meiosis , 2003, Cell.

[62]  T. Petes,et al.  2 Meiotic Sister Chromatid Recombination , 1995 .

[63]  D. Zickler,et al.  From early homologue recognition to synaptonemal complex formation , 2006, Chromosoma.

[64]  G. Roeder,et al.  A yeast acts in (Cis) to inhibit meiotic gene conversion of adjacent sequences , 1988, Cell.

[65]  N. Kleckner,et al.  Crossover/Noncrossover Differentiation, Synaptonemal Complex Formation, and Regulatory Surveillance at the Leptotene/Zygotene Transition of Meiosis , 2004, Cell.

[66]  A. Goldman,et al.  Meiotic recombination hotspots. , 1995, Annual review of genetics.