Modulating crossover positioning by introducing large structural changes in chromosomes

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• 作者：Antoine Ederveen (1)
  Yuching Lai (2) (3)
  Marc A van Driel (2) (4)
  Tom Gerats (1)
  Janny L Peters (1)
  
  1. Department of Molecular Plant Physiology ; Radboud University Nijmegen ; Institute for Water and Wetland Research (IWWR) ; Heyendaalseweg 135 ; 6525 AJ ; Nijmegen ; The Netherlands
  2. Netherlands Bioinformatics Centre ; 260 NBIC ; P.O. Box 9101 ; 6500 HB ; Nijmegen ; The Netherlands
  3. The Delft Bioinformatics Lab ; Department of Intelligent Systems ; Delft University of Technology ; Mekelweg 4 ; 2628 CD ; Delft ; The Netherlands
  4. Current affiliation ; Philips Research ; High Tech Campus 11 ; 5656 AE ; Eindhoven ; The Netherlands
  
• 关键词：Arabidopsis thaliana ; Meiosis ; Crossover positioning ; Recombination frequency ; Chromosome modifications ; Deletion ; Inversion ; Gamma ; irradiation
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：1,064 KB
• 参考文献：1. Osman, K, Higgins, JD, Sanchez-Moran, E, Armstrong, SJ, Franklin, FCH (2011) Pathways to meiotic recombination in Arabidopsis thaliana. New Phytol 190: pp. 523-44 2011.03665.x" target="_blank" title="It opens in new window">CrossRef
  2. Edlinger, B, Sch枚gelhofer, P (2011) Have a break: determinants of meiotic DNA double strand break (DSB) formation and processing in plants. J Exp Bot 62: pp. 1545-63 21" target="_blank" title="It opens in new window">CrossRef
  3. Drouaud, J, Mercier, R, Chelysheva, L, B茅rard, A, Falque, M, Martin, O (2007) Sex-specific crossover distribution and variations in interference level along Arabidopsis thaliana chromosome 4. PLoS Genet 3: pp. e106 CrossRef
  4. Gireaut, L, Falque, M, Drouaud, J, Pereira, L, Martin, OC, M茅zard, C (2011) Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet 7: pp. e1002354 2354" target="_blank" title="It opens in new window">CrossRef
  5. Bita, CE, Zenoni, S, Vriezen, WH, Mariani, C, Pezzotti, M, Gerats, T (2011) Temperature stress differentially modulates transcription in meiotic anthers of heat-tolerant and heat-sensitive tomato plants. BMC Genomics 12: pp. 384 2164-12-384" target="_blank" title="It opens in new window">CrossRef
  6. Kovalchuk, O, Titov, V, Hohn, B, Kovalchuk, I (2001) A sensitive transgenic plant system to detect toxic inorganic compounds in the environment. Nat Biotechnol 19: pp. 568-72 27" target="_blank" title="It opens in new window">CrossRef
  7. Schuermann, D, Molinier, J, Fritsch, O, Hohn, B (2005) The dual nature of homologous recombination in plants. Trends Genet 21: pp. 171-81 2005.01.002" target="_blank" title="It opens in new window">CrossRef
  8. Keeney, S, Giroux, CN, Kleckner, N (1997) Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 88: pp. 375-84 2-8674(00)81876-0" target="_blank" title="It opens in new window">CrossRef
  9. Cornu, A, Farcy, E, Mousset, C (1989) A genetic basis for variations in meiotic recombination in Petunia hybrida. Genome 32: pp. 46-53 CrossRef
  10. Crismani, W, Girard, C, Froger, N, Padrillo, M, Santos, JL, Chelysheva, L (2012) FANCM limits meiotic crossovers. Science 336: pp. 1588-90 26/science.1220381" target="_blank" title="It opens in new window">CrossRef
  11. Choi, K, Zhao, X, Kelly, KA, Venn, O, Higgins, JD, Yelina, NE (2013) Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters. Nat Genet 45: pp. 1327-36 2766" target="_blank" title="It opens in new window">CrossRef
  12. Brick, K, Smagulova, F, Khil, P, Camerini-Otero, DR, Petukhova, CV (2012) Genetic recombination is directed away from functional genomic elements in mice. Nature 485: pp. 642-5 CrossRef
  13. Kaback, DB, Guacci, V, Barber, D, Mahon, JW (1992) Chromosome size-dependent control of meiotic recombination. Science 256: pp. 228-35 26/science.1566070" target="_blank" title="It opens in new window">CrossRef
  14. Kaback, DB, Barber, D, Mahon, J, Lamb, J, You, J (1999) Chromosome size-dependent control of meiotic reciprocal recombination in Saccharomyces cerevisiae: the role of crossover interference. Genetics 152: pp. 1475-86
  15. Gerats, AGM, Vlaming, P, Maizonnier, D (1984) Recombination behaviour and gene transfer in Petunia hybrida after pollen irradiation. Mol Gen Genet 198: pp. 57-61 28701" target="_blank" title="It opens in new window">CrossRef
  16. Wijnker, E, Jong, H (2007) Managing meiotic recombination in plant breeding. Trends Plant Sci 13: pp. 640-6 2008.09.004" target="_blank" title="It opens in new window">CrossRef
  17. Vizir, IY, Anderson, ML, Wilson, ZA, Mulligan, BJ (1994) Isolation of deficiencies in the Arabidopsis genome by 纬-irradiation of pollen. Genetics 137: pp. 1111-9
  18. Britt, AB (1999) Molecular genetics of plant DNA repair in higher organisms. Trends Plant Sci 4: pp. 20-5 CrossRef
  19. Naito, K, Kusaba, M, Shikazono, N, Takano, T, Tanaka, A, Tanisaka, T (2005) Transmissible and nontransmissible mutations induced by irradiating arabidopsis thaliana pollen with 纬-rays and carbon ions. Genetics 169: pp. 881-9 CrossRef
  20. Britt, A (1996) DNA damage and repair in plants. Annu Rev Plant Physiol Plant Mol Biol 47: pp. 75-100 CrossRef
  21. Wallace, DC (1992) Mitochondrial genetics: a paradigm for aging and degenerative diseases. Science 256: pp. 628-32 26/science.1533953" target="_blank" title="It opens in new window">CrossRef
  22. Paques, F, Haber, JE (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol and Mol Boil Rev 63: pp. 349-404
  23. Gorbunova, V, Levy, AA (1999) How plants make ends meet: DNA double-strand break repair. Trends Plant Sci 4: pp. 263-9 2" target="_blank" title="It opens in new window">CrossRef
  24. Cornu, A, Maizonnier, D (1979) Enhanced non-disjunction and recombination as consequences of 纬-induced deficiencies in Petunia hybrida. Mut Res 61: pp. 57-63 27-5107(79)90006-X" target="_blank" title="It opens in new window">CrossRef
  25. Yang, C, Mulligan, BJ, Wilson, ZA (2004) Molecular genetic analysis of pollen irradiation mutagenesis in Arabidopsis. New Phytol 164: pp. 279-88 2004.01182.x" target="_blank" title="It opens in new window">CrossRef
  26. Honys, D, Twell, D (2003) Comparative analysis of the Arabidopsis pollen transcriptome. Plant Physiol 132: pp. 640-52 20925" target="_blank" title="It opens in new window">CrossRef
  27. Chaudhury, AM, Koltunow, A, Payne, T, Luo, M, Tucker, MR, Dennis, ES (2001) Control of early seed development. Annu Rev Cell Dev Biol 17: pp. 677-99 CrossRef
  28. Haecker, A, Gross-Hardt, R, Geiges, B, Sarkar, A, Breuninger, H, Herrmann, M (2004) Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development 131: pp. 657-68 242/dev.00963" target="_blank" title="It opens in new window">CrossRef
  29. Hardtke, CS, Berleth, T (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 17: pp. 1405-11 CrossRef
  30. Basu-Roy, S, Gauthier, F, Gireaut, L, M茅zard, C, Falcke, M, Martin, OC (2013) Hot regions of noninterfering crossovers coexist with a nonuniformly interfering pathway in Arabidopsis thaliana. Genetics 195: pp. 769-79 CrossRef
  31. Fransz, PF, Armstrong, SJ, Jong, H, Parnell, LD, Drunen, C, Dean, C (2000) Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100: pp. 367-76 2-8674(00)80672-8" target="_blank" title="It opens in new window">CrossRef
  32. Kleckner, N, Zickler, D, Jones, GH, Dekker, J, Padmore, R, Henle, J (2004) A mechanical basis for chromosome function. Proc Natl Acad Sci 101: pp. 12592-7 2724101" target="_blank" title="It opens in new window">CrossRef
  33. Truong, HT, Ramos, AM, Yalcin, F, Ruiter, M, Poel, HJA, Huvenaars, KHJ (2012) Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations. PLoS One 7: pp. e37565 CrossRef
  34. Gan, X, Stegle, O, Behr, J, Steffen, JG, Drewe, P, Hildebrand, KL (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: pp. 419-23 CrossRef
  35. Ziolkowski PA, Koczyk G, Galganski L, Sadowski J. Genome sequence comparison of Col and L / er lines reveals the dynamic nature of / Arabidopsis chromosomes. Nucleic acids research / . 2009:1鈥?3. doi:10.1093/nar/gkp183
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Crossing over assures the correct segregation of the homologous chromosomes to both poles of the dividing meiocyte. This exchange of DNA creates new allelic combinations thus increasing the genetic variation present in offspring. Crossovers are not uniformly distributed along chromosomes; rather there are preferred locations where they may take place. The positioning of crossovers is known to be influenced by both exogenous and endogenous factors as well as structural features inherent to the chromosome itself. We have introduced large structural changes into Arabidopsis chromosomes and report their effects on crossover positioning. Results The introduction of large deletions and putative inversions silenced recombination over the length of the structural change. In the majority of cases analyzed, the total recombination frequency over the chromosomes was unchanged. The loss of crossovers at the sites of structural change was compensated for by increases in recombination frequencies elsewhere on the chromosomes, mostly in single intervals of one to three megabases in size. Interestingly, two independent cases of induced structural changes in the same chromosomal interval were found on both chromosomes 1 and 2. In both cases, compensatory increases in recombination frequencies were of similar strength and took place in the same chromosome region. In contrast, deletions in chromosome arms carrying the nucleolar organizing region did not change recombination frequencies in the remainder of those chromosomes. Conclusions When taken together, these observations show that changes in the physical structure of the chromosome can have large effects on the positioning of COs within that chromosome. Moreover, different reactions to induced structural changes are observed between and within chromosomes. However, the similarity in reaction observed when looking at chromosomes carrying similar changes suggests a direct causal relation between induced change and observed reaction.