#PAGE_PARAMS# #ADS_HEAD_SCRIPTS# #MICRODATA#

Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots


During formation of sperm and eggs chromosomes exchange DNA in a process known as recombination, creating new combinations responsible for much of the enormous diversity in populations. In some mammals, including humans, the locations of recombination are chosen by a DNA-binding protein named PRDM9. Importantly, there are tens to hundreds of different variations of the Prdm9 gene (termed alleles), many of which are predicted to bind a unique DNA sequence. This high frequency of variation results in many individuals having two different copies of Prdm9, and several lines of evidence indicate that alleles compete to initiate recombination. In seeking to understand the mechanism of this competition we found that Prdm9 activity is sensitive to the number of gene copies present, suggesting that availability of this protein is a limiting factor during recombination. Moreover, we found that variant forms of PRDM9 protein can physically interact suggesting that when this happens one variant can influence which hotspots will become activated. Genetic crosses in mice support these observations; the presence of a dominant Prdm9 allele can completely suppress recombination at some locations. We conclude that allele-dominance of PRDM9 is a consequence of protein-protein interaction and competition for DNA binding in a limited pool of molecules, thus shaping the recombination landscape in natural populations.


Vyšlo v časopise: Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots. PLoS Genet 11(9): e32767. doi:10.1371/journal.pgen.1005512
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005512

Souhrn

During formation of sperm and eggs chromosomes exchange DNA in a process known as recombination, creating new combinations responsible for much of the enormous diversity in populations. In some mammals, including humans, the locations of recombination are chosen by a DNA-binding protein named PRDM9. Importantly, there are tens to hundreds of different variations of the Prdm9 gene (termed alleles), many of which are predicted to bind a unique DNA sequence. This high frequency of variation results in many individuals having two different copies of Prdm9, and several lines of evidence indicate that alleles compete to initiate recombination. In seeking to understand the mechanism of this competition we found that Prdm9 activity is sensitive to the number of gene copies present, suggesting that availability of this protein is a limiting factor during recombination. Moreover, we found that variant forms of PRDM9 protein can physically interact suggesting that when this happens one variant can influence which hotspots will become activated. Genetic crosses in mice support these observations; the presence of a dominant Prdm9 allele can completely suppress recombination at some locations. We conclude that allele-dominance of PRDM9 is a consequence of protein-protein interaction and competition for DNA binding in a limited pool of molecules, thus shaping the recombination landscape in natural populations.


Zdroje

1. Baudat F, Imai Y, de Massy B (2013) Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 14: 794–806. doi: 10.1038/nrg3573 24136506

2. Paigen K, Petkov P (2010) Mammalian recombination hot spots: properties, control and evolution. Nat Rev Genet 11: 221–233. doi: 10.1038/nrg2712 20168297

3. Axelsson E, Webster MT, Ratnakumar A, Ponting CP, Lindblad-Toh K (2012) Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Res 22: 51–63. doi: 10.1101/gr.124123.111 22006216

4. Munoz-Fuentes V, Di Rienzo A, Vila C (2011) Prdm9, a major determinant of meiotic recombination hotspots, is not functional in dogs and their wild relatives, wolves and coyotes. PLoS One 6: e25498. doi: 10.1371/journal.pone.0025498 22102853

5. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836–840. doi: 10.1126/science.1183439 20044539

6. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, et al. (2010) Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327: 876–879. doi: 10.1126/science.1182363 20044541

7. Parvanov ED, Petkov PM, Paigen K (2010) Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835. doi: 10.1126/science.1181495 20044538

8. Buard J, Barthes P, Grey C, de Massy B (2009) Distinct histone modifications define initiation and repair of meiotic recombination in the mouse. EMBO J 28: 2616–2624. doi: 10.1038/emboj.2009.207 19644444

9. Baker CL, Kajita S, Walker M, Petkov PM, Paigen K (2014) PRDM9 binding organizes hotspot nucleosomes and limits Holliday junction migration. Genome Res 24: 724–732. doi: 10.1101/gr.170167.113 24604780

10. Brick K, Smagulova F, Khil P, Camerini-Otero RD, Petukhova GV (2012) Genetic recombination is directed away from functional genomic elements in mice. Nature 485: 642–645. doi: 10.1038/nature11089 22660327

11. Smagulova F, Gregoretti IV, Brick K, Khil P, Camerini-Otero RD, et al. (2011) Genome-wide analysis reveals novel molecular features of mouse recombination hotspots. Nature 472: 375–378. doi: 10.1038/nature09869 21460839

12. Keeney S (2008) Spo11 and the Formation of DNA Double-Strand Breaks in Meiosis. Genome dynamics and stability 2: 81–123. 21927624

13. Hayashi K, Yoshida K, Matsui Y (2005) A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. Nature 438: 374–378. 16292313

14. Irie S, Tsujimura A, Miyagawa Y, Ueda T, Matsuoka Y, et al. (2009) Single-nucleotide polymorphisms of the PRDM9 (MEISETZ) gene in patients with nonobstructive azoospermia. J Androl 30: 426–431. doi: 10.2164/jandrol.108.006262 19168450

15. Miyamoto T, Koh E, Sakugawa N, Sato H, Hayashi H, et al. (2008) Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest. J Assist Reprod Genet 25: 553–557. doi: 10.1007/s10815-008-9270-x 18941885

16. Mihola O, Trachtulec Z, Vlcek C, Schimenti JC, Forejt J (2009) A mouse speciation gene encodes a meiotic histone H3 methyltransferase. Science 323: 373–375. doi: 10.1126/science.1163601 19074312

17. Berg IL, Neumann R, Lam KW, Sarbajna S, Odenthal-Hesse L, et al. (2010) PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans. Nat Genet 42: 859–863. doi: 10.1038/ng.658 20818382

18. Berg IL, Neumann R, Sarbajna S, Odenthal-Hesse L, Butler NJ, et al. (2011) Variants of the protein PRDM9 differentially regulate a set of human meiotic recombination hotspots highly active in African populations. Proc Natl Acad Sci U S A 108: 12378–12383. doi: 10.1073/pnas.1109531108 21750151

19. Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, et al. (2011) The landscape of recombination in African Americans. Nature 476: 170–175. doi: 10.1038/nature10336 21775986

20. Grey C, Barthes P, Chauveau-Le Friec G, Langa F, Baudat F, et al. (2011) Mouse PRDM9 DNA-binding specificity determines sites of histone H3 lysine 4 trimethylation for initiation of meiotic recombination. PLoS Biol 9: e1001176. doi: 10.1371/journal.pbio.1001176 22028627

21. Groeneveld LF, Atencia R, Garriga RM, Vigilant L (2012) High diversity at PRDM9 in chimpanzees and bonobos. PLoS One 7: e39064. doi: 10.1371/journal.pone.0039064 22768294

22. Auton A, Fledel-Alon A, Pfeifer S, Venn O, Segurel L, et al. (2012) A fine-scale chimpanzee genetic map from population sequencing. Science 336: 193–198. doi: 10.1126/science.1216872 22422862

23. Schwartz JJ, Roach DJ, Thomas JH, Shendure J (2014) Primate evolution of the recombination regulator PRDM9. Nat Commun 5: 4370. doi: 10.1038/ncomms5370 25001002

24. Sandor C, Li W, Coppieters W, Druet T, Charlier C, et al. (2012) Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle. PLoS Genet 8: e1002854. doi: 10.1371/journal.pgen.1002854 22844258

25. Steiner CC, Ryder OA (2013) Characterization of Prdm9 in equids and sterility in mules. PLoS One 8: e61746. doi: 10.1371/journal.pone.0061746 23613924

26. Parvanov ED, Ng SH, Petkov PM, Paigen K (2009) Trans-regulation of mouse meiotic recombination hotspots by Rcr1. PLoS Biol 7: e36. doi: 10.1371/journal.pbio.1000036 19226189

27. Neumann R, Jeffreys AJ (2006) Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation. Hum Mol Genet 15: 1401–1411. 16543360

28. Pratto F, Brick K, Khil P, Smagulova F, Petukhova GV, et al. (2014) DNA recombination. Recombination initiation maps of individual human genomes. Science 346: 1256442. doi: 10.1126/science.1256442 25395542

29. Segurel L, Leffler EM, Przeworski M (2011) The case of the fickle fingers: how the PRDM9 zinc finger protein specifies meiotic recombination hotspots in humans. PLoS Biol 9: e1001211. doi: 10.1371/journal.pbio.1001211 22162947

30. Baker CL, Kajita S, Walker M, Saxl RL, Raghupathy N, et al. (2015) PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination. PLoS Genet 11: e1004916. doi: 10.1371/journal.pgen.1004916 25568937

31. Billings T, Parvanov ED, Baker CL, Walker M, Paigen K, et al. (2013) DNA binding specificities of the long zinc-finger recombination protein PRDM9. Genome Biol 14: R35. doi: 10.1186/gb-2013-14-4-r35 23618393

32. Hinch AG, Altemose N, Noor N, Donnelly P, Myers SR (2014) Recombination in the human Pseudoautosomal region PAR1. PLoS Genet 10: e1004503. doi: 10.1371/journal.pgen.1004503 25033397

33. Eram MS, Bustos SP, Lima-Fernandes E, Siarheyeva A, Senisterra G, et al. (2014) Trimethylation of histone H3 lysine 36 by human methyltransferase PRDM9 protein. J Biol Chem 289: 12177–12188. doi: 10.1074/jbc.M113.523183 24634223

34. Sun F, Fujiwara Y, Reinholdt LG, Hu J, Saxl RL, et al. (2015) Nuclear localization of PRDM9 and its role in meiotic chromatin modifications and homologous synapsis. Chromosoma.

35. Fairfield H, Gilbert GJ, Barter M, Corrigan RR, Curtain M, et al. (2011) Mutation discovery in mice by whole exome sequencing. Genome Biol 12: R86. doi: 10.1186/gb-2011-12-9-r86 21917142

36. Flachs P, Mihola O, Simecek P, Gregorova S, Schimenti JC, et al. (2012) Interallelic and intergenic incompatibilities of the Prdm9 (Hst1) gene in mouse hybrid sterility. PLoS Genet 8: e1003044. doi: 10.1371/journal.pgen.1003044 23133405

37. Weiss J, Hurley LA, Harris RM, Finlayson C, Tong M, et al. (2012) ENU mutagenesis in mice identifies candidate genes for hypogonadism. Mamm Genome 23: 346–355. doi: 10.1007/s00335-011-9388-5 22258617

38. Flachs P, Bhattacharyya T, Mihola O, Pialek J, Forejt J, et al. (2014) Prdm9 incompatibility controls oligospermia and delayed fertility but no selfish transmission in mouse intersubspecific hybrids. PLoS One 9: e95806. doi: 10.1371/journal.pone.0095806 24756080

39. Dzur-Gejdosova M, Simecek P, Gregorova S, Bhattacharyya T, Forejt J (2012) Dissecting the genetic architecture of F1 hybrid sterility in house mice. Evolution 66: 3321–3335. doi: 10.1111/j.1558-5646.2012.01684.x 23106700

40. Bhattacharyya T, Gregorova S, Mihola O, Anger M, Sebestova J, et al. (2013) Mechanistic basis of infertility of mouse intersubspecific hybrids. Proc Natl Acad Sci U S A 110: E468–477. doi: 10.1073/pnas.1219126110 23329330

41. Fog CK, Galli GG, Lund AH (2012) PRDM proteins: important players in differentiation and disease. Bioessays 34: 50–60. doi: 10.1002/bies.201100107 22028065

42. Hohenauer T, Moore AW (2012) The Prdm family: expanding roles in stem cells and development. Development 139: 2267–2282. doi: 10.1242/dev.070110 22669819

43. Huang S, Shao G, Liu L (1998) The PR domain of the Rb-binding zinc finger protein RIZ1 is a protein binding interface and is related to the SET domain functioning in chromatin-mediated gene expression. J Biol Chem 273: 15933–15939. 9632640

44. Davis CA, Haberland M, Arnold MA, Sutherland LB, McDonald OG, et al. (2006) PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. Molecular and cellular biology 26: 2626–2636. 16537907

45. Friedman JR, Fredericks WJ, Jensen DE, Speicher DW, Huang XP, et al. (1996) KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes & development 10: 2067–2078.

46. Urrutia R (2003) KRAB-containing zinc-finger repressor proteins. Genome Biol 4: 231. 14519192

47. Edelstein LC, Collins T (2005) The SCAN domain family of zinc finger transcription factors. Gene 359: 1–17. 16139965

48. Buard J, Rivals E, Dunoyer de Segonzac D, Garres C, Caminade P, et al. (2014) Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite. PLoS One 9: e85021. doi: 10.1371/journal.pone.0085021 24454780

49. Kono H, Tamura M, Osada N, Suzuki H, Abe K, et al. (2014) Prdm9 polymorphism unveils mouse evolutionary tracks. DNA Res 21: 315–326. doi: 10.1093/dnares/dst059 24449848

50. Shultz KL, Donahue LR, Bouxsein ML, Baylink DJ, Rosen CJ, et al. (2003) Congenic strains of mice for verification and genetic decomposition of quantitative trait loci for femoral bone mineral density. J Bone Miner Res 18: 175–185. 12568393

51. Anderson LK, Reeves A, Webb LM, Ashley T (1999) Distribution of crossing over on mouse synaptonemal complexes using immunofluorescent localization of MLH1 protein. Genetics 151: 1569–1579. 10101178

52. Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890. 12724300

53. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, et al. (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A 103: 10352–10357. 16801547

54. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. doi: 10.1093/bioinformatics/btp324 19451168

55. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137. doi: 10.1186/gb-2008-9-9-r137 18798982

56. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37: W202–208. doi: 10.1093/nar/gkp335 19458158

57. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, et al. (2012) Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481: 389–393. doi: 10.1038/nature10730 22217937

58. Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, et al. (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 39: e35. doi: 10.1093/nar/gkq1287 21177645

59. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841–842. doi: 10.1093/bioinformatics/btq033 20110278

Štítky
Genetika Reprodukčná medicína

Článok vyšiel v časopise

PLOS Genetics


2015 Číslo 9
Najčítanejšie tento týždeň
Najčítanejšie v tomto čísle
Kurzy

Zvýšte si kvalifikáciu online z pohodlia domova

Aktuální možnosti diagnostiky a léčby litiáz
nový kurz
Autori: MUDr. Tomáš Ürge, PhD.

Všetky kurzy
Prihlásenie
Zabudnuté heslo

Zadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.

Prihlásenie

Nemáte účet?  Registrujte sa

#ADS_BOTTOM_SCRIPTS#