-
Články
- Časopisy
- Kurzy
- Témy
- Kongresy
- Videa
- Podcasty
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.1005512Souhrn
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
Článek The Chromatin Protein DUET/MMD1 Controls Expression of the Meiotic Gene during Male Meiosis inČlánek Tissue-Specific Gain of RTK Signalling Uncovers Selective Cell Vulnerability during Embryogenesis
Článok vyšiel v časopisePLOS Genetics
Najčítanejšie tento týždeň
2015 Číslo 9- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
-
Všetky články tohto čísla
- Retraction: RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells
- Signaling from Within: Endocytic Trafficking of the Robo Receptor Is Required for Midline Axon Repulsion
- A Splice Region Variant in Lowers Non-high Density Lipoprotein Cholesterol and Protects against Coronary Artery Disease
- The Chromatin Protein DUET/MMD1 Controls Expression of the Meiotic Gene during Male Meiosis in
- A NIMA-Related Kinase Suppresses the Flagellar Instability Associated with the Loss of Multiple Axonemal Structures
- Slit-Dependent Endocytic Trafficking of the Robo Receptor Is Required for Son of Sevenless Recruitment and Midline Axon Repulsion
- Expression of Concern: Protein Under-Wrapping Causes Dosage Sensitivity and Decreases Gene Duplicability
- Mutagenesis by AID: Being in the Right Place at the Right Time
- Identification of as a Genetic Modifier That Regulates the Global Orientation of Mammalian Hair Follicles
- Bridges Meristem and Organ Primordia Boundaries through , , and during Flower Development in
- Evaluating the Performance of Fine-Mapping Strategies at Common Variant GWAS Loci
- KLK5 Inactivation Reverses Cutaneous Hallmarks of Netherton Syndrome
- Differential Expression of Ecdysone Receptor Leads to Variation in Phenotypic Plasticity across Serial Homologs
- Receptor Polymorphism and Genomic Structure Interact to Shape Bitter Taste Perception
- Cognitive Function Related to the Gene Acquired from an LTR Retrotransposon in Eutherians
- Critical Function of γH2A in S-Phase
- Arabidopsis AtPLC2 Is a Primary Phosphoinositide-Specific Phospholipase C in Phosphoinositide Metabolism and the Endoplasmic Reticulum Stress Response
- XBP1-Independent UPR Pathways Suppress C/EBP-β Mediated Chondrocyte Differentiation in ER-Stress Related Skeletal Disease
- Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood
- A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism
- Cell Cycle Regulates Nuclear Stability of AID and Determines the Cellular Response to AID
- A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in
- Tissue-Specific Gain of RTK Signalling Uncovers Selective Cell Vulnerability during Embryogenesis
- RAB-10-Dependent Membrane Transport Is Required for Dendrite Arborization
- Basolateral Endocytic Recycling Requires RAB-10 and AMPH-1 Mediated Recruitment of RAB-5 GAP TBC-2 to Endosomes
- Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes
- ARID1A Is Essential for Endometrial Function during Early Pregnancy
- Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele
- An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in
- Photoreceptor Specificity in the Light-Induced and COP1-Mediated Rapid Degradation of the Repressor of Photomorphogenesis SPA2 in Arabidopsis
- Autophosphorylation of the Bacterial Tyrosine-Kinase CpsD Connects Capsule Synthesis with the Cell Cycle in
- Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots
- Rescheduling Behavioral Subunits of a Fixed Action Pattern by Genetic Manipulation of Peptidergic Signaling
- A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary
- Cell-Autonomous Gβ Signaling Defines Neuron-Specific Steady State Serotonin Synthesis in
- Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests
- The RCC1 Family Protein TCF1 Regulates Freezing Tolerance and Cold Acclimation through Modulating Lignin Biosynthesis
- The AMPK, Snf1, Negatively Regulates the Hog1 MAPK Pathway in ER Stress Response
- The Parkinson’s Disease-Associated Protein Kinase LRRK2 Modulates Notch Signaling through the Endosomal Pathway
- Multicopy Single-Stranded DNA Directs Intestinal Colonization of Enteric Pathogens
- Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses
- Three Different Pathways Prevent Chromosome Segregation in the Presence of DNA Damage or Replication Stress in Budding Yeast
- Identification of Four Mouse Diabetes Candidate Genes Altering β-Cell Proliferation
- The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity
- Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in
- Genome Sequence and Transcriptome Analyses of : Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)
- Ty3 Retrotransposon Hijacks Mating Yeast RNA Processing Bodies to Infect New Genomes
- FUS Interacts with HSP60 to Promote Mitochondrial Damage
- Point Mutations in Centromeric Histone Induce Post-zygotic Incompatibility and Uniparental Inheritance
- Genome-Wide Association Study with Targeted and Non-targeted NMR Metabolomics Identifies 15 Novel Loci of Urinary Human Metabolic Individuality
- Outer Hair Cell Lateral Wall Structure Constrains the Mobility of Plasma Membrane Proteins
- A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen
- A Genetic Selection for Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis
- PLOS Genetics
- Archív čísel
- Aktuálne číslo
- Informácie o časopise
Najčítanejšie v tomto čísle- Arabidopsis AtPLC2 Is a Primary Phosphoinositide-Specific Phospholipase C in Phosphoinositide Metabolism and the Endoplasmic Reticulum Stress Response
- Bridges Meristem and Organ Primordia Boundaries through , , and during Flower Development in
- KLK5 Inactivation Reverses Cutaneous Hallmarks of Netherton Syndrome
- XBP1-Independent UPR Pathways Suppress C/EBP-β Mediated Chondrocyte Differentiation in ER-Stress Related Skeletal Disease
Prihlásenie#ADS_BOTTOM_SCRIPTS#Zabudnuté hesloZadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
- Časopisy