Sequence features of HLA-DRB1 locus define putative basis for gene conversion and point mutations

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Von Salomé, Jenny ^b,c,d   Kukkonen, Jyrki P ^a,c,d  

^a UNIVERSITY OF HELSINKI   (Finland)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^c ÅBO AKADEMI UNIVERSITY   (Finland)

^d UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CPG DINUCLEOTIDE; DINUCLEOTIDE; HLA DR1 ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; DNA; HLA DR ANTIGEN; HLA-DRB1 ANTIGEN;

ANTIBODY COMBINING SITE; ANTIGEN DETECTION; ARTICLE; CPG ISLAND; DNA CLEAVAGE; DNA POLYMORPHISM; DNA REPAIR; EXON; GENE CONVERSION; GENE FREQUENCY; GENE LOCUS; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC RECOMBINATION; HOMOLOGOUS RECOMBINATION; HUMAN; HUMAN CELL; POINT MUTATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; ALLELE; BINDING SITE; DNA BASE COMPOSITION; GENE; GENETIC VARIABILITY; GENETICS; NUCLEOTIDE SEQUENCE;

ALLELES; BASE COMPOSITION; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; CPG ISLANDS; DNA; EXONS; GENE CONVERSION; GENES, MHC CLASS II; HLA-DR ANTIGENS; HUMANS; POINT MUTATION; RECOMBINATION, GENETIC; VARIATION (GENETICS);

EID: 44649148271     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-228     Document Type: Article

References (64)

1. Gruss A Michel B The replication-recombination connection: Insights from genomics Curr Opin Microbiol 2001, 4(5):595-601. 10.1016/ S1369-5274(00)00256-3 11587938
2. West SC Molecular views of recombination proteins and their control Nat Rev Mol Cell Biol 2003, 4(6):435-445. 10.1038/nrm1127 12778123
3. Haber JE Recombination: A frank view of exchanges and vice versa Curr Opin Cell Biol 2000, 12(3):286-292. 10.1016/S0955-0674(00)00090-9 10801454
4. van Rijk A Bloemendal H Molecular mechanisms of exon shuffling: illegitimate recombination Genetica 2003, 118(2-3):245-249. 10.1023/ A:1024138600624 12868613
5. Wurtele H Little KC Chartrand P Illegitimate DNA integration in mammalian cells Gene Ther 2003, 10(21):1791-1799. 10.1038/sj.gt.3302074 12960968
6. Robinson J Waller MJ Parham P de Groot N Bontrop R Kennedy LJ Stoehr P Marsh SG IMGT/HLA and IMGT/MHC: Sequence databases for the study of the major histocompatibility complex Nucleic Acids Res 2003, 31(1):311-314. 165517 12520010 10.1093/nar/gkg070
7. IMGT/HLA Database http://www.ebi.ac.uk/imgt/hla
8. Hogstrand K Bohme J A determination of the frequency of gene conversion in unmanipulated mouse sperm Proc Natl Acad Sci U S A 1994, 91(21):9921-9925. 44929 7937918 10.1073/pnas.91.21.9921
9. Titus-Trachtenberg EA Rickards O De Stefano GF Erlich HA Analysis of HLA class II haplotypes in the Cayapa Indians of Ecuador: A novel DRB1 allele reveals evidence for convergent evolution and balancing selection at position 86 Am J Hum Genet 1994, 55(1):160-167. 1918223 8023844
10. Ohta T Gene conversion vs point mutation in generating variability at the antigen recognition site of major histocompatibility complex loci J Mol Evol 1995, 41(2):115-119. 10.1007/BF00170662 7666440
11. Zangenberg G Huang MM Arnheim N Erlich H New HLA-DPB1 alleles generated by interallelic gene conversion detected by analysis of sperm Nat Genet 1995, 10(4):407-414. 10.1038/ng0895-407 7670490
12. von Salome J Gyllensten U Bergstrom TF Full-length sequence analysis of the HLA-DRB1 locus suggests a recent origin of alleles Immunogenetics 2007, 59(4):261-271. 10.1007/s00251-007-0196-8 17345114
13. Gorski J Mach B Polymorphism of human Ia antigens: Gene conversion between two DR beta loci results in a new HLA-D/DR specificity Nature 1986, 322(6074):67-70. 10.1038/322067a0 3459965
14. Gyllensten UB Sundvall M Erlich HA Allelic diversity is generated by intraexon sequence exchange at the DRB1 locus of primates Proc Natl Acad Sci U S A 1991, 88(9):3686-3690. 51517 2023919 10.1073/pnas.88.9.3686
15. Wakeley J Substitution-rate variation among sites and the estimation of transition bias Mol Biol Evol 1994, 11(3):436-442. 8015437
16. Purvis A Bromham L Estimating the transition/transversion ratio from independent pairwise comparisons with an assumed phylogeny J Mol Evol 1997, 44(1):112-119. 10.1007/PL00006117 9010143
17. Yang Z Yoder AD Estimation of the transition/transversion rate bias and species sampling J Mol Evol 1999, 48(3):274-283. 10.1007/PL00006470 10093216
18. Sved J Bird A The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model Proc Natl Acad Sci U S A 1990, 87(12):4692-4696. 54183 2352943 10.1073/pnas.87.12.4692
19. Abeysinghe SS Chuzhanova N Krawczak M Ball EV Cooper DN Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs Hum Mutat 2003, 22(3):229-244. 10.1002/humu.10254 12938088
20. Ball EV Stenson PD Abeysinghe SS Krawczak M Cooper DN Chuzhanova NA Microdeletions and microinsertions causing human genetic disease: Common mechanisms of mutagenesis and the role of local DNA sequence complexity Hum Mutat 2005, 26(3):205-213. 10.1002/humu.20212 16086312
21. Ramsden DA McBlane JF van Gent DC Gellert M Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage Embo J 1996, 15(12):3197-3206. 450263 8670820
22. Cuomo CA Mundy CL Oettinger MA DNA sequence and structure requirements for cleavage of V(D)J recombination signal sequences Mol Cell Biol 1996, 16(10):5683-5690. 231568 8816481
23. Dunnick W Hertz GZ Scappino L Gritzmacher C DNA sequences at immunoglobulin switch region recombination sites Nucleic Acids Res 1993, 21(3):365-372. 309126 8441648 10.1093/nar/21.3.365
24. Smith GR Homologous recombination near and far from DNA breaks: alternative roles and contrasting views Annu Rev Genet 2001, 35:243-274. 10.1146/annurev.genet.35.102401.090509 11700284
25. Wyatt RT Rudders RA Zelenetz A Delellis RA Krontiris TG BCL2 oncogene translocation is mediated by a chi-like consensus J Exp Med 1992, 175(6):1575-1588. 2119260 1588282 10.1084/jem.175.6.1575
26. Veljkovic E Dzodic R Neskovic G Stanojevic B Milovanovic Z Opric M Dimitrijevic B Sequence variant in the intron 10 of the RET oncogene in a patient with microfollicular thyroid carcinoma with medullar differentiation: Implications for newly generated chi-like sequence Med Oncol 2004, 21(4):319-324. 10.1385/MO:21:4:319 15579915
27. Xie F Wang X Cooper DN Chuzhanova N Fang Y Cai X Wang Z Wang H A novel Alu-mediated 61-kb deletion of the von Willebrand factor (VWF) gene whose breakpoints co-locate with putative matrix attachment regions Blood Cells Mol Dis 2006, 36(3):385-391. 10.1016/j.bcmd.2006.03.003 16690331
28. Krawczak M Cooper DN Gene deletions causing human genetic disease: mechanisms of mutagenesis and the role of the local DNA sequence environment Hum Genet 1991, 86(5):425-441. 10.1007/BF00194629 2016084
29. Schmucker B Krawczak M Meiotic microdeletion breakpoints in the BRCA1 gene are significantly associated with symmetric DNA-sequence elements Am J Hum Genet 1997, 61(6):1454-1456. 1716079 9399889 10.1086/301631
30. Helleday T Lo J van Gent DC Engelward BP DNA double-strand break repair: From mechanistic understanding to cancer treatment DNA Repair (Amst) 2007, 6(7):923-935. 10.1016/j.dnarep.2007.02.006 17363343
31. Jaulin C Perrin A Abastado JP Dumas B Papamatheakis J Kourilsky P Polymorphism in mouse and human class I H-2 and HLA genes is not the result of random independent point mutations Immunogenetics 1985, 22(5):453-470. 10.1007/BF00418091 3934067
32. Hogstrand K Bohme J Gene conversion of major histocompatibility complex genes is associated with CpG-rich regions Immunogenetics 1999, 49(5):446-455. 10.1007/s002510050518 10199921
33. Marais G Biased gene conversion: Implications for genome and sex evolution Trends Genet 2003, 19(6):330-338. 10.1016/ S0168-9525(03)00116-1 12801726
34. Duret L Eyre-Walker A Galtier N A new perspective on isochore evolution Gene 2006, 385:71-74. 10.1016/j.gene.2006.04.030 16971063
35. Takai D Jones PA Comprehensive analysis of CpG islands in human chromosomes 21 and 22 Proc Natl Acad Sci U S A 2002, 99(6):3740-3745. 122594 11891299 10.1073/pnas.052410099
36. Tanay A O'Donnell AH Damelin M Bestor TH Hyperconserved CpG domains underlie Polycomb-binding sites Proc Natl Acad Sci U S A 2007, 104(13):5521-5526. 1838490 17376869 10.1073/pnas.0609746104
37. Zhu J Schiestl RH Topoisomerase I involvement in illegitimate recombination in Saccharomyces cerevisiae Mol Cell Biol 1996, 16(4):1805-1812. 231167 8657156
38. Nakagawa K Morishima N Shibata T An endonuclease with multiple cutting sites, Endo.SceI, initiates genetic recombination at its cutting site in yeast mitochondria Embo J 1992, 11(7):2707-2715. 556746 1628629
39. Stoddard BL Homing endonuclease structure and function Q Rev Biophys 2005, 38(1):49-95. 10.1017/S0033583505004063 16336743
40. Amor M Parker KL Globerman H New MI White PC Mutation in the CYP21B gene (Ile-172 - Asn) causes steroid 21-hydroxylase deficiency Proc Natl Acad Sci U S A 1988, 85(5):1600-1604. 279821 3257825 10.1073/pnas.85.5.1600
41. Blanco MG Boan F Barros P Castano JG Gomez-Marquez J Generation of DNA double-strand breaks by two independent enzymatic activities in nuclear extracts J Mol Biol 2005, 351(5):995-1006. 10.1016/j.jmb.2005.06.065 16051267
42. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22(22):4673-4680. 308517 7984417 10.1093/nar/22.22.4673
43. Jukes TH Cantor CR Evolution of protein molecules Mammalian Protein Metabolism New York, Academic Press Munro, H.N 1969:21-32.
44. Kumar S Tamura K Nei M MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Brief Bioinform 2004, 5(2):150-163. 10.1093/bib/5.2.150 15260895
45. Rozas J Sanchez-DelBarrio JC Messeguer X Rozas R DnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 2003, 19(18):2496-2497. 10.1093/bioinformatics/btg359 14668244
46. Pride DT SWAAP - A tool for analyzing substitutions and similarity in multiple alignments http://www.bacteriamuseum.org/SWAAP/SwaapPage.htm
47. Simonsson T G-quadruplex DNA structures - variations on a theme Biol Chem 2001, 382(4):621-628. 10.1515/BC.2001.073 11405224
48. Burge S Parkinson GN Hazel P Todd AK Neidle S Quadruplex DNA: Sequence, topology and structure Nucleic Acids Res 2006, 34(19):5402-5415. 1636468 17012276 10.1093/nar/gkl655
49. Ferec C Casals T Chuzhanova N Macek M Jr. Bienvenu T Holubova A King C McDevitt T Castellani C Farrell PM Sheridan M Pantaleo SJ Loumi O Messaoud T Cuppens H Torricelli F Cutting GR Williamson R Ramos MJ Pignatti PF Raguenes O Cooper DN Audrezet MP Chen JM Gross genomic rearrangements involving deletions in the CFTR gene: Characterization of six new events from a large cohort of hitherto unidentified cystic fibrosis chromosomes and meta-analysis of the underlying mechanisms Eur J Hum Genet 2006, 14(5):567-576. 10.1038/sj.ejhg.5201590 16493442
50. Tsai CL Chatterji M Schatz DG DNA mismatches and GC-rich motifs target transposition by the RAG1/RAG2 transposase Nucleic Acids Res 2003, 31(21):6180-6190. 275461 14576304 10.1093/nar/gkg819
51. van Gent DC Hoeijmakers JH Kanaar R Chromosomal stability and the DNA double-stranded break connection Nat Rev Genet 2001, 2(3);196-206. 10.1038/35056049 11256071
52. Lee HH Niu DM Lin RW Chan P Lin CY Structural analysis of the chimeric CYP21P/CYP21 gene in steroid 21-hydroxylase deficiency J Hum Genet 2002, 47(10):517-522. 10.1007/s100380200077 12376740
53. Chou CL Morrison SL A common sequence motif near nonhomologous recombination breakpoints involving Ig sequences J Immunol 1993, 150(12):5350-5360. 8515063
54. Borgato L Bonizzato A Lunardi C Dusi S Andrioli G Scarperi A Corrocher R A 1.1-kb duplication in the p67-phox gene causes chronic granulomatous disease Hum Genet 2001, 108(6):504-510. 10.1007/s004390100526 11499676
55. Krowczynska AM Rudders RA Krontiris TG The human minisatellite consensus at breakpoints of oncogene translocations Nucleic Acids Res 1990, 18(5);1121-1127. 330424 1969618 10.1093/nar/18.5.1121
56. Bullock P Champoux JJ Botchan M Association of crossover points with topoisomerase I cleavage sites: A model for nonhomologous recombination Science 1985, 230(4728):954-958. 10.1126/science.2997924 2997924
57. Fry M Loeb LA A DNA polymerase alpha pause site is a hot spot for nucleotide misinsertion Proc Natl Acad Sci U S A 1992, 89(2):763-767. 48319 1731352 10.1073/pnas.89.2.763
58. Kunkel TA The mutational specificity of DNA polymerase-beta during in vitro DNA synthesis. Production of frameshift, base substitution, and deletion mutations J Biol Chem 1985, 260(9):5787-5796. 3988773
59. Kunkel TA The mutational specificity of DNA polymerases-alpha and -gamma during in vitro DNA synthesis J Biol Chem 1985, 260(23):12866-12874. 3930505
60. Sander M Hsieh TS Drosophila topoisomerase II double-strand DNA cleavage: Analysis of DNA sequence homology at the cleavage site Nucleic Acids Res 1985, 13(4):1057-1072. 341056 2987816 10.1093/nar/13.4.1057
61. Gale KC Osheroff N Intrinsic intermolecular DNA ligation activity of eukaryotic topoisomerase II. Potential roles in recombination J Biol Chem 1992, 267(17):12090-12097. 1318309
62. Jeffreys AJ Wilson V Thein SL Hypervariable 'minisatellite' regions in human DNA Nature 1985, 314(6006):67-73. 10.1038/314067a0 3856104
63. Myers S Bottolo L Freeman C McVean G Donnelly P A fine-scale map of recombination rates and hotspots across the human genome Science 2005, 310(5746):321-324. 10.1126/science.1117196 16224025
64. Chuzhanova NA Anassis EJ Ball EV Krawczak M Cooper DN Meta-analysis of indels causing human genetic disease: Mechanisms of mutagenesis and the role of local DNA sequence complexity Hum Mutat 2003, 21(1):28-44. 10.1002/humu.10146 12497629