The RHNumtS compilation: Features and bioinformatics approaches to locate and quantify Human NumtS

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Lascaro, Daniela ^a   Castellana, Stefano ^a   Gasparre, Giuseppe ^b   Romeo, Giovanni ^b   Saccone, Cecilia ^a   Attimonelli, Marcella ^a  

^a UNIVERSITY OF BARI   (Italy)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA; MITOCHONDRIAL DNA; PROTEIN NUMTS;

ARTICLE; BIOINFORMATICS; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA SEQUENCE; HUMAN; MITOCHONDRIAL GENETICS; POLYMERASE CHAIN REACTION; PROTEIN LOCALIZATION; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE DATABASE; BIOLOGY; CELL NUCLEUS; CHROMOSOME MAP; COMPARATIVE STUDY; GENETICS; GENOME; GENOMICS; ISOCHORE; METHODOLOGY; MITOCHONDRIAL GENOME; NUCLEIC ACID DATABASE; REFERENCE VALUE; SEQUENCE ALIGNMENT; VALIDATION STUDY;

EUKARYOTA;

CELL NUCLEUS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA, MITOCHONDRIAL; GENOME, HUMAN; GENOME, MITOCHONDRIAL; GENOMICS; HUMANS; ISOCHORES; POLYMERASE CHAIN REACTION; REFERENCE VALUES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 47249160395     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-267     Document Type: Article

References (49)

1. Bensasson D Zhang D Hartl DL Hewitt GM Mitochondrial pseudogenes: evolution's misplaced witnesses Trends Ecol Evol 2001, 16(6):314-321. 11369110 10.1016/S0169-5347(01)02151-6
2. Du Buy HG Riley FL Hybridization between the nuclear and kinetoplast DNAs of Leishmania enriettii and between nuclear and mitochondrial DNAs of mouse liver Proc Nat Acad Sci USA 1967, 57:790-797. 335577 16591532 10.1073/pnas.57.3.790
3. Farrelly F Butow RA Rearranged mitochondrial genes in the yeast nuclear genome Nature 1983, 301:296-301. 10.1038/301296a0 6296698
4. Gellissen G Bradfield JY White BN Wyatt GR Mitochondrial DNA sequences in the nuclear genome of a locust Nature 1983, 301:631-634. 10.1038/ 301631a0 6298629
5. Wright RM Cummings DJ Integration of mitochondrial gene sequences within the nuclear genome during senescence in a fungus Nature 1983, 302:86-88. 10.1038/302086a0 6828161
6. Jacobs HT Posakony JW Grula JW Roberts JW Xin JH Britten RJ Davidson EH Mitochondrial DNA sequences in the nuclear genome of Strongylocentrotus purpuratus J Mol Biol 1983, 165:609-632. 10.1016/S0022-2836(83)80270-8 6687903
7. Tsuzuki T Nomiyama H Setoyama C Maeda S Shimada K Presence of mitochondrial DNA like sequences in the human nuclear DNA Gene 1983, 25:223-229. 10.1016/0378-1119(83)90226-3 6662364
8. Kemble RJ Mans RJ Gabay-Laughnan S Laughnan JR Sequences homologous to episomal mitochondrial DNAs in the maize nuclear genome Nature 1983, 304:744-747. 10.1038/304744a0
9. Hadler HI Dimitrijevic B Mahalingam R Mitochondrial DNA and nuclear DNA from normal rat liver have a common sequence Genomics 1983, 22:487-489.
10. Lopez JV Yuhki N Masuda R Modi W O'brien SJ Numt a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat J Mol Evol 1994, 39:174-190. 7932781
11. Bravi CM Parson W Numts Revisited Human Mitochondrial DNA and the Evolution of Homo Sapiens Springer-Verlag, Berlin Heidelberg Bandelt V, Macaulay M, Richards HJ 2006, chapter 3 Part 1, 31.
12. Gherman A Chen PE Teslovich TM Stankiewicz P Withers M Kashuk CS Chakravarti A Lupski JR Cutler DJ Katsanis N Population Bottlenecks as a Potential Major Shaping Force of Human Genome Architecture PLoS Genet 2007, 3(7):e119. 1925129 17658953 10.1371/journal.pgen.0030119
13. Zischler H von Haeseler A Paabo S A nuclear fossil of the mitochondrial D-loop and the origin of the modern humans Nature 1995, 378:489-492. 10.1038/378489a0 7477404
14. Andrews RM Kubacka I Chinnery PF Lightowlers RN Turnbull DM Howell N Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA Nat Genet 1999, 23(2):147. 10.1038/13779 10508508
15. Yuan JD Shi JX Meng GX An LG Hu GX Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome Cell Res 1999, 9:281-290. 10.1038/sj.cr.7290027 10628837
16. Ricchetti M Tekaia F Dujon B Continued colonization of the Human Genome by mitochondrial DNA Plos Biology 2004, 2(9):e273. 515365 15361937 10.1371/journal.pbio.0020273
17. Antunes A Ramos MJ Discovery of a large number of previously unrecognised mitochondrial pseudogenes in fish genomes Genomics 2005, 86(6):708-717. 10.1016/j.ygeno.2005.08.002 16176867
18. Venkatesh B Dandona N Brenner S Fugu genome does not contain mitochondrial pseudogenes Genomics 2006, 87:307-310. 10.1016/ j.ygeno.2005.11.007 16386876
19. Behura SK Analysis of nuclear copies of mitochondrial sequences in honey bee Apis mellifera genome Mol Biol and Evol 2007, 24(7):1492-505. 10.1093/molbev/msm068
20. Woodward SR Weyand NJ Bunnell M DNA sequence from Cretaceous period bone fragments Science 1995, 268:1194. 10.1126/science.268.5214.1194 17840632
21. Wallace DC Stugard C Murdock D Schurr T Brown MD Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations Proc Natl Acad Sci USA 1997, 94(26):14900-14905. 25135 9405711 10.1073/pnas.94.26.14900
22. Adcock GJ Dennis ES Easteal S Huttley GA Jermiin LS Peacock WJ Thorne A Mitochondrial DNA sequences in ancient Australians: Implications for modern human origins Proc Natl Acad Sci USA 2001, 98(2):537-42. 14622 11209053 10.1073/pnas.98.2.537
23. Hazkani-Covo E Sorek R Graur D Evolutionary dynamics of large NUMTs in the Human Genome: Rarity of independent insertions and Abundance of Post-insertion duplications J Mol Evol 2003, 56:169-174. 10.1007/ s00239-002-2390-5 12574863
24. Schmitz J Piskurek O Zischler H Forty million years of independent evolution: A mitochondrial gene and its corresponding nuclear pseudogene in primates J Mol Evol 2005, 61(1):1-11. 10.1007/s00239-004-0293-3 16007490
25. Lopez JV Culver M Stephens JC Johnson WE O'Brien SJ Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals Mol Biol Evol 1997, 14(3):277-86. 9066795
26. Mishmar D Ruiz-Pesini E Brandon M Wallace DC Mitochondrial DNA like sequences in the Nucleus (NUMTs):INsights onto our african origins and the mechanism of foreign DNA integration Human mutation 2004, 23:125-133. 10.1002/humu.10304 14722916
27. Tourmen Y Baris O Dessen P Jacques C Malthiery Y Reynier P Structure and chromosomal distribution of human mitochondrial pseudogenes Genomics 2002, 80(1):71-77. 10.1006/geno.2002.6798 12079285
28. Mourier T Hansen AJ Willerslev E Arctander P The Human Genome Project reveals a continuous transfer of Large Mitochondrial Fragments to the Nucleus Mol Biol and Evol 2001, 18:1833-1837.
29. Woischnick M Moraes CT Pattern of organization of human mitochondrial pseudogenes in the nuclear genome Genome Res 2002, 12:885-893. 1383742 12045142 10.1101/gr.227202. Article published online before print in May 2002
30. Bensasson D Feldman MW Petrov DA Rates of DNA duplication and Insertion in the Human Genome J Mol Evol 2004, 57(3):343-354. 14629044 10.1007/ s00239-003-2485-7
31. Hazkani-Covo E Graur D A Comparative Analysis of Numt Evolution in Human and Chimpazee Mol Biol Evol 2007, 24(1):13-8. 10.1093/molbev/msl149 17056643
32. Parr RL Maki J Reguly B Dakubo GD Aguirre A Wittock R Robinson K Jakupciak JP Thayer RE The pseudomitochondrial genome influences mistakes in heteroplasmy interpretation BMC Genomics 2006, 7:185. 1538596 16859552 10.1186/1471-2164-7-185
33. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
34. Altschul SF Boguski MS Gish W Wootton JC Issues in searching molecular sequence databases Nature Genet 1994, 6:119-129. 10.1038/ng0294-119 8162065
35. Kent WJ BLAT - The BLAST-Like Alignment Tool Genome Res 2002, 12(4):656-664. 187518 11932250 10.1101/gr.229202. Article published online before March 2002
36. Madden T The BLAST sequence analysis tool NCBI Handbook part 3. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook
37. Collura R Stewart CB Insertions and duplications of mtDNA in the nuclear genomes of Old World Monkeys and Hominoids Nature 1995, 378:485-489. 10.1038/378485a0 7477403
38. UCSC Genome Browser http://genome.ucsc.edu/
39. NCBI Map viewer http://www.ncbi.nlm.nih.gov/mapview
40. Bernardi G Isochores and the evolutionary genomics of vertebrates Gene 2000, 241(1):3-17. 10.1016/S0378-1119(99)00485-0 10607893
41. Costantini M Clay O Auletta F Bernardi G An isochore map of human chromosomes Genome Res 2006, 16(4):536-541. 1457033 16597586 10.1101/ gr.4910606
42. Ishiguro N Nakajima A Horiuchi M Shinagawa M Multiple nuclear pseudogenes of mitochondrial DNA exist in the canine genome Mamm Genome 2002, 13(7):365-72. 10.1007/s00335-001-2139-2 12140679
43. Attimonelli M Accetturo M Santamaria M Lascaro D Scioscia G Pappada G Russo L Zanchetta L Tommaseo-Ponzetta M HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research BMC Bioinformatics 2005, 6(Suppl 4):S4. 1866381 16351753 10.1186/1471-2105-6-S4-S4
44. Pesole G Prunella N Liuni S Attimonelli M Saccone C WordUP: An efficient algorithm for discovering statistically significant patterns in DNA sequences Nucl Acids Res 1992, 20(11):2871-2875. 336935 1614873 10.1093/ nar/20.11.2871
45. Entrez home http://www.ncbi.nlm.nih.gov/Entrez
46. Katoh K Misawal K Kuma K Miyata T MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Research 2002, 30(14):3059-3066. 135756 12136088 10.1093/nar/gkf436
47. Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 2004, 5:113. 517706 15318951 10.1186/1471-2105-5-113
48. EBI home http://www.ebi.ac.uk
49. Blast2 site http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi