A study on genomic distribution and sequence features of human long inverted repeats reveals species-specific intronic inverted repeats

FEBS Journal

Volumn 276, Issue 7, 2009, Pages 1986-1998

  Wang, Yong ^a   Leung, Frederick C C ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Human; Intron; Long inverted repeat; Primates; Stem loop

Indexed keywords

PALINDROMIC DNA;

ARTICLE; CELL COMMUNICATION; CELL MATURATION; CHIMPANZEE; EXON; GENE CONTROL; INTRON; INVERTED REPEAT; NERVOUS SYSTEM DEVELOPMENT; ORTHOLOGY; PRIORITY JOURNAL; RHESUS MONKEY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

MACACA MULATTA; PAN; PRIMATES;

EID: 62149126551     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2009.06930.x     Document Type: Article

References (48)

1. Lobachev KS, Stenger JE, Kozyreva OG, Jurka J, Gordenin DA Resnick MA (2000) Inverted Alu repeats unstable in yeast are excluded from the human genome. EMBO J 19, 3822 3830.
2. Lobachev KS, Shor BM, Tran HT, Taylor W, Keen JD, Resnick MA Gordenin DA (1998) Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae. Genetics 148, 1507 1524.
3. Gordenin DA, Lobachev KS, Degtyareva NP, Malkova AL, Perkins E Resnick MA (1993) Inverted DNA repeats: a source of eukaryotic genomic instability. Mol Cell Biol 13, 5315 5322.
4. Tanaka H, Tapscott SJ, Trask BJ Yao M-C (2002) Short inverted repeats initiate gene amplification through the formation of a large DNA palindrome in mammalian cells. Proc Natl Acad Sci USA 99, 8772 8777.
5. Lin C-T, Lin W-H, Lyu YL Whang-Peng J (2001) Inverted repeats as genetic elements for promoting DNA inverted duplication: implications in gene amplification. Nucleic Acids Res 29, 3529 3538.
6. Gotter AL, Nimmakayalu MA, Jalali GR, Hacker AM, Vorstman J, Conforto Duffy D, Medne L Emanuel BS (2007) A palindrome-driven complex rearrangement of 22q11.2 and 8q24.1 elucidated using novel technologies. Genome Res 17, 470 481.
7. Nag DK Kurst A (1997) A 140-bp-long palindromic sequence induces double strand breaks during meiosis in the yeast Saccharomyces cerevisiae. Genetics 146, 835 847.
8. Collick A, Drew J, Penberth J, Bois P, Luckett J, Scaerou F, Jeffreys A Reik W (1996) Instability of long inverted repeats within mouse transgenes. EMBO J 15, 1163 1171.
9. Katz RA, Gravuer K Skalka AM (1998) A preferred target DNA structure for retroviral integrase in vitro. J Bio Chem 273, 24190 24195.
10. Inagaki K, Lewis SM, Wu X, Ma C, Munroe DJ, Fuess S, Storm TA, Kay MA Nakai H (2007) DNA palindromes with a modest arm length of >20 base pairs are a significant target for recombinant adeno-associated virus vector integration in the liver, muscles, and heart in mice. J Virol 81, 11290 11303.
11. Voineagu I, Narayanan V, Lobachev KS Mirkin SM (2008) Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Pro Nat Aca Sci USA 105, 9936 9941.
12. Stenger JE, Lobachev KS, Gordenin D, Darden TA, Jurka J Resnick MA (2001) Biased distribution of inverted and direct Alus in the human genome: Implications for insertion, exclusion, and genome stability. Genome Res 11, 12 27.
13. Akgun E, Zahn J, Baumes S, Brown G, Liang F, Romanienko PJ, Lewis S Jasin M (1997) Palindrome resolution and recombination in the mammalian germ line. Mol Cell Biol 17, 5559 5570.
14. Piriyapongsa J (2007) A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS ONE 2, e203.
15. Montgomery MK, Xu S Fire A (1998) RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci USA 95, 15502 15507.
16. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281.
17. Moss EG, Lee RC Ambros V (1997) The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88, 637 646.
18. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR Ruvkun G (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403, 901 906.
19. Schramke V, Sheedy DM, Denli AM, Bonila C, Ekwall K, Hannon GJ Allshire RC (2005) RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435, 1275 1279.
20. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833 1837.
21. Glucksmann MA, Markiewicz P, Malone C Rothman-Denes LB (1992) Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition. Cell 70, 491 500.
22. Kim EL, Peng H, Esparza FM, Maltchenko SZ Stachowiak MK (1998) Cruciform-extruding regulatory element controls cell-specific activity of the tyrosine hydroxylase gene promoter. Nucleic Acids Res 26, 1793 1800.
23. Spiro C McMurray CT (1997) Switching of DNA secondary structure in proenkephalin transcriptional regulation. J Bio Chem 272, 33145 33152.
24. Christopher E, Pearson CE, Zorbas H, Price GB Zannis-Hadjopoulos M (1996) Inverted repeats, stem-loops, and cruciforms: significance for initiation of DNA replication. J Cell Biochem 63, 1 22.
25. McAlinden A, Havlioglu N, Liang L, Davies SR Sandell LJ (2005) Alternative splicing of type II procollagen exon 2 is regulated by the combination of a weak 5′ splice site and an adjacent intronic stem-loop cis element. J Biol Chem 280, 32700 32711.
26. Baraniak AP, Lasda EL, Wagner EJ Garcia-Blanco MA (2003) A stem structure in fibroblast growth factor receptor 2 transcripts mediates cell-type-specific splicing by approximating intronic control elements. Mol Cell Biol 23, 9327 9337.
27. Miyaso H, Okumura M, Kondo S, Higashide S, Miyajima H Imaizumi K (2003) An intronic splicing enhancer element in survival motor neuron (SMN) pre-mRNA. J Biol Chem 278, 15825 15831.
28. Chen Y Stephan W (2003) Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene. Proc Natl Acad Sci USA 100, 11499 11504.
29. Lisnić B, Svetec I-K, Šarić H, Nikolić I Zgaga Z (2005) Palindrome content of the yeast Saccharomyces cerevisiae genome. Curr Genet 47, 289 297.
30. Lu L, Jia H, Dröge P Li J (2007) The human genome-wide distribution of DNA palindromes. Funct Integr Genomics 7, 221 227.
31. Zhao G, Chang KY, Varley K Stormo GD (2007) Evidence for active maintenance of inverted repeat structures identified by a comparative genomic approach. PLoS ONE 2, e262.
32. Warburton PE, Giordano J, Cheung F, Gelfand Y Benson G (2004) Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res 14, 1861 1869.
33. Wang Y Leung FCC (2006) Long inverted repeats in eukaryotic genomes: recombinogenic motifs determine genomic plasticity. FEBS Lett 580, 1277 1284.
34. Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M et al. (2004) The DNA sequence and biology of human chromosome 19. Nature 428, 529 539.
35. Hüttenhofer A, Schattner P Polacek N (2005) Non-coding RNAs: hope or hype? Trends Genet 21, 289 297.
36. Achaz G, Netter P Coissac E (2001) Study of intrachromosomal duplications among the eukaryote genomes. Mol Biol Evol 18, 2280 2288.
37. International Human Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409, 860 921.
38. Edelmann L, Spiteri E, Koren K, Pulijaal V, Bialer MG, Shanske A, Goldberg R Morrow BE (2001) AT-rich palindromes mediate the constitutional t(11;22) translocation. Am J Hum Genet 68, 1 13.
39. Hefferon TW, Groman JD, Yurk CE Cutting GR (2004) A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing. Proc Natl Acad Sci USA 101, 3504 3509.
40. Hui J, Hung L-H, Heiner M, Schreiner S, Neumüller N, Reither G, Haas SA Bindereif A (2005) Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing. EMBO J 24, 1988 1998.
41. Waldman AS, Tran H, Goldsmith EC Resnick MA (1999) Long inverted repeats are an at-risk motif for recombination in mammalian cells. Genetics 153, 1873 1883.
42. Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM Trask BJ (2005) Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 437, 94 100.
43. Myers S, Bottolo L, Freeman C, McVean G Donnelly P (2005) A fine-scale map of recombination rates and hotspots across the human genome. Science 310, 321 324.
44. Bird AP (1995) Gene number, noise reduction and biological complexity. Trends Genet 11, 94 100.
45. Claverie J-M (2001) Gene number: what if there are only 30,000 human genes? Science 291, 1255 1257.
46. Bacolla A, Larson JE, Collins JR, Li J, Milosavljevic A, Stenson PD, Cooper DN Wells RD (2008) Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties. Genome Res 18, 1545 1553.
47. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674 3676.
48. Blüthgen N, Brand K, Cajavec B, Swat M, Herzel H Beule D (2005) Biological profiling of gene groups utilizing gene ontology. Genome Inform 16, 106 115.