Gene properties and chromatin state influence the accumulation of transposable elements in genes

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Zhang, Ying ^a,b   Mager, Dixie L ^a,b  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTOME; DNA DIRECTED DNA POLYMERASE ALPHA;

ARTICLE; CHROMATIN; CONTROLLED STUDY; COW; DEVELOPMENT; DNA SEQUENCE; EMBRYONIC STEM CELL; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENETIC CONSERVATION; HISTONE MODIFICATION; HUMAN; HUMAN GENOME; METABOLISM; MOUSE; NONHUMAN; PROMOTER REGION; TISSUE SPECIFICITY; TRANSPOSON; ANIMAL; CATTLE; CHROMOSOME MAP; DNA BASE COMPOSITION; GENE EXPRESSION REGULATION; GENETICS; GENOME; METHYLATION; PROTEIN BINDING; SPECIES DIFFERENCE;

MAMMALIA;

ANIMALS; BASE COMPOSITION; CATTLE; CHROMATIN; CHROMOSOME MAPPING; DNA POLYMERASE II; DNA TRANSPOSABLE ELEMENTS; EMBRYONIC STEM CELLS; GENE EXPRESSION; GENOME; HISTONES; HUMANS; METHYLATION; MICE; MUTAGENESIS, INSERTIONAL; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 84855858788     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030158     Document Type: Article

References (44)

1. McClintock B, (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci U S A 36: 344-355.
2. Smit AF, (1996) The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6: 743-748.
3. Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE, (2008) Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition. Genome Res 18: 869-880.
4. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, et al. (2010) LINE-1 retrotransposition activity in human genomes. Cell 141: 1159-1170.
5. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, et al. (2009) The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324: 522-528.
6. Oldridge M, Zackai EH, McDonald-McGinn DM, Iseki S, Morriss-Kay GM, et al. (1999) De novo alu-element insertions in FGFR2 identify a distinct pathological basis for Apert syndrome. Am J Hum Genet 64: 446-461.
7. Chen JM, Stenson PD, Cooper DN, Ferec C, (2005) A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 117: 411-427.
8. Maksakova IA, Romanish MT, Gagnier L, Dunn CA, van de Lagemaat LN, et al. (2006) Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet 2: e2.
9. Cohen CJ, Lock WM, Mager DL, (2009) Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448: 105-114.
10. Hasler J, Strub K, (2006) Alu elements as regulators of gene expression. Nucleic Acids Res 34: 5491-5497.
11. Walters RD, Kugel JF, Goodrich JA, (2009) InvAluable junk: the cellular impact and function of Alu and B2 RNAs. IUBMB Life 61: 831-837.
12. Prudhomme S, Bonnaud B, Mallet F, (2005) Endogenous retroviruses and animal reproduction. Cytogenet Genome Res 110: 353-364.
13. Black SG, Arnaud F, Palmarini M, Spencer TE, (2010) Endogenous retroviruses in trophoblast differentiation and placental development. Am J Reprod Immunol 64: 255-264.
14. Biemont C, (2010) A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics 186: 1085-1093.
15. Cordaux R, Batzer MA, (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10: 691-703.
16. Feschotte C, (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405.
17. Brookfield JF, (2005) The ecology of the genome- mobile DNA elements and their hosts. Nat Rev Genet 6: 128-136.
18. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
19. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
20. Cutter AD, Good JM, Pappas CT, Saunders MA, Starrett DM, et al. (2005) Transposable element orientation bias in the Drosophila melanogaster genome. J Mol Evol 61: 733-741.
21. Medstrand P, van de Lagemaat LN, Mager DL, (2002) Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res 12: 1483-1495.
22. van de Lagemaat LN, Medstrand P, Mager DL, (2006) Multiple effects govern endogenous retrovirus survival patterns in human gene introns. Genome Biol 7: R86.
23. Zhang Y, Romanish MT, Mager DL, (2011) Distributions of transposable elements reveal hazardous zones in Mammalian introns. PLoS Comput Biol 7: e1002046.
24. Grover D, Majumder PP, C BR, Brahmachari SK, Mukerji M, (2003) Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol 20: 1420-1424.
25. Mortada H, Vieira C, Lerat E, (2010) Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species. J Mol Evol 71: 180-191.
26. Sironi M, Menozzi G, Comi GP, Cereda M, Cagliani R, et al. (2006) Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol 7: R120.
27. Jjingo D, Huda A, Gundapuneni M, Marino-Ramirez L, Jordan IK, (2011) Effect of the transposable element environment of human genes on gene length and expression. Genome Biol Evol 3: 259-271.
28. Fontanillas P, Hartl DL, Reuter M, (2007) Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLoS Genet 3: e210.
29. Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, et al. (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42: 631-634.
30. Jjingo D, Huda A, Gundapuneni M, Marino-Ramirez L, Jordan IK, (2011) Effect of the transposable element environment of human genes on gene length and expression. Genome Biol Evol.
31. Graham T, Boissinot S, (2006) The genomic distribution of L1 elements: the role of insertion bias and natural selection. J Biomed Biotechnol 2006 75327.
32. Smit AF, (1999) Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9: 657-663.
33. Malik HS, Eickbush TH, (1998) The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINEs. Mol Biol Evol 15: 1123-1134.
34. Adelson DL, Raison JM, Edgar RC, (2009) Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc Natl Acad Sci U S A 106: 12855-12860.
35. Simons C, Pheasant M, Makunin IV, Mattick JS, (2006) Transposon-free regions in mammalian genomes. Genome Res 16: 164-172.
36. Maere S, Heymans K, Kuiper M, (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: 3448-3449.
37. Rebollo R, Horard B, Hubert B, Vieira C, (2010) Jumping genes and epigenetics: Towards new species. Gene 454: 1-7.
38. Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, et al. (2008) Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res 18: 46-59.
39. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
40. Spivakov M, Fisher AG, (2007) Epigenetic signatures of stem-cell identity. Nat Rev Genet 8: 263-271.
41. Karimi MM, Goyal P, Maksakova IA, Bilenky M, Leung D, et al. (2011) DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs. Cell Stem Cell 8: 676-687.
42. Baillie JK, Barnett MW, Upton KR, Gerhardt DJ, Richmond TA, et al. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479: 534-537.
43. Gasior SL, Preston G, Hedges DJ, Gilbert N, Moran JV, et al. (2007) Characterization of pre-insertion loci of de novo L1 insertions. Gene 390: 190-198.
44. Brady T, Lee YN, Ronen K, Malani N, Berry CC, et al. (2009) Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev 23: 633-642.