Epigenetic regulation of transposable element derived human gene promoters

Gene

Volumn 475, Issue 1, 2011, Pages 39-48

  Huda, Ahsan ^a   Bowen, Nathan J ^a   Conley, Andrew B ^a   Jordan, I King ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Chromatin; Gene expression; Gene regulation; Histone modifications; Transposable elements

Indexed keywords

HISTONE;

ARTICLE; CELL LINE; CELL LINEAGE; CELL TYPE; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; HISTONE MODIFICATION; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; RETROPOSON; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; TRANSPOSON;

CELL LINE; DNA TRANSPOSABLE ELEMENTS; EPIGENOMICS; GENOME-WIDE ASSOCIATION STUDY; HISTONES; HUMANS; PROMOTER REGIONS, GENETIC;

MAMMALIA;

EID: 79952007022     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2010.12.010     Document Type: Article

References (68)

1. Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. Molecular biology of the cell. Garland Science 2002.
2. Atanackovic D., et al. Expression of cancer-testis antigens as possible targets for antigen-specific immunotherapy in head and neck squamous cell carcinoma. Cancer Biol Ther 2006, 5:1218-1225.
3. Bannert N., Kurth R. Retroelements and the human genome: new perspectives on an old relation. Proc Natl Acad Sci USA 2004, 101(Suppl 2):14572-14579.
4. Barski A., et al. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837.
5. Bejerano G., et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006, 441:87-90.
6. Birney E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
7. Brosius J., Gould S.J. On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci USA 1992, 89:10706-10710.
8. Celniker S.E., et al. Unlocking the secrets of the genome. Nature 2009, 459:927-930.
9. Chen, Y.T., Chadburn, A., Lee, P., Hsu, M., Ritter, E., Chiu, A., Gnjatic, S., Pfreundschuh, M., Knowles, D.M. and Old, L.J., 2010. Expression of cancer testis antigen CT45 in classical Hodgkin lymphoma and other B-cell lymphomas. Proc Natl Acad Sci U S A 107, pp. 3093-8.
10. Cohen C.J., Lock W.M., Mager D.L. Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 2009, 448:105-114.
11. Conley A.B., Piriyapongsa J., Jordan I.K. Retroviral promoters in the human genome. Bioinformatics 2008, 24:1563-1567.
12. Doolittle W.F., Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature 1980, 284:601-603.
13. Dunn C.A., Medstrand P., Mager D.L. An endogenous retroviral long terminal repeat is the dominant promoter for human beta1, 3-galactosyltransferase 5 in the colon. Proc Natl Acad Sci USA 2003, 100:12841-12846.
14. Dunn C.A., Romanish M.T., Gutierrez L.E., van de Lagemaat L.N., Mager D.L. Transcription of two human genes from a bidirectional endogenous retrovirus promoter. Gene 2006, 366:335-342.
15. Fazzari M.J., Greally J.M. Epigenomics: beyond CpG islands. Nat Rev Genet 2004, 5:446-455.
16. Feschotte C. Transposable elements and the evolution of regulatory networks. Nat Rev Genet 2008, 9:397-405.
17. Gendrel A.V., Lippman Z., Yordan C., Colot V., Martienssen R.A. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 2002, 297:1871-1873.
18. Gould S.J., Vrba E.S. Exaptation; a missing term in the science of form. Paleobiology 1982, 8:4-15.
19. Grewal S.I., Elgin S.C. Transcription and RNA interference in the formation of heterochromatin. Nature 2007, 447:399-406.
20. Grewal S.I., Jia S. Heterochromatin revisited. Nat Rev Genet 2007, 8:35-46.
21. Henikoff S., Matzke M.A. Exploring and explaining epigenetic effects. Trends Genet 1997, 13:293-295.
22. Hsu F., Kent W.J., Clawson H., Kuhn R.M., Diekhans M., Haussler D. The UCSC known genes. Bioinformatics 2006, 22:1036-1046.
23. Huda A., Marino-Ramirez L., Jordan I.K. Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. Mob DNA 2010, 1:2.
24. Jordan I.K., Rogozin I.B., Glazko G.V., Koonin E.V. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 2003, 19:68-72.
25. Kapitonov V., Jurka J. The age of Alu subfamilies. J Mol Evol 1996, 42:59-65.
26. Karolchik D., et al. The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31:51-54.
27. Karolchik D., et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res 2004, 32:D493-D496.
28. Kidwell M.G., Lisch D.R. Transposable elements and host genome evolution. Trends Ecol Evol 2000, 15:95-99.
29. Kondo Y., Issa J.P. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J Biol Chem 2003, 278:27658-27662.
30. Kuno K., Matsushima K. The IL-1 receptor signaling pathway. J Leukoc Biol 1994, 56:542-547.
31. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
32. Langowski J.L., et al. IL-23 promotes tumour incidence and growth. Nature 2006, 442:461-465.
33. Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 2002, 3:662-673.
34. Lippman Z., et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 2004, 430:471-476.
35. Marino-Ramirez L., Jordan I.K. Transposable element derived DNaseI-hypersensitive sites in the human genome. Biol Direct 2006, 1:20.
36. Marino-Ramirez L., Lewis K.C., Landsman D., Jordan I.K. Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet Genome Res 2005, 110:333-341.
37. Martens J.H., et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 2005, 24:800-812.
38. Matsui T., et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 2010, 464:927-931.
39. Matzke M.A., Mette M.F., Matzke A.J. Transgene silencing by the host genome defense: implications for the evolution of epigenetic control mechanisms in plants and vertebrates. Plant Mol Biol 2000, 43:401-415.
40. McDonald J.F. Transposable elements, gene silencing and macroevolution. Trends Ecol Evol 1998, 13:94-95.
41. McDonald J.F., Matzke M.A., Matzke A.J. Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenet Genome Res 2005, 110:242-249.
42. Medstrand P., Landry J.R., Mager D.L. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J Biol Chem 2001, 276:1896-1903.
43. Medstrand P., van de Lagemaat L.N., Dunn C.A., Landry J.R., Svenback D., Mager D.L. Impact of transposable elements on the evolution of mammalian gene regulation. Cytogenet Genome Res 2005, 110:342-352.
44. Mikkelsen T.S., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
45. Miller C.J., Okoniewski M.J., Yates T. Description of exonmap: simple analysis and annotation tools for Affymetrix exon arrays 2007.
46. Morgan H.D., Sutherland H.G., Martin D.I., Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 1999, 23:314-318.
47. Orgel L.E., Crick F.H. Selfish DNA: the ultimate parasite. Nature 1980, 284:604-607.
48. Pauler F.M., et al. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 2009, 19(2):221-233.
49. Piriyapongsa J., Jordan I.K. A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS ONE 2007, 2:e203.
50. Polavarapu N., Marino-Ramirez L., Landsman D., McDonald J.F., Jordan I.K. Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics 2008, 9:226.
51. Romanish M.T., Lock W.M., van de Lagemaat L.N., Dunn C.A., Mager D.L. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet 2007, 3:e10.
52. Rosenbloom K.R., et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 2010, 38:D620-D625.
53. Samuelson L.C., Wiebauer K., Snow C.M., Meisler M.H. Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution. Mol Cell Biol 1990, 10:2513-2520.
54. Santangelo A.M., de Souza F.S., Franchini L.F., Bumaschny V.F., Low M.J., Rubinstein M. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet 2007, 3:1813-1826.
55. Siepel A., Pollard K.S., Haussler D. New methods for detecting lineage-specific selection., 10th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '06) 2006.
56. Silva J.C., Shabalina S.A., Harris D.G., Spouge J.L., Kondrashovi A.S. Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genet Res 2003, 82:1-18.
57. Slotkin R.K., Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 2007, 8:272-285.
58. Sokal R.R., Rohlf J.F. Biometry: The Principles and Practice of Statistics in Biological Research 1981, W. H. Freeman, San Francisco.
59. Soriano P., Meunier-Rotival M., Bernardi G. The distribution of interspersed repeats is nonuniform and conserved in the mouse and human genomes. Proc Natl Acad Sci USA 1983, 80:1816-1820.
60. Sturn A., Quackenbush J., Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics 2002, 18:207-208.
61. Suzuki M.M., Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008, 9:465-476.
62. van de Lagemaat L.N., Landry J.R., Mager D.L., Medstrand P. Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions. Trends Genet 2003, 19:530-536.
63. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 2002, 297:1833-1837.
64. Wang Z., et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 2008, 40:897-903.
65. Weil C., Martienssen R. Epigenetic interactions between transposons and genes: lessons from plants. Curr Opin Genet Dev 2008, 18:188-192.
66. Whitelaw E., Martin D.I. Retrotransposons as epigenetic mediators of phenotypic variation in mammals. Nat Genet 2001, 27:361-365.
67. Yoder J.A., Walsh C.P., Bestor T.H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 1997, 13:335-340.
68. Zhang X.Y., et al. Identification and expression analysis of alternatively spliced isoforms of human interleukin-23 receptor gene in normal lymphoid cells and selected tumor cells. Immunogenetics 2006, 57:934-943.