Prediction of transposable element derived enhancers using chromatin modification profiles

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Huda, Ahsan ^a   Tyagi, Eishita ^a   Mariño Ramírez, Leonardo ^b,c   Bowen, Nathan J ^a   Jjingo, Daudi ^a   Jordan, I King ^a,c  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c PanAmerican Bioinformatics Institute   (Colombia)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; TRANSCRIPTION FACTOR;

ARTICLE; CELL LINEAGE; CELL SPECIFICITY; CELL TYPE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; ENHANCER REGION; EPIGENETICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENOME ANALYSIS; HEMATOPOIETIC CELL; HISTONE MODIFICATION; MATHEMATICAL MODEL; PREDICTION; PROCESS MODEL; PROMOTER REGION; TRANSPOSON; CELL LINE; CELL STRAIN K 562; CHROMATIN; ERYTHROID PRECURSOR CELL; GENE EXPRESSION; GENETIC EPIGENESIS; HUMAN; HUMAN GENOME; METABOLISM; PROCEDURES;

CELL LINE; CHROMATIN; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; ERYTHROID PRECURSOR CELLS; GENE EXPRESSION; GENOME, HUMAN; HISTONES; HUMANS; K562 CELLS; METHODS; TRANSCRIPTION FACTORS;

EID: 80455131284     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027513     Document Type: Article

References (41)

1. Doolittle WF, Sapienza C, (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.
2. Orgel LE, Crick FH, (1980) Selfish DNA: the ultimate parasite. Nature 284: 604-607.
3. Hickey DA, (1982) Selfish DNA: a sexually-transmitted nuclear parasite. Genetics 101: 519-531.
4. Kidwell MG, Lisch DR, (2000) Transposable elements and host genome evolution. Trends Ecol Evol 15: 95-99.
5. Kidwell MG, Lisch DR, (2001) Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution Int J Org Evolution 55: 1-24.
6. Hambor JE, Mennone J, Coon ME, Hanke JH, Kavathas P, (1993) Identification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8 alpha gene. Mol Cell Biol 13: 7056-7070.
7. Yang Z, Boffelli D, Boonmark N, Schwartz K, Lawn R, (1998) Apolipoprotein(a) gene enhancer resides within a LINE element. J Biol Chem 273: 891-897.
8. Santangelo AM, de Souza FS, Franchini LF, Bumaschny VF, Low MJ, et al. (2007) Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet 3: 1813-1826.
9. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, et al. (2008) Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A 105: 4220-4225.
10. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, et al. (2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441: 87-90.
11. Marino-Ramirez L, Jordan IK, (2006) Transposable element derived DNaseI-hypersensitive sites in the human genome. Biol Direct 1: 20.
12. Gross DS, Garrard WT, (1988) Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57: 159-197.
13. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
14. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
15. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
16. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
17. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, et al. (2010) ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 38: D620-625.
18. Hatzis P, Talianidis I, (2002) Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol Cell 10: 1467-1477.
19. Wang Q, Carroll JS, Brown M, (2005) Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell 19: 631-642.
20. Maston GA, Evans SK, Green MR, (2006) Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 7: 29-59.
21. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457: 854-858.
22. Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, et al. (2007) Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet 3: e136.
23. Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, et al. (2006) CAGE: cap analysis of gene expression. Nat Methods 3: 211-222.
24. Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100: 15776-15781.
25. Smit AFA, Hubley R, Green P, (1996) RepeatMasker Open-3.0.
26. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462-467.
27. Kohany O, Gentles AJ, Hankus L, Jurka J, (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics 7: 474.
28. Cohen CJ, Lock WM, Mager DL, (2009) Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448: 105-114.
29. Feschotte C, (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9: 397-405.
30. Silva JC, Shabalina SA, Harris DG, Spouge JL, Kondrashovi AS, (2003) 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 82: 1-18.
31. Huda A, Marino-Ramirez L, Jordan IK, (2010) Epigenetic histone modifications of human transposable elements: genome defense versus exaptation. Mob DNA 1: 2.
32. Machon O, van den Bout CJ, Backman M, Rosok O, Caubit X, et al. (2002) Forebrain-specific promoter/enhancer D6 derived from the mouse Dach1 gene controls expression in neural stem cells. Neuroscience 112: 951-966.
33. Nobrega MA, Ovcharenko I, Afzal V, Rubin EM, (2003) Scanning human gene deserts for long-range enhancers. Science 302: 413.
34. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169-181.
35. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
36. 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.
37. Miller CJ, Okoniewski MJ, Yates T, (2007) Description of exonmap: simple analysis and annotation tools for Affymetrix exon arrays.
38. Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res 31: 51-54.
39. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32: D493-496.
40. Sturn A, Quackenbush J, Trajanoski Z, (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18: 207-208.
41. Sokal RR, Rohlf JF, (1981) Biometry: The Principles and Practice of Statistics in Biological Research. San Francisco W. H. Freeman.