Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Zhang, Zhihua ^a   Zhang, Michael Q ^a  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BODY REGIONS; HISTONE MODIFICATION; HOUSEKEEPING GENE; MUSCLE CELL; PREDICTIVE POWER; PROTEIN-CODING; PROTEIN-CODING GENES; REGULATORY ELEMENTS;

CHROMOSOMES; PROTEINS; RNA; T-CELLS; TISSUE;

GENE EXPRESSION;

HISTONE; MICRORNA;

ANTIBODY SPECIFICITY; ARTICLE; ARTIFICIAL INTELLIGENCE; CD4+ T LYMPHOCYTE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HISTONE CODE; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REGULATORY SEQUENCE; SKELETAL MUSCLE;

ARTIFICIAL INTELLIGENCE; BASE SEQUENCE; CD4-POSITIVE T-LYMPHOCYTES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HISTONE CODE; HISTONES; HUMANS; MICRORNAS; MUSCLE, SKELETAL; ORGAN SPECIFICITY; PROMOTER REGIONS, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 79955807556     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-155     Document Type: Article

References (55)

1. Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2006, 7:29-59. 10.1146/annurev.genom.7.080505.115623, 16719718.
2. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132(5):887-898. 10.1016/j.cell.2008.02.022, 18329373.
3. Allis CD, Jenuwein T, Reinberg D. Epigenetics. 2007, Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
4. Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, Stoeckert CJ. Promoter features related to tissue specificity as measured by Shannon entropy. Genome biol 2005, 6(4):R33. 10.1186/gb-2005-6-4-r33, 1088961, 15833120.
5. Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278(1):167-181. 10.1006/jmbi.1998.1700, 9571041.
6. Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11(9):1559-1566. 10.1101/gr.180601, 311083, 11544200.
7. Smith AD, Sumazin P, Zhang MQ. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci USA 2005, 102(5):1560-1565. 10.1073/pnas.0406123102, 547828, 15668401.
8. Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Mol Syst Biol 2007, 3:73. 1800356, 17224917.
9. Smith AD, Sumazin P, Xuan Z, Zhang MQ. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci USA 2006, 103(16):6275-6280. 10.1073/pnas.0508169103, 1458868, 16606849.
10. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009, 459(7243):108-112. 10.1038/nature07829, 2910248, 19295514.
11. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309(5740):1559-1563.
12. Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006, 38(6):626-635. 10.1038/ng1789, 16645617.
13. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 2008, 40(7):897-903. 10.1038/ng.154, 2769248, 18552846.
14. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129(4):823-837. 10.1016/j.cell.2007.05.009, 17512414.
15. Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 2009, 4(1):80-93. 10.1016/j.stem.2008.11.011, 2785912, 19128795.
16. Karlic R, Chung HR, Lasserre J, Vlahovicek K, Vingron M. Histone modification levels are predictive for gene expression. Proc Natl Acad Sci USA 2010, 107(7):2926-2931. 10.1073/pnas.0909344107, 2814872, 20133639.
17. Pekowska A, Benoukraf T, Ferrier P, Spicuglia S. A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Res 2010, 20:1493-1502. 10.1101/gr.109389.110, 2963813, 20841431.
18. Zhao XY, Xuan ZY, Zhang MQ. Boosting with stumps for predicting transcription start sites. Genome biology 2007, 8(2):R17. 10.1186/gb-2007-8-2-r17, 1852414, 17274821.
19. Wang XW, Xuan ZY, Zhao XY, Li YD, Zhang MQ. High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res 2009, 19(2):266-275. 2652208, 18997002.
20. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 2004, 101(16):6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
21. Bajic VB, Seah SH, Chong A, Zhang G, Koh JL, Brusic V. Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics 2002, 18(1):198-199. 10.1093/bioinformatics/18.1.198, 11836231.
22. Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet 2001, 29(4):412-417. 10.1038/ng780, 11726928.
23. Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, Johnstone S, Guenther MG, Johnston WK, Wernig M, Newman J, et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 2008, 134(3):521-533. 10.1016/j.cell.2008.07.020, 2586071, 18692474.
24. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448(7153):553-560. 10.1038/nature06008, 2921165, 17603471.
25. Roh TY, Cuddapah S, Cui K, Zhao K. The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci USA 2006, 103(43):15782-15787. 10.1073/pnas.0607617103, 1613230, 17043231.
26. Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006, 103(5):1412-1417. 10.1073/pnas.0510310103, 1345710, 16432200.
27. Bajic VB, Tan SL, Suzuki Y, Sugano S. Promoter prediction analysis on the whole human genome. Nat Biotechnol 2004, 22(11):1467-1473. 10.1038/nbt1032, 15529174.
28. Abeel T, Saeys Y, Bonnet E, Rouze P, Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 2008, 18(2):310-323. 10.1101/gr.6991408, 2203629, 18096745.
29. Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Genome-wide functional analysis of human 5'untranslated region introns. Genome biol 2010, 11(3):R29. 2864569, 20222956.
30. Nogami H, Hoshino R, Ogasawara K, Miyamoto S, Hisano S. Region-specific expression and hormonal regulation of the first exon variants of rat prolactin receptor mRNA in rat brain and anterior pituitary gland. J Neuroendocrinol 2007, 19(8):583-593. 10.1111/j.1365-2826.2007.01565.x, 17620100.
31. Turner JD, Schote AB, Macedo JA, Pelascini LP, Muller CP. Tissue specific glucocorticoid receptor expression, a role for alternative first exon usage?. Biochem Pharmacol 2006, 72(11):1529-1537. 10.1016/j.bcp.2006.07.005, 16930562.
32. Roh TY, Wei G, Farrell CM, Zhao K. Genome-wide prediction of conserved and non-conserved enhancers by histone acetylation patterns. Genome Res 2007, 17(1):74-81. 1716270, 17135569.
33. Schones DE, Zhao K. Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 2008, 9(3):179-191. 10.1038/nrg2270, 18250624.
34. Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, et al. Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. Immunity 2009, 30(1):155-167. 10.1016/j.immuni.2008.12.009, 2722509, 19144320.
35. Lorincz MC, Dickerson DR, Schmitt M, Groudine M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 2004, 11(11):1068-1075. 10.1038/nsmb840, 15467727.
36. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346.
37. Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, et al. Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res 2009, 19(2):255-265. 2652207, 19074369.
38. Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res 2009, 19(6):1044-1056. 10.1101/gr.088773.108, 2694474, 19273619.
39. Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol 2010, 28(10):1057-1068. 10.1038/nbt.1685, 20944598.
40. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 2010, 466(7303):253-257. 10.1038/nature09165, 20613842.
41. Heintzman ND, Stuart RK, Hon G, Fu YT, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu CX, Ching KA, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007, 39(3):311-318. 10.1038/ng1966, 17277777.
42. Roh TY, Cuddapah S, Zhao K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 2005, 19(5):542-552. 10.1101/gad.1272505, 551575, 15706033.
43. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 2007, 130(1):77-88. 10.1016/j.cell.2007.05.042, 17632057.
44. Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008, 322(5909):1845-1848. 10.1126/science.1162228, 2833333, 19056941.
45. Core LJ, Lis JT. Transcription regulation through promoter-proximal pausing of RNA polymerase II. Science 2008, 319(5871):1791-1792. 10.1126/science.1150843, 2833332, 18369138.
46. Seila AC, Calabrese JM, Levine SS, Yeo GW, Rahl PB, Flynn RA, Young RA, Sharp PA. Divergent transcription from active promoters. Science 2008, 322(5909):1849-1851. 10.1126/science.1162253, 2692996, 19056940.
47. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116(2):281-297. 10.1016/S0092-8674(04)00045-5, 14744438.
48. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136(2):215-233. 10.1016/j.cell.2009.01.002, 19167326.
49. Cai X, Hagedorn CH, Cullen BR. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 2004, 10(12):1957-1966. 10.1261/rna.7135204, 1370684, 15525708.
50. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN. MicroRNA genes are transcribed by RNA polymerase II. EMBO J 2004, 23(20):4051-4060. 10.1038/sj.emboj.7600385, 524334, 15372072.
51. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 2006, 13(12):1097-1101. 10.1038/nsmb1167, 17099701.
52. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007, 129(7):1401-1414. 10.1016/j.cell.2007.04.040, 2681231, 17604727.
53. Xuan Z, Zhao F, Wang J, Chen G, Zhang MQ. Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome biol 2005, 6(8):R72. 10.1186/gb-2005-6-8-r72, 1273639, 16086854.
54. Hastie T, Tibshirani R, Friedman J. The elements of satistical learning: Data mining, inference, and prediction. 2000, New York: Springer-Verlag.
55. Breiman L, Friedman J, Olshen R, Storne C. Classification and regression trees. 1984, Belmont, CA: Wadsworth International Group.