Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq

Nucleic Acids Research

Volumn 39, Issue 4, 2011, Pages 1408-1418

  Liu, Yi ^a   Han, Dali ^a   Han, Yixing ^a   Yan, Zheng ^a   Xie, Bin ^b   Li, Jing ^a   Qiao, Nan ^a   Hu, Haiyang ^a   Khaitovich, Philipp ^a,c   Gao, Yuan ^b   Han, Jing Dong J ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; LYSINE; MESSENGER RNA; TRANSFER RNA;

AB INITIO CALCULATION; ALGORITHM; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; BRAIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GENOME; MACACA; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN MODIFICATION; RELIABILITY; RNA SEQUENCE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

ALGORITHMS; ANIMALS; CHROMATIN IMMUNOPRECIPITATION; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; LYSINE; MACACA MULATTA; MOLECULAR SEQUENCE ANNOTATION; RNA, MESSENGER; RNA, SMALL UNTRANSLATED; ROC CURVE; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION INITIATION SITE;

MACACA MULATTA; PRIMATES;

EID: 79952350327     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq956     Document Type: Article

References (24)

1. Gibbs, R.A., Rogers, J., Katze, M.G., Bumgarner, R., Weinstock, G.M., Mardis, E.R., Remington, K.A., Strausberg, R.L., Venter, J.C., Wilson, R.K. et al. (2007) Evolutionary, biomedical insights from the rhesus macaque genome. Science, 316, 222-234. (Pubitemid 46633091)
2. Guigo, R., Dermitzakis, E.T., Agarwal, P., Ponting, C.P., Parra, G., Reymond, A., Abril, J.F., Keibler, E., Lyle, R., Ucla, C. et al. (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1, 019 additional genes. Proc. Natl Acad. Sci. USA, 100, 1140-1145. (Pubitemid 36183969)
3. Parra, G., Agarwal, P., Abril, J.F., Wiehe, T., Fickett, J.W. and Guigo, R. (2003) Comparative gene prediction in human and mouse. Genome Res., 13, 108-117.
4. Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41. (Pubitemid 34679498)
5. Kent, W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
6. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65. (Pubitemid 46056171)
7. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I. and Zhao, K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837. (Pubitemid 46802390)
8. Mikkelsen, T.S., Ku, M., Jaffe, D.B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.K., Koche, R.P. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560. (Pubitemid 47206934)
9. Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
10. Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, A. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl Acad. Sci. USA, 106, 11667-11672.
11. Yu, H., Zhu, S., Zhou, B., Xue, H. and Han, J.D. (2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res., 18, 1314-1324.
12. Wang, X., Xuan, Z., Zhao, X., Li, Y. and Zhang, M.Q. (2009) High-resolution human core-promoter prediction with CoreBoost-HM. Genome Res., 19, 266-275.
13. Karlic, R., Chung, H.R., Lasserre, J., Vlahovicek, K. and Vingron, M. (2010) Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA, 107, 2926-2931.
14. Fei, T., Xia, K., Li, Z., Zhou, B., Zhu, S., Chen, H., Zhang, J., Chen, Z., Xiao, H., Han, J.D. et al. (2010) Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate determination. Genome Res., 20, 36-44.
15. Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
16. Zang, C., Schones, D.E., Zeng, C., Cui, K., Zhao, K. and Peng, W. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics, 25, 1952-1958.
17. Friedman, J., Hastie, T. and Tibshirani, R. (2000) Additive logistic regression: a statistical view of boosting. Annals Stat., 28, 337-407. (Pubitemid 33227445)
18. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold, B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621-628. (Pubitemid 351911867)
19. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
20. Zhao, X., Xuan, Z. and Zhang, M.Q. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol., 8, R17.
21. Taft, R.J., Kaplan, C.D., Simons, C. and Mattick, J.S. (2009) Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle, 8, 2332-2338.
22. Landry, J., Sharov, A.A., Piao, Y., Sharova, L.V., Xiao, H., Southon, E., Matta, J., Tessarollo, L., Zhang, Y.E., Ko, M.S. et al. (2008) Essential role of chromatin remodeling protein Bptf in early mouse embryos and embryonic stem cells. PLoS Genet., 4, e1000241.
23. Li, H., Ilin, S., Wang, W., Duncan, E.M., Wysocka, J., Allis, C.D. and Patel, D.J. (2006) Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature, 442, 91-95. (Pubitemid 44064215)
24. Kwon, S.Y., Xiao, H., Wu, C. and Badenhorst, P. (2009) Alternative splicing of NURF301 generates distinct NURF chromatin remodeling complexes with altered modified histone binding specificities. PLoS Genet., 5, e1000574.