EMdeCODE: A novel algorithm capable of reading words of epigenetic code to predict enhancers and retroviral integration sites and to identify H3R2me1 as a distinctive mark of coding versus non-coding genes

Nucleic Acids Research

Volumn 41, Issue 3, 2013, Pages

  Santoni, Federico Andrea ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN;

ACCURACY; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; EPIGENETICS; GENE; GENETIC ALGORITHM; GENETIC CODE; H3R2ME1 GENE; HISTONE MODIFICATION; PREDICTIVE VALUE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROMOTER REGION; PROTEIN PROCESSING; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; VIRUS DNA CELL DNA INTERACTION;

ALGORITHMS; CHROMATIN IMMUNOPRECIPITATION; ENHANCER ELEMENTS, GENETIC; EPIGENESIS, GENETIC; GENES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; RETROVIRIDAE; RNA, LONG UNTRANSLATED; VIRUS INTEGRATION;

EID: 84873657043     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1214     Document Type: Article

References (41)

1. Bird,A. (2007) Perceptions of epigenetics. Nature, 447, 396-398.
2. Jirtle,R.L. and Skinner,M.K. (2007) Environmental epigenomics and disease susceptibility. Nat. Rev. Genet., 8, 253-262.
3. Spivakov,M. and Fisher,A.G. (2007) Epigenetic signatures of stem-cell identity. Nat. Rev. Genet., 8, 263-271.
4. Nightingale,K.P., O'Neill,L.P. and Turner,B.M. (2006) Histone modifications: Signalling receptors and potential elements of a heritable epigenetic code. Curr. Opin. Genet. Dev., 16, 125-136.
5. Santoni,F.A., Hartley,O. and Luban,J. (2010) Deciphering the code for retroviral integration target site selection. PLoS Comput. Biol., 6, e1001008.
6. Turner,B.M. (2007) Defining an epigenetic code. Nat. Cell Biol., 9, 2-6.
7. Huff,J.T., Plocik,A.M., Guthrie,C. and Yamamoto,K.R. (2010) Reciprocal intronic and exonic histone modification regions in humans. Nat. Struct. Mol. Biol., 17, 1495-1499.
8. Hon,G., Ren,B. and Wang,W. (2008) ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput. Biol., 4, e1000201.
9. Ernst,J. and Kellis,M. (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol., 28, 817-825.
10. Hoffman,M.M., Buske,O.J., Wang,J., Weng,Z., Bilmes,J.A. and Noble,W.S. (2012) Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods, 9, 473-476.
11. van Steensel,B., Braunschweig,U., Filion,G.J., Chen,M., van Bemmel,J.G. and Ideker,T. (2010) Bayesian network analysis of targeting interactions in chromatin. Genome Res., 20, 190-200.
12. Firpi,H.A., Ucar,D. and Tan,K. (2010) Discover regulatory DNA elements using chromatin signatures and artificial neural network. Bioinformatics, 26, 1579-1586.
13. Heintzman,N.D., Stuart,R.K., Hon,G., Fu,Y., Ching,C.W., Hawkins,R.D., Barrera,L.O., Van Calcar,S., Qu,C., Ching,K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39, 311-318.
14. Micsinai,M., Parisi,F., Strino,F., Asp,P., Dynlacht,B.D. and Kluger,Y. (2012) Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res., 40, e70.
15. Heinz,S., Benner,C., Spann,N., Bertolino,E., Lin,Y.C., Laslo,P., Cheng,J.X., Murre,C., Singh,H. and Glass,C.K. (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
16. Song,Q. and Smith,A.D. (2011) Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics, 27, 870-871.
17. Pepke,S., Wold,B. and Mortazavi,A. (2009) Computation for ChIP-seq and RNA-seq studies. Nat. Methods, 6, S22-S32.
18. Boyle,A.P., Guinney,J., Crawford,G.E. and Furey,T.S. (2008) F-Seq: A feature density estimator for high-throughput sequence tags. Bioinformatics, 24, 2537-2538.
19. Bilmes,J.A. (1997) A gentle tutorial on the EM algorithm and application to Gaussian Mixtures and Baum-Welch. Technical Report TR-97-021, ICSI
20. Won,K.J., Chepelev,I., Ren,B. and Wang,W. (2008) Prediction of regulatory elements in mammalian genomes using chromatin signatures. BMC Bioinformatics, 9, 547.
21. Robertson,G., Hirst,M., Bainbridge,M., Bilenky,M., Zhao,Y., Zeng,T., Euskirchen,G., Bernier,B., Varhol,R., Delaney,A. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 4, 651-657.
22. Visel,A., Blow,M.J., Li,Z., Zhang,T., Akiyama,J.A., Holt,A., Plajzer-Frick,I., Shoukry,M., Wright,C., Chen,F. et al. (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature, 457, 854-858.
23. Ferretti,V., Poitras,C., Bergeron,D., Coulombe,B., Robert,F. and Blanchette,M. (2007) PReMod: A database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res., 35, D122-D126.
24. Wang,Z., Zang,C., Cui,K., Schones,D.E., Barski,A., Peng,W. and Zhao,K. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell, 138, 1019-1031.
25. Heintzman,N.D., Hon,G.C., Hawkins,R.D., Kheradpour,P., Stark,A., Harp,L.F., Ye,Z., Lee,L.K., Stuart,R.K., Ching,C.W. et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature, 459, 108-112.
26. Boyle,A.P., Davis,S., Shulha,H.P., Meltzer,P., Margulies,E.H., Weng,Z., Furey,T.S. and Crawford,G.E. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell, 132, 311-322.
27. Morris,S.A., Rao,B., Garcia,B.A., Hake,S.B., Diaz,R.L., Shabanowitz,J., Hunt,D.F., Allis,C.D., Lieb,J.D. and Strahl,B.D. (2007) Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification. J. Biol. Chem., 282, 7632-7640.
28. Valouev,A., Johnson,S.M., Boyd,S.D., Smith,C.L., Fire,A.Z. and Sidow,A. (2011) Determinants of nucleosome organization in primary human cells. Nature, 474, 516-520.
29. Wang,Z., Zang,C., Rosenfeld,J.A., Schones,D.E., Barski,A., Cuddapah,S., Cui,K., Roh,T.Y., Peng,W., Zhang,M.Q. et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet., 40, 897-903.
30. Rada-Iglesias,A., Bajpai,R., Swigut,T., Brugmann,S.A., Flynn,R.A. and Wysocka,J. (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature, 470, 279-283.
31. Creyghton,M.P., Cheng,A.W., Welstead,G.G., Kooistra,T., Carey,B.W., Steine,E.J., Hanna,J., Lodato,M.A., Frampton,G.M., Sharp,P.A. et al. (2011) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA, 107, 21931-21936.
32. 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.
33. Ugarkovic,D. (ed.), (2011) Long Non-Coding RNAs. Springer-Verlag, New York
34. Barski,A., Chepelev,I., Liko,D., Cuddapah,S., Fleming,A.B., Birch,J., Cui,K., White,R.J. and Zhao,K. (2010) Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nat. Struct. Mol. Biol., 17, 629-634.
35. Rahl,P.B., Lin,C.Y., Seila,A.C., Flynn,R.A., McCuine,S., Burge,C.B., Sharp,P.A. and Young,R.A. (2010) c-Myc regulates transcriptional pause release. Cell, 141, 432-445. 36. Guttman,M. and Rinn,J.L. (2012) Modular regulatory principles of large non-coding RNAs. Nature, 482, 339-346.
36. Tanaka,Y., Katagiri,Z., Kawahashi,K., Kioussis,D. and Kitajima,S. (2007) Trithorax-group protein ASH1 methylates histone H3 lysine 36. Gene, 397, 161-168.
37. An,W., Kim,J. and Roeder,R.G. (2004) Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell, 117, 735-748.
38. Kirmizis,A., Santos-Rosa,H., Penkett,C.J., Singer,M.A., Green,R.D. and Kouzarides,T. (2009) Distinct transcriptional outputs associated with mono- and dimethylated histone H3 arginine 2. Nat. Struct. Mol. Biol., 16, 449-451.
39. Migliori,V., Muller,J., Phalke,S., Low,D., Bezzi,M., Mok,W.C., Sahu,S.K., Gunaratne,J., Capasso,P., Bassi,C. et al. (2012) Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance. Nat. Struct. Mol. Biol., 19, 136-144.
40. Lewinski,M.K., Yamashita,M., Emerman,M., Ciuffi,A., Marshall,H., Crawford,G., Collins,F., Shinn,P., Leipzig,J., Hannenhalli,S. et al. (2006) Retroviral DNA integration: viral and cellular determinants of target-site selection. PLoS Pathog., 2, e60.
41. Wu,X., Li,Y., Crise,B. and Burgess,S.M. (2003) Transcription start regions in the human genome are favored targets for MLV integration. Science, 300, 1749-1751.