ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome

PLoS Computational Biology

Volumn 4, Issue 10, 2008, Pages

  Hon, Gary ^a   Ren, Bing ^a,b   Wang, Wei ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFORMATION USE; LANTHANUM COMPOUNDS; TRANSCRIPTION; UNSUPERVISED LEARNING;

CIS-REGULATORY ELEMENTS; EPIGENETICS; FUNCTIONAL GENOMICS; GENE STRUCTURE; GENETIC INFORMATION; GENOMICS; HISTONE MODIFICATION; HUMAN GENOMES; PROBABILISTICS APPROACH; REGULATORY ELEMENTS;

GENOME;

HISTONE; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN; CHROMATIN STRUCTURE; CONTROLLED STUDY; HUMAN; HUMAN GENOME; OUTCOME ASSESSMENT; PROTEIN MICROARRAY; SEQUENCE ANALYSIS; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; CHROMATIN IMMUNOPRECIPITATION; DNA MICROARRAY; ENHANCER REGION; GENETICS; GENOME; HELA CELL; METABOLISM; PROMOTER REGION; PROTEIN PROCESSING; STATISTICAL MODEL; STATISTICS; TRANSCRIPTION INITIATION SITE;

ARTIFICIAL INTELLIGENCE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; ENHANCER ELEMENTS (GENETICS); GENOME, HUMAN; HELA CELLS; HISTONES; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS (GENETICS); PROTEIN PROCESSING, POST-TRANSLATIONAL; TRANSCRIPTION INITIATION SITE;

EID: 55549118625     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000201     Document Type: Article

References (35)

1. Millar CB, Grunstein M (2006) Genome-wide patterns of histone modifications in yeast. Nat Rev Mol Cell Biol 7: 657-666.
2. Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, et al. (2006) A genomic code for nucleosome positioning. Nature 442: 772-778.
3. Roh TY, Cuddapah S, Cui K, Zhao K (2006) The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A 103: 15782-15787.
4. Grant PA (2001) A tale of histone modifications. Genome Biol 2: REVIEWS0003.
5. Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, et al. (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431: 873-878.
6. Nathan D, Ingvarsdottir K, Sterner DE, Bylebyl GR, Dokmanovic M, et al. (2006) Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev 20: 966-976.
7. Sims RJ 3rd, Reinberg D (2006) Histone H3 Lys 4 methylation: caught in a bind? Genes Dev 20: 2779-2786.
8. Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, et al. (2005) Direct isolation and identification of promoters in the human genome. Genome Res 15: 830-839.
9. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, et al. (2005) A high-resolution map of active promoters in the human genome. Nature 436: 876-880.
10. Bergink S, Salomons FA, Hoogstraten D, Groothuis TA, de Waard H, et al. (2006) DNA damage triggers nucleotide excision repair-dependent monoubiquitylation of histone H2A. Genes Dev 20: 1343-1352.
11. Cimini D, Mattiuzzo M, Torosantucci L, Degrassi F (2003) Histone hyperacetylation in mitosis prevents sister chromatid separation and produces chromosome segregation defects. Mol Biol Cell 14: 3821-3833.
12. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293: 1074-1080.
13. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, et al. (2005) Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3: e328. doi:10.1371/journal.pbio.0030328.
14. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517-527.
15. 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.
16. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
17. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
18. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
19. Zheng M, Barrera LO, Ren B, Wu YN (2005) ChIP-chip: Data, Model, and Analysis. Los Angeles (California): Department of Statistics, University of California Los Angeles.
20. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, et al. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A 103: 12457-12462.
21. Benner CFGA, Subramaniam S, Glass C (2006) HOMER: An Algorithm for the De Novo Discovery of cis-Regulatory Elements from High Throughput Data. La Jolla (California): University of California San Diego.
22. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
23. Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33: D501-D504.
24. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, et al. (2006) DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods 3: 503-509.
25. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15: 1034-1050.
26. Blanchette M, Bataille AR, Chen X, Poitras C, Laganiere J, et al. (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 16: 656-668.
27. 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. doi:10.1371/journal.pgen. 0030136.
28. 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.
29. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322.
30. Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, et al. (2006) ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22: 637-640.
31. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell 124: 207-219.
32. Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, et al. (2006) High-resolution computational models of genome binding events. Nat Biotechnol 24: 963-970.
33. ENCODE_Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
34. Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, et al. (2005) Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation. Proc Natl Acad Sci U S A 102: 1998-2003.
35. Kim J, Bhinge AA, Morgan XC, Iyer VR (2005) Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat Methods 2: 47-53.