An integrative approach to understanding the combinatorial histone code at functional elements

Bioinformatics

Volumn 29, Issue 18, 2013, Pages 2231-2237

  Lai, William K M ^a   Buck, Michael J ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; CHROMATIN; NUCLEOSOME;

ALGORITHM; ARTICLE; CHEMISTRY; CHROMATIN; CLASSIFICATION; GENE EXPRESSION; GENETICS; GENOMICS; HISTONE CODE; METABOLISM; METHODOLOGY; NUCLEOSOME; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; PROCEDURES;

ALGORITHMS; CHROMATIN; GENE EXPRESSION; GENOMICS; HISTONE CODE; NUCLEOSOMES; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

EID: 84883484883     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt382     Document Type: Article

References (36)

1. Albert,I. et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature, 446, 572-576.
2. Batta,K. et al. (2011) Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes Dev., 25, 2254-2265.
3. Brickner,D.G. et al. (2007) H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol., 5, e81.
4. Chan,C.T. et al. (2012) Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat. Commun., 3, 937.
5. Crooks,G.E. et al. (2004) WebLogo: A sequence logo generator. Genome Res., 14, 1188-1190.
6. Doyon,Y. et al. (2004) Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol. Cell. Biol., 24, 1884-1896.
7. Eaton,M.L. et al. (2010) Conserved nucleosome positioning defines replication origins. Genes Dev., 24, 748-753.
8. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
9. ENCODE. (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol., 9, e1001046.
10. Ernst,J. and Kellis,M. (2012) ChromHMM: Automating chromatin-state discovery and characterization. Nat. Methods, 9, 215-216.
11. Givens,R.M. et al. (2012) Chromatin architectures at fission yeast transcriptional promoters and replication origins. Nucleic Acids Res., 40, 7176-7189.
12. Guillemette,B. et al. (2011) H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation. PLoS Genet., 7, e1001354.
13. Hall,M. et al. (2009) The WEKA Data Mining Software: An update. SIGKDD Explor., 11, 10-18.
14. Hanlon,S.E. et al. (2011) The stress response factors Yap6, Cin5, Phd1, and Skn7 direct targeting of the conserved co-repressor Tup1-Ssn6 in S. cerevisiae. PLoS One, 6, e19060.
15. Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
16. Hesselberth,J.R. et al. (2009) Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat. Methods, 6, 283-289.
17. Hoffman,M.M. et al. (2012) Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods, 9, 473-476.
18. Irlbacher,H. et al. (2005) Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression. Genes Dev., 19, 1811-1822.
19. Kirmizis,A. et al. (2007) Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature, 449, 928-932.
20. Lai,W.K. and Buck,M.J. (2010) ArchAlign: Coordinate-free chromatin alignment reveals novel architectures. Genome Biol., 11, R126.
21. Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
22. Liu,C.L. et al. (2005) Single-nucleosome mapping of histone modifications in S.cerevisiae. PLoS Biol., 3, e328.
23. MacIsaac,K.D. et al. (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
24. Pan,J. et al. (2011) A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation. Cell, 144, 719-731.
25. Pan,X. and Heitman,J. (2000) Sok2 regulates yeast pseudohyphal differentiation via a transcription factor cascade that regulates cell-cell adhesion. Mol. Cell. Biol., 20, 8364-8372.
26. Pelleg,D. and Moore,A. (2000) X-means: Extending K-means with efficient estimation of the number of clusters. In: Proceedings of the Seventeenth International Conference on Machine Learning. Stanford, CA, USA, pp. 727-734.
27. Pokholok,D.K. et al. (2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell, 122, 517-527.
28. Rando,O.J. (2012) Combinatorial complexity in chromatin structure and function: Revisiting the histone code. Curr. Opin. Genet. Dev., 22, 148-155.
29. Rizzo,J.M. et al. (2011) Tup1 stabilizes promoter nucleosome positioning and occupancy at transcriptionally plastic genes. Nucleic Acids Res., 39, 8803-8819.
30. Rizzo,J.M. et al. (2012) Standardized collection of MNase-seq experiments enables unbiased dataset comparisons. BMC Mol. Biol., 13, 15.
31. Trapnell,C. et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
32. Venters,B.J. and Pugh,B.F. (2009) How eukaryotic genes are transcribed. Crit. Rev. Biochem. Mol. Biol., 44, 117-141.
33. Weiner,A. et al. (2010) High-resolution nucleosome mapping reveals transcriptiondependent promoter packaging. Genome Res., 20, 90-100.
34. Xu,Z. et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature, 457, 1033-1037.
35. Yassour,M. et al. (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc. Natl Acad. Sci. USA, 106, 3264-3269.
36. Yeang,C.H. et al. (2005) Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol., 6, R62.