Calculating the statistical significance of physical clusters of co-regulated genes in the genome: The role of chromatin in domain-wide gene regulation

Nucleic Acids Research

Volumn 32, Issue 5, 2004, Pages 1798-1807

  Chang, Cheng Fu ^a   Wai, Ka Man ^a   Patterton, Hugh G ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; CHROMATIN; CHROMATIN STRUCTURE; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE LOCUS; GENE SILENCING; GENOME ANALYSIS; HETEROCHROMATIN; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN; PROTEIN MICROARRAY; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS; TELOMERE; EVALUATION; FUNGAL GENE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; PHYSIOLOGY; REPRODUCIBILITY; STATISTICAL MODEL;

PYXIS; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

HISTONE DEACETYLASE; NUCLEAR PROTEIN; REPRESSOR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; SILENT INFORMATION REGULATOR PROTEIN; SIR2 PROTEIN, S CEREVISIAE; SIR3 PROTEIN, S CEREVISIAE; SIR4 PROTEIN, S CEREVISIAE; SIRTUIN; TUP1 PROTEIN, S CEREVISIAE;

CHROMATIN; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, FUNGAL; HISTONE DEACETYLASES; MODELS, STATISTICAL; NUCLEAR PROTEINS; REPRESSOR PROTEINS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE; SIRTUINS; SOFTWARE; TELOMERE;

EID: 3042526849     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh507     Document Type: Article

References (39)

1. Cohen,B.A., Mitra,R.D., Hughes,J.D. and Church,G.M. (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genet., 26, 183-186.
2. de Haan,G., Bystrykh,L.V., Weersing,E., Dontje,B., Geiger,H., Ivanova,N., Lemischka,I.R., Vellenga,E. and Van Zant,G. (2002) A genetic and genomic analysis identifies a cluster of genes associated with hematopoietic cell turnover. Blood, 100, 2056-2062.
3. Roy,P.J., Stuart,J.M., Lund,J. and Kim,S.K. (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature, 418, 975-979.
4. Spellman,P.T. and Rubin,G.M. (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol., 1, 5.
5. Zhang,H., Pan,K.H. and Cohen,S.N. (2003) Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci. Proc. Natl Acad. Sci. USA, 100, 3251-3256.
6. Orlando,V., Jane,E.P., Chinwalla,V., Harte,P.J. and Paro,R. (1998) Binding of trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis. EMBO J., 17, 5141-5150.
7. Bi,X., Braunstein,M., Shei,G.J. and Broach,J.R. (1999) The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing. Proc. Natl Acad. Sci. USA, 96, 11934-11939.
8. Plath,K., Mlynarczyk-Evans,S., Nusinow,D.A. and Panning,B. (2002) Xist RNA and the mechanism of X chromosome inactivation. Annu. Rev. Genet., 36, 233-278.
9. Litt,M.D., Simpson,M., Gaszner,M., Allis,C.D. and Felsenfeld,G. (2001) Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science, 293, 2453-2455.
10. Moretti,P. and Shore,D. (2001) Multiple interactions in Sir protein recruitment by Rap1p at silencers and telomeres in yeast. Mol. Cell. Biol., 21, 8082-8094.
11. Wolffe,A.P. (1998) Chromatin: Structure and Function. Academic Press, New York, NY.
12. Strahl,B.D. and Allis,C.D. (2000) The language of covalent histone modifications. Nature, 403, 41-45.
13. Bannister,A.J., Zegerman,P., Partridge,J.F., Miska,E.A., Thomas,J.O., Allshire,R.C. and Kouzarides,T. (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature, 410, 120-124.
14. Braunstein,M., Sobel,R.E., Allis,C.D., Turner,B.M. and Broach,J.R. (1996) Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol., 16, 4349-4356.
15. Caron,H., van Schaik,B., van der Mee,M., Baas,F., Riggins,G., van Sluis,P., Hermus,M.C., van Asperen,R., Boon,K., Voute,P.A. et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science, 291, 1289-1292.
16. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
17. Seoighe,C., Federspiel,N., Jones,T., Hansen,N., Bivolarovic,V., Surzycki,R., Tamse,R., Komp,C., Huizar,L., Davis,R.W. et al. (2000) Prevalence of small inversions in yeast gene order evolution. Proc. Natl Acad. Sci. USA, 97, 14433-14437.
18. Feller,W. (1961) An Introduction to Probability Theory and its Applications. John Wiley & Sons, New York, NY.
19. Peterson,C.L. and Tamkun,J.W. (1995) The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem. Sci., 20, 143-146.
20. Sudarsanam,P., Iyer,V.R., Brown,P.O. and Winston,F. (2000) Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 97, 3364-3369.
21. Hecht,A., Laroche,T., Strahl-Bolsinger,S., Gasser,S.M. and Grunstein,M. (1995) Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell, 80, 583-592.
22. Ducker,C.E. and Simpson,R.T. (2000) The organized chromatin domain of the repressed yeast a cell-specific gene STE6 contains two molecules of the corepressor Tup1p per nucleosome. EMBO J., 19, 400-409.
23. DeRisi,J.L., Iyer,V.R. and Brown,P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
24. Fritze,C.E., Verschueren,K., Strich,R. and Easton,E.R. (1997) Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J., 16, 6495-6509.
25. Imai,S., Armstrong,C.M., Kaeberlein,M. and Guarente,L. (2000) Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature, 403, 795-800.
26. Carmen,A.A., Milne,L. and Grunstein,M. (2002) Acetylation of the yeast histone H4 N terminus regulates its binding to heterochromatin protein SIR3. J. Biol. Chem., 277, 4778-4781.
27. Rusche,L.N., Kirchmaier,A.L. and Rine,J. (2002) Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell, 13, 2207-2222.
28. Meneghini,M., Wu,M. and Madhani,H. (2003) Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell, 112, 725-736.
29. Tzamarias,D. and Struhl,K. (1994) Functional dissection of the yeast Cyc8-Tup1 transcriptional co-repressor complex. Nature, 369, 758-761.
30. Edmondson,D.G., Smith,M.M. and Roth,S.Y. (1996) Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. Genes Dev., 10, 1247-1259.
31. Schuller,J. and Lehming,N. (2003) The cyclin in the RNA polymerase holoenzyme is a target for the transcriptional repressor Tup1p in Saccharomyces cerevisiae. J. Mol. Microbiol. Biotechnol., 5, 199-205.
32. Gromoller,A. and Lehming,N. (2000) Srb7p is a physical and physiological target of Tup1p. EMBO J., 19, 6845-6852.
33. Kerkmann,K. and Lehming,N. (2001) Genome-wide expression analysis of a Saccharomyces cerevisiae strain deleted for the Tup1p-interacting protein Cdc73p. Curr. Genet., 39, 284-290.
34. Cherry,J.M., Adler,C., Ball,C., Chervitz,S.A., Dwight,S.S., Hester,E.T., Jia,Y., Juvik,G., Roe,T., Schroeder,M. et al. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res., 26, 73-79.
35. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25-29.
36. Boa,S., Coert,C. and Patterton,H.G. (2003) Saccharomyces cerevisiae Set1p is a methyltransferase specific for lysine 4 of histone H3 and is required for efficient gene expression. Yeast, 20, 827-835.
37. Briggs,S.D., Bryk,M., Strahl,B.D., Cheung,W.L., Davie,J.K., Dent,S.Y., Winston,F. and Allis,C.D. (2001) Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev., 15, 3286-3295.
38. Nislow,C., Ray,E. and Pillus,L. (1997) SET1, a yeast member of the trithorax family, functions in transcriptional silencing and diverse cellular processes. Mol. Biol. Cell, 8, 2421-2436.
39. Wyrick,J.J., Holstege,F.C., Jennings,E,G., Causton,H.C., Shore,D., Grunstein,M., Lander,E.S. and Young,R.A. (1999) Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast, Nature, 402, 418-421.