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

Physical clusters of co-regulated, but apparently functionally unrelated, genes are present in many genomes. Despite the important implication that the genomic environment contributes appreciably to the regulation of gene expression, no simple statistical method has been described to identify physical clusters of co-regulated genes. Here we report the development of a model that allows the direct calculation of the significance of such clusters. We have implemented the derived statistical relation in a software program, Pyxis, and have analyzed a selection of Saccharomyces cerevisiae gene expression microarray data sets. We have identified many gene clusters where constituent genes exhibited a regulatory dependence on proteins previously implicated in chromatin structure. Specifically, we found that Tup1p-dependent gene domains were enriched close to telomeres, which suggested a new role for Tup1p in telomere silencing. In addition, we identified Sir2p-, Sir3p- and Sir4p-dependent clusters, which suggested the presence of Sir-mediated heterochromatin in previously unidentified regions of the yeast genome. We also showed the presence of Sir4p-dependent gene clusters bordering the HMRa heterothallic locus, which suggested leaky termination of the heterochromatin by the boundary elements. These results demonstrate the utility of Pyxis in identifying possible higher order genomic features that may contribute to gene regulation in extended domains.

[1]  T. Liesegang.  The human transcriptome map: Clustering of highly expressed genes in chromosomal domains. Caron H, ∗ van Schaik B, van der Mee M, et al. Science 2001;291:1289–1292. , 2001 .

[2]  Hiten D. Madhani,et al.  Conserved Histone Variant H2A.Z Protects Euchromatin from the Ectopic Spread of Silent Heterochromatin , 2003, Cell.

[3]  H. Patterton,et al.  Saccharomyces cerevisiae Set1p is a methyltransferase specific for lysine 4 of histone H3 and is required for efficient gene expression , 2003, Yeast.

[4]  D. Edmondson,et al.  Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4. , 1996, Genes & development.

[5]  Stanley N Cohen,et al.  Senescence-specific gene expression fingerprints reveal cell-type-dependent physical clustering of up-regulated chromosomal loci , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  David Botstein,et al.  SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..

[7]  C. Nislow,et al.  SET1, a yeast member of the trithorax family, functions in transcriptional silencing and diverse cellular processes. , 1997, Molecular biology of the cell.

[8]  C. Peterson,et al.  The SWI-SNF complex: a chromatin remodeling machine? , 1995, Trends in biochemical sciences.

[9]  R. Simpson,et al.  The organized chromatin domain of the repressed yeast a cell‐specific gene STE6 contains two molecules of the corepressor Tup1p per nucleosome , 2000, The EMBO journal.

[10]  N. Lehming,et al.  Genome-wide expression analysis of a Saccharomyces cerevisiae strain deleted for the Tup1p-interacting protein Cdc73p , 2001, Current Genetics.

[11]  J. Broach,et al.  The yeast HML I silencer defines a heterochromatin domain boundary by directional establishment of silencing. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[12]  K. Struhl,et al.  Functional dissection of the yeast Cyc8–Tupl transcriptional co-repressor complex , 1994, Nature.

[13]  B. Hamkalo,et al.  Chromatin Structure and Function , 1979, NATO Advanced Study Institutes Series.

[14]  R. E. Esposito,et al.  Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA , 1997, The EMBO journal.

[15]  Andreas Hecht,et al.  Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: A molecular model for the formation of heterochromatin in yeast , 1995, Cell.

[16]  Andrew J. Bannister,et al.  Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain , 2001, Nature.

[17]  F. Baas,et al.  The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains , 2001, Science.

[18]  N. Lehming,et al.  The Cyclin in the RNA Polymerase Holoenzyme Is a Target for the Transcriptional Repressor Tup1p in Saccharomyces cerevisiae , 2003, Journal of Molecular Microbiology and Biotechnology.

[19]  Dmitri A. Nusinow,et al.  Xist RNA and the mechanism of X chromosome inactivation. , 2002, Annual review of genetics.

[20]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[21]  Claudio Nicolini,et al.  Chromatin Structure and Function , 1979, NATO Advanced Study Institutes Series.

[22]  J. Davie,et al.  Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. , 2001, Genes & development.

[23]  R. Paro,et al.  Binding of Trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis , 1998, The EMBO journal.

[24]  Lisa Milne,et al.  Acetylation of the Yeast Histone H4 N Terminus Regulates Its Binding to Heterochromatin Protein SIR3* , 2002, The Journal of Biological Chemistry.

[25]  B M Turner,et al.  Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern , 1996, Molecular and cellular biology.

[26]  William Feller,et al.  An Introduction to Probability Theory and Its Applications , 1951 .

[27]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[28]  David Shore,et al.  Multiple Interactions in Sir Protein Recruitment by Rap1p at Silencers and Telomeres in Yeast , 2001, Molecular and Cellular Biology.

[29]  E. Vellenga,et al.  A genetic and genomic analysis identifies a cluster of genes associated with hematopoietic cell turnover. , 2002, Blood.

[30]  N. Lehming,et al.  Srb7p is a physical and physiological target of Tup1p , 2000, The EMBO journal.

[31]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[32]  Gerald M Rubin,et al.  Evidence for large domains of similarly expressed genes in the Drosophila genome , 2002, Journal of biology.

[33]  P. Brown,et al.  Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[34]  B. Barrell,et al.  Prevalence of small inversions in yeast gene order evolution. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Joshua M. Stuart,et al.  Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans , 2002, Nature.

[36]  John J. Wyrick,et al.  Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast , 1999, Nature.

[37]  L. Guarente,et al.  Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase , 2000, Nature.

[38]  G. Church,et al.  A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression , 2000, Nature Genetics.

[39]  Jasper Rine,et al.  Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. , 2002, Molecular biology of the cell.

[40]  C. Allis,et al.  Correlation Between Histone Lysine Methylation and Developmental Changes at the Chicken β-Globin Locus , 2001, Science.

[41]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.