in Saccharomyces cerevisiae

Recent studies have revealed that transcription of noncoding, intergenic DNA is abundant among eukaryotes. However, the functions of this transcription are poorly understood. We have previously shown that in Saccharomyces cerevisiae, expression of an intergenic transcript, SRG1, represses the transcription of the adjacent gene, SER3, by transcription interference. We now show that SRG1 transcription is regulated by serine, thereby conferring regulation of SER3, a serine biosynthetic gene. This regulation requires Cha4, a serine-dependent activator that binds to the SRG1 promoter and is required for SRG1 induction in the presence of serine. Furthermore, two coactivator complexes, SAGA and Swi/Snf, are also directly required for activation of SRG1 and transcription interference of SER3. Taken together, our results elucidate a physiological role for intergenic transcription in the regulation of SER3. Moreover, our results demonstrate a mechanism by which intergenic transcription allows activators to act indirectly as repressors.

[1]  John R Yates,et al.  Deubiquitination of Histone H2B by a Yeast Acetyltransferase Complex Regulates Transcription* , 2004, Journal of Biological Chemistry.

[2]  P. Fraser,et al.  Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus. , 2000, Molecular cell.

[3]  Employment Opportunities , 2004, IEEE Engineering in Medicine and Biology Magazine.

[4]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[5]  E. Sánchez-Herrero,et al.  Spatially ordered transcription of regulatory DNA in the bithorax complex of Drosophila. , 1989, Development.

[6]  S. Gottesman.  The small RNA regulators of Escherichia coli: roles and mechanisms*. , 2004, Annual review of microbiology.

[7]  F. Karch,et al.  Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing. , 2002, Development.

[8]  S. Merchant,et al.  Reciprocal Expression of Two Candidate Di-Iron Enzymes Affecting Photosystem I and Light-Harvesting Complex Accumulation , 2002, The Plant Cell Online.

[9]  P. Schjerling,et al.  Cha4p of Saccharomyces cerevisiae activates transcription via serine/threonine response elements. , 1996, Genetics.

[10]  N. Proudfoot.  Transcriptional interference and termination between duplicated α-globin gene constructs suggests a novel mechanism for gene regulation , 1986, Nature.

[11]  D. Moazed.  Mechanisms of Gene Silencing , 2001 .

[12]  F. Winston,et al.  Evidence that Swi/Snf directly represses transcription in S. cerevisiae. , 2002, Genes & development.

[13]  B. Birren,et al.  Sequencing and comparison of yeast species to identify genes and regulatory elements , 2003, Nature.

[14]  P. Avner,et al.  Employment opportunities for non‐coding RNAs , 2004, FEBS letters.

[15]  T. Tuschl,et al.  Mechanisms of gene silencing by double-stranded RNA , 2004, Nature.

[16]  F. Winston,et al.  Analysis of the yeast SPT3 gene and identification of its product, a positive regulator of Ty transcription. , 1986, Nucleic acids research.

[17]  Eli Eisenberg,et al.  Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome , 2005, BMC Genomics.

[18]  S. P. Fodor,et al.  Large-Scale Transcriptional Activity in Chromosomes 21 and 22 , 2002, Science.

[19]  R. Paro,et al.  Transcription through Intergenic Chromosomal Memory Elements of the Drosophila Bithorax Complex Correlates with an Epigenetic Switch , 2002, Molecular and Cellular Biology.

[20]  R. Paro,et al.  Intergenic transcription through a polycomb group response element counteracts silencing. , 2005, Genes & development.

[21]  Fred Winston,et al.  Functional Organization of the Yeast SAGA Complex: Distinct Components Involved in Structural Integrity, Nucleosome Acetylation, and TATA-Binding Protein Interaction , 1999, Molecular and Cellular Biology.

[22]  A. Dudley,et al.  The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. , 1999, Genes & development.

[23]  E. Schadt,et al.  Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. , 2005, Trends in genetics : TIG.

[24]  L. Fulton,et al.  Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting , 2003, Science.

[25]  John J. Wyrick,et al.  Genome-wide location and function of DNA binding proteins. , 2000, Science.

[26]  W. Bender,et al.  Transcription activates repressed domains in the Drosophila bithorax complex. , 2002, Development.

[27]  B. Cullen,et al.  Transcriptional interference in avian retroviruses—implications for the promoter insertion model of leukaemogenesis , 1984, Nature.

[28]  F. Winston,et al.  Analysis of a Mutant Histone H3 That Perturbs the Association of Swi/Snf with Chromatin , 2004, Molecular and Cellular Biology.

[29]  A. Happel,et al.  A mutant tRNA affects delta-mediated transcription in Saccharomyces cerevisiae. , 1992, Genetics.

[30]  P. Brown,et al.  Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae , 2003, Genome Biology.

[31]  R. Morse,et al.  Global and specific transcriptional repression by the histone H3 amino terminus in yeast , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  J. Mattick.  Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[33]  K. Yamamoto,et al.  Essential role of Swp73p in the function of yeast Swi/Snf complex. , 1996, Genes & development.

[34]  E. Cho,et al.  Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. , 2000, Genes & development.

[35]  R. Young,et al.  RNA polymerase II subunit composition, stoichiometry, and phosphorylation , 1990, Molecular and cellular biology.

[36]  J. Ranish,et al.  Positive and negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. , 2004, Genes & development.

[37]  Leah Barrera,et al.  A high-resolution map of active promoters in the human genome , 2005, Nature.

[38]  M. Brandriss,et al.  Proline-independent binding of PUT3 transcriptional activator protein detected by footprinting in vivo , 1991, Molecular and cellular biology.

[39]  R. J. Reece,et al.  Modulation of transcription factor function by an amino acid: activation of Put3p by proline , 2003, The EMBO journal.

[40]  A. Hüttenhofer,et al.  Non-coding RNAs: hope or hype? , 2005, Trends in genetics : TIG.

[41]  A. Sparks,et al.  Using the transcriptome to annotate the genome , 2002, Nature Biotechnology.

[42]  K. Shearwin,et al.  Transcriptional interference--a crash course. , 2005, Trends in genetics : TIG.

[43]  S. Cumberledge,et al.  Characterization of two RNAs transcribed from the cis-regulatory region of the abd-A domain within the Drosophila bithorax complex. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[44]  M. Carlson,et al.  Molecular analysis of SNF2 and SNF5, genes required for expression of glucose-repressible genes in Saccharomyces cerevisiae , 1986, Molecular and cellular biology.

[45]  G. Helt,et al.  Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.

[46]  S. Cawley,et al.  Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs , 2004, Cell.

[47]  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.

[48]  T. Maniatis,et al.  Role of transcriptional interference in the Drosophila melanogaster Adh promoter switch , 1989, Nature.

[49]  F. Winston,et al.  SPT20/ADA5 encodes a novel protein functionally related to the TATA-binding protein and important for transcription in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[50]  K. Struhl,et al.  Current Protocols in Molecular Biology (New York: Greene Publishing Associates and Wiley-Interscience). Host-Range Shuttle System for Gene Insertion into the Chromosomes of Gram-negative Bacteria. , 1988 .

[51]  F. Winston,et al.  Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. , 1997, Genetics.

[52]  B. Séraphin,et al.  Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.

[53]  L. Gansheroff,et al.  The Saccharomyces cerevisiae SPT7 gene encodes a very acidic protein important for transcription in vivo. , 1995, Genetics.

[54]  R. Somerville,et al.  Interaction in vivo between strong closely spaced constitutive promoters. , 1979, Journal of molecular biology.

[55]  Thomas E. Royce,et al.  Global Identification of Human Transcribed Sequences with Genome Tiling Arrays , 2004, Science.

[56]  D. Hogness,et al.  Novel transcripts from the Ultrabithorax domain of the bithorax complex. , 1987, Genes & development.

[57]  Ali Shilatifard,et al.  Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. , 2003, Genes & development.

[58]  S. Cawley,et al.  Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. , 2004, Genome research.

[59]  J. Boeke,et al.  Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications , 1998, Yeast.

[60]  Emily Bernstein,et al.  RNA meets chromatin. , 2005, Genes & development.

[61]  R. J. Reece,et al.  Eukaryotic transcription factors as direct nutrient sensors. , 2005, Trends in biochemical sciences.

[62]  F. Winston,et al.  The Saccharomyces cerevisiae SPT8 gene encodes a very acidic protein that is functionally related to SPT3 and TATA-binding protein. , 1994, Genetics.

[63]  G. Storz,et al.  An abundance of RNA regulators. , 2005, Annual review of biochemistry.

[64]  B. Panning,et al.  Epigenetic gene regulation by noncoding RNAs. , 2003, Current opinion in cell biology.

[65]  A. Dudley,et al.  Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae. , 1999, Genetics.

[66]  Fred Winston,et al.  Construction of a set of convenient saccharomyces cerevisiae strains that are isogenic to S288C , 1995, Yeast.

[67]  J. Rowley,et al.  Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Fred Winston,et al.  Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene , 2004, Nature.

[69]  R Ohba,et al.  Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. , 1997, Genes & development.

[70]  S. Cases,et al.  Transcription of unr ( pstream of ‐ as) down‐modulates N‐ras expression in vivo , 1997, FEBS letters.