title: Regulon-specific control of transcription elongation across the yeast genome.
abstract: Transcription elongation by RNA polymerase II was often considered an invariant non-regulated process. However, genome-wide studies have shown that transcriptional pausing during elongation is a frequent phenomenon in tightly-regulated metazoan genes. Using a combination of ChIP-on-chip and genomic run-on approaches, we found that the proportion of transcriptionally active RNA polymerase II (active versus total) present throughout the yeast genome is characteristic of some functional gene classes, like those related to ribosomes and mitochondria. This proportion also responds to regulatory stimuli mediated by protein kinase A and, in relation to cytosolic ribosomal-protein genes, it is mediated by the silencing domain of Rap1. We found that this inactive form of RNA polymerase II, which accumulates along the full length of ribosomal protein genes, is phosphorylated in the Ser5 residue of the CTD, but is hypophosphorylated in Ser2. Using the same experimental approach, we show that the in vivo-depletion of FACT, a chromatin-related elongation factor, also produces a regulon-specific effect on the expression of the yeast genome. This work demonstrates that the regulation of transcription elongation is a widespread, gene class-dependent phenomenon that also affects housekeeping genes.
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain.
authors.forename: Vicent
authors.initials: V
authors.lastname: Pelechano
authors.forename: Silvia
authors.initials: S
authors.lastname: Jimeno-González
authors.forename: Alfonso
authors.initials: A
authors.lastname: Rodríguez-Gil
authors.forename: José
authors.initials: J
authors.lastname: García-Martínez
authors.forename: José E
authors.initials: JE
authors.lastname: Pérez-Ortín
authors.forename: Sebastián
authors.initials: S
authors.lastname: Chávez
mesh_terms: D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D016681:Genome, Fungal; D006609:High Mobility Group Proteins / Q000235:genetics / Q000378:metabolism; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D018085:Regulon; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; C541535:FACT protein, S cerevisiae; D006609:High Mobility Group Proteins; D029701:Saccharomyces cerevisiae Proteins; D035602:Transcriptional Elongation Factors; D012319:RNA Polymerase II
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