title: The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.
abstract: In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3'/5' RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in both cases. We detected a subset of elongation-related factors that are important for maintaining the wild-type profiles of active transcription, including DSIF, Mediator, factors related to the methylation of histone H3-lysine 4, the Bur CDK and the RNA polymerase II subunit Rpb9. We conducted a more detailed investigation of the alterations caused by rpb9Delta to find that Rpb9 contributes to the intragenic profiles of active transcription by influencing the probability of arrest of RNA polymerase II.
authors.affiliation: Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Rodríguez-Gil
authors.forename: José
authors.initials: J
authors.lastname: García-Martínez
authors.forename: Vicent
authors.initials: V
authors.lastname: Pelechano
authors.forename: María de la Cruz
authors.initials: Mde L
authors.lastname: Muñoz-Centeno
authors.forename: Vincent
authors.initials: V
authors.lastname: Geli
authors.forename: José E
authors.initials: JE
authors.lastname: Pérez-Ortín
authors.forename: Sebastián
authors.initials: S
authors.lastname: Chávez
mesh_terms: D005800:Genes, Fungal; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D012319:RNA Polymerase II / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D014158:Transcription, Genetic; D035602:Transcriptional Elongation Factors / Q000235:genetics / Q000502:physiology*
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D035602:Transcriptional Elongation Factors; D012319:RNA Polymerase II; C509257:Rpb9 protein, S cerevisiae
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