title: Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.
abstract: The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution following a new biotin-based genomic run-on (BioGRO) technique. Compared with conventional profiling with chromatin immunoprecipitation, the analysis of the BioGRO profiles in Saccharomyces cerevisiae shows that RNA polymerase II has unique activity profiles at both gene ends, which are highly dependent on positioned nucleosomes. This is the first demonstration of the in vivo influence of positioned nucleosomes on transcription elongation. The particular features at the 5' end and around the polyadenylation site indicate that this polymerase undergoes extensive specific-activity regulation in the initial and final transcription elongation phases. The genes encoding for ribosomal proteins show distinctive features at both ends. BioGRO also provides the first nascentome analysis for RNA polymerase III, which indicates that transcription of tRNA genes is poorly regulated at the individual copy level. The present study provides a novel perspective of the transcription cycle that incorporates inactivation/reactivation as an important aspect of RNA polymerase dynamics.
authors.affiliation: Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Jordán-Pla
authors.affiliation: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Ishaan
authors.identifier: http://orcid.org/0000-0002-2595-3049
authors.initials: I
authors.lastname: Gupta
authors.affiliation: Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain.
authors.forename: Lola
authors.initials: L
authors.lastname: de Miguel-Jiménez
authors.affiliation: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA.
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.affiliation: Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain.
authors.forename: Sebastián
authors.initials: S
authors.lastname: Chávez
authors.affiliation: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Vicent
authors.initials: V
authors.lastname: Pelechano
authors.affiliation: Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain jose.e.perez@uv.es.
authors.forename: José E
authors.initials: JE
authors.lastname: Pérez-Ortín
mesh_terms: D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D009707:Nucleosomes / Q000378:metabolism*; D012319:RNA Polymerase II / Q000378:metabolism*; D012320:RNA Polymerase III / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D061805:Transcription Elongation, Genetic; D061806:Transcription Termination, Genetic; D014158:Transcription, Genetic
chemical_list: D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II; D012320:RNA Polymerase III