title: Defects in the NC2 repressor affect both canonical and non-coding RNA polymerase II transcription initiation in yeast.
abstract: BACKGROUND
  The formation of the pre-initiation complex in eukaryotic genes is a key step in transcription initiation. The TATA-binding protein (TBP) is a universal component of all pre-initiation complexes for all kinds of RNA polymerase II (RNA pol II) genes, including those with a TATA or a TATA-like element, both those that encode proteins and those that transcribe non-coding RNAs. Mot1 and the negative cofactor 2 (NC2) complex are regulators of TBP, and it has been shown that depletion of these factors in yeast leads to defects in the control of transcription initiation that alter cryptic transcription levels in selected yeast loci.
  
  
  RESULTS
  In order to cast light on the molecular functions of NC2, we performed genome-wide studies in conditional mutants in yeast NC2 essential subunits Ydr1 and Bur6. Our analyses show a generally increased level of cryptic transcription in all kinds of genes upon depletion of NC2 subunits, and that each kind of gene (canonical or ncRNAs, TATA or TATA-like) shows some differences in the cryptic transcription pattern for each NC2 mutant.
  
  
  CONCLUSIONS
  We conclude that NC2 plays a general role in transcription initiation in RNA polymerase II genes that is related with its known TBP interchange function from free to promoter bound states. Therefore, loss of the NC2 function provokes increases in cryptic transcription throughout the yeast genome. Our results also suggest functional differences between NC2 subunits Ydr1 and Bur6.
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain. ngomez@mrc-lmb.cam.ac.uk.|Present address: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. ngomez@mrc-lmb.cam.ac.uk.
authors.forename: Natalia
authors.initials: N
authors.lastname: Gómez-Navarro
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain. antonio.jordan@su.se.|Present address: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, SE-106 91, Sweden. antonio.jordan@su.se.
authors.forename: Antonio
authors.initials: A
authors.lastname: Jordán-Pla
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain. francisco.estruch@uv.es.
authors.forename: Francisco
authors.initials: F
authors.lastname: Estruch
authors.affiliation: Departamento de Bioquímica y Biología Molecular, Facultad de Biológicas and ERI Biotecmed, Universitat de València, Dr. Moliner 50, E-46100, Burjassot, Valencia, Spain. jose.e.perez@uv.es.
authors.forename: José
authors.initials: J
authors.lastname: E Pérez-Ortín
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D010750:Phosphoproteins / Q000235:genetics*; D012319:RNA Polymerase II / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D035181:TATA-Box Binding Protein / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D018528:ATP-Binding Cassette Transporters; C403190:BUR6 protein, S cerevisiae; C092438:PDR5 protein, S cerevisiae; D010750:Phosphoproteins; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; C075995:down-regulator of transcription 1; D012319:RNA Polymerase II