title: The evolutionarily conserved Pol II flap loop contributes to proper transcription termination on short yeast genes.
abstract: Current models of transcription termination factor recruitment to the RNA polymerase II (Pol II) transcription complex rely exclusively on the direct interaction between the termination factor and phosphorylated isoforms of the Pol II C-terminal domain (CTD). Here, we report that the Pol II flap loop is needed for physical interaction of Pol II with the Pcf11/Clp1 subcomplex of cleavage factor IA (CF IA), which functions in both 3? end processing and Pol II termination, and for proper termination of short RNAs in vitro and in vivo. Deletion of the flap loop reduces the in vivo interaction of Pol II with CF IA but increases the association of Nrd1 during stages of the transcription cycle when the CTD is predominantly Ser5 phosphorylated. We propose a model in which the flap loop coordinates a binding equilibrium between the competing termination factors Pcf11 and Nrd1 to Pol II during termination of short RNA synthesis.
authors.affiliation: Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA.
authors.forename: Erika
authors.initials: E
authors.lastname: Pearson
authors.affiliation: Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA. Electronic address: claire.moore@tufts.edu.
authors.forename: Claire
authors.initials: C
authors.lastname: Moore
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D021901:DNA, Intergenic; D019143:Evolution, Molecular; D005800:Genes, Fungal; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010766:Phosphorylation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012319:RNA Polymerase II / Q000737:chemistry* / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism*; D017384:Sequence Deletion; D013329:Structure-Activity Relationship; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D012333:RNA, Messenger; D020537:RNA, Small Nucleolar; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II; C580821:RPB2 protein, S cerevisiae