title: In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1-dependent transcription termination.
abstract: The Nrd1-Nab3-Sen1 (NNS) complex pathway is responsible for transcription termination of cryptic unstable transcripts and sn/snoRNAs. The NNS complex recognizes short motifs on the nascent RNA, but the presence of these sequences alone is not sufficient to define a functional terminator. We generated a homogeneous set of several hundreds of artificial, NNS-dependent terminators with an in vivo selection approach. Analysis of these terminators revealed novel and extended sequence determinants for transcription termination and NNS complex binding as well as supermotifs that are critical for termination. Biochemical and structural data revealed that affinity and specificity of RNA recognition by Nab3p relies on induced fit recognition implicating an α-helical extension of the RNA recognition motif. Interestingly, the same motifs can be recognized by the NNS or the mRNA termination complex depending on their position relative to the start of transcription, suggesting that they function as general transcriptional insulators to prevent interference between the non-coding and the coding yeast transcriptomes.
authors.affiliation: Centre de Génétique Moléculaire, Gif sur Yvette, Paris, France.
authors.forename: Odil
authors.initials: O
authors.lastname: Porrua
authors.forename: Fruzsina
authors.initials: F
authors.lastname: Hobor
authors.forename: Jocelyne
authors.initials: J
authors.lastname: Boulay
authors.forename: Karel
authors.initials: K
authors.lastname: Kubicek
authors.forename: Yves
authors.initials: Y
authors.lastname: D'Aubenton-Carafa
authors.forename: Rajani Kanth
authors.initials: RK
authors.lastname: Gudipati
authors.forename: Richard
authors.initials: R
authors.lastname: Stefl
authors.forename: Domenico
authors.initials: D
authors.lastname: Libri
mesh_terms: D020816:Amino Acid Motifs / Q000502:physiology; D000595:Amino Acid Sequence; D004265:DNA Helicases / Q000737:chemistry / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D008969:Molecular Sequence Data; D009687:Nuclear Proteins / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D020365:RNA Helicases / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D052156:SELEX Aptamer Technique; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism*; D061806:Transcription Termination, Genetic
chemical_list: C090564:NAB3 protein, S cerevisiae; C491211:NRD1 protein, S cerevisiae; D009687:Nuclear Proteins; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; C542347:SEN1 protein, S cerevisiae; D004265:DNA Helicases; D020365:RNA Helicases