In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1 dependent transcription termination

PORRUA-FUERTE, Odil, Fruzsina HÓBOR, Jocelyne BOULAY, Karel KUBÍČEK, Yves D’AUBENTON-CARAFA, Rajani Kanth GUDIPATI, Richard ŠTEFL and Domenico LIBRI. In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1 dependent transcription termination. EMBO Journal. NEW YORK: NATURE PUBLISHING GROUP, vol. 31, No 19, p. 3935-3948. ISSN 0261-4189. doi:10.1038/emboj.2012.237. 2012.

Basic information

• Original name: In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1 dependent transcription termination
• Authors: PORRUA-FUERTE, Odil (724 Spain), Fruzsina HÓBOR (348 Hungary, belonging to the institution), Jocelyne BOULAY (250 France), Karel KUBÍČEK (203 Czech Republic, belonging to the institution), Yves D’AUBENTON-CARAFA (250 France), Rajani Kanth GUDIPATI (250 France), Richard ŠTEFL (203 Czech Republic, belonging to the institution) and Domenico LIBRI (250 France, guarantor).
• Edition: EMBO Journal, NEW YORK, NATURE PUBLISHING GROUP, 2012, 0261-4189.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: Genetics and molecular biology
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 9.822
• RIV identification code: RIV/00216224:14740/12:00057509
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1038/emboj.2012.237
• UT WoS: 000309656600015
• Keywords in English: cryptic unstable transcripts; transcription termination; Nrd1p-Nab3p-Sen1p complex; hidden transcription; transcriptional insulators
• Tags: ok, rivok
• Tags: International impact, Reviewed

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 a-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.

Links

• ED1.1.00/02.0068, research and development project: Name: CEITEC - central european institute of technology
• GAP305/10/1490, research and development project: Name: Strukturní podstata ukončení transkripce nezávislé na poly(A) signálu

Investor: Czech Science Foundation

• GBP305/12/G034, research and development project: Name: Centrum biologie RNA