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

J 2012

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 et. al.

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

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

Genetics and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

Abstract

V originále

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

Citovat

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, 2012, vol. 31, No 19, p. 3935-3948. ISSN 0261-4189. Available from: https://dx.doi.org/10.1038/emboj.2012.237.

@article{988334,
   author = {PorruaandFuerte, Odil and Hóbor, Fruzsina and Boulay, Jocelyne and Kubíček, Karel and D’AubentonandCarafa, Yves and Gudipati, Rajani Kanth and Štefl, Richard and Libri, Domenico},
   article_location = {NEW YORK},
   article_number = {19},
   doi = {http://dx.doi.org/10.1038/emboj.2012.237},
   keywords = {cryptic unstable transcripts; transcription termination; Nrd1p-Nab3p-Sen1p complex; hidden transcription; transcriptional insulators},
   language = {eng},
   issn = {0261-4189},
   journal = {EMBO Journal},
   title = {In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1 dependent transcription termination},
   url = {http://www.nature.com/emboj/journal/v31/n19/abs/emboj2012237a.html},
   volume = {31},
   year = {2012}
}

TY  - JOUR
ID  - 988334
AU  - Porrua-Fuerte, Odil - Hóbor, Fruzsina - Boulay, Jocelyne - Kubíček, Karel - D’Aubenton-Carafa, Yves - Gudipati, Rajani Kanth - Štefl, Richard - Libri, Domenico
PY  - 2012
TI  - In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1 dependent transcription termination
JF  - EMBO Journal
VL  - 31
IS  - 19
SP  - 3935-3948
EP  - 3935-3948
PB  - NATURE PUBLISHING GROUP
SN  - 02614189
KW  - cryptic unstable transcripts
KW  - transcription termination
KW  - Nrd1p-Nab3p-Sen1p complex
KW  - hidden transcription
KW  - transcriptional insulators
UR  - http://www.nature.com/emboj/journal/v31/n19/abs/emboj2012237a.html
L2  - http://www.nature.com/emboj/journal/v31/n19/abs/emboj2012237a.html
N2  - 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.
ER  -

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. \textit{EMBO Journal}. NEW YORK: NATURE PUBLISHING GROUP, 2012, vol.~31, No~19, p.~3935-3948. ISSN~0261-4189. Available from: https://dx.doi.org/10.1038/emboj.2012.237.

Detailed Information on Publication Record