A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication.

Nucleic Acids Research
Andrew TuplinDavid J Evans

Abstract

The RNA structure and long-range interactions of the SL9266 cis-acting replication element located within the NS5B coding region of hepatitis C virus (HCV) were determined using selective 2'-hydroxyl acylation analysed by primer extension. Marked differences were found in the long-range interactions of SL9266 when the two widely used genotype 2a JFH-1 (HCVcc) and genotype 1b Con1b sub-genomic replicon systems were compared. In both genomes, there was evidence for interaction of the sub-terminal bulge loop of SL9266 and sequences around nucleotide 9110, though the replication phenotype of genomes bearing mutations that disrupted this interaction was fundamentally different. In contrast, a 'kissing loop' interaction between the terminal loop of SL9266 and sequences in the 3'-untranslated X-tail was only detectable in JFH-1-based genomes. In the latter, where both long-range interactions are present, they were independent, implying that SL9266 forms the core of an extended pseudoknot. The presence of the 'kissing loop' interaction inhibited the formation of SL9571 in the 3'-X-tail, an RNA structure implicated in genome replication. We propose that, SL9266 may contribute a switch function that modulates the mutually incompatible tr...Continue Reading

References

Oct 29, 1996·Proceedings of the National Academy of Sciences of the United States of America·R Giegé
Aug 8, 1998·Genes & Development·A V Gamarnik, R Andino
Jul 15, 2000·Seminars in Liver Disease·A Wasley, M J Alter
Dec 9, 2000·Science·K J BlightC M Rice
Jan 11, 2001·Journal of Virology·V LohmannR Bartenschlager
Mar 22, 2002·Journal of Virology·Thomas PietschmannRalf Bartenschlager
Oct 23, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jens BukhRalf Bartenschlager
Feb 14, 2003·Journal of Virology·Volker LohmannRalf Bartenschlager
Mar 1, 2003·Journal of Virology·MinKyung Yi, Stanley M Lemon
Nov 9, 2004·Advances in Virus Research·Ralf BartenschlagerThomas Pietschmann
Jun 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jin ZhongFrancis V Chisari
Jun 11, 2005·Science·Brett D LindenbachCharles M Rice
Oct 24, 2006·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Carla KuikenUNKNOWN Los Alamos HIV Database Group
Feb 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Laura K McMullanCharles M Rice
Oct 19, 2007·Journal of Virology·Shihyun You, Charles M Rice
Aug 21, 2008·Methods in Molecular Biology·Nicholas R Markham, Michael Zuker
Jul 17, 2009·RNA·Cristina Romero-López, Alfredo Berzal-Herranz
Sep 29, 2009·Biochimica Et Biophysica Acta·Ying LiuAniko V Paul
Oct 21, 2010·Seminars in Liver Disease·Marion Poenisch, Ralf Bartenschlager

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Citations

Sep 21, 2013·Nucleic Acids Research·Cristina Romero-LópezAlfredo Berzal-Herranz
Jun 17, 2014·Nature Reviews. Microbiology·Beth L Nicholson, K Andrew White
Sep 15, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alba Fernández-SanlésAlfredo Berzal-Herranz
Aug 29, 2013·Reviews in Medical Virology·Cristina Romero-López, Alfredo Berzal-Herranz
Mar 22, 2016·Virology·Guillaume N FichesMichael R Beard
Sep 14, 2012·The Journal of General Virology·Brendan A PalmerLiam J Fanning
Sep 19, 2015·Nucleic Acids Research·Peter AshtonK Andrew White
Aug 11, 2015·Nature Reviews. Microbiology·You LiStanley M Lemon
Mar 31, 2015·Cellular and Molecular Life Sciences : CMLS·Cyril MasanteCarmelo Di Primo
Jan 13, 2015·Virus Research·Selena M SaganPeter Sarnow
Jun 12, 2016·Bioinformatics·Markus Fricke, Manja Marz
Feb 7, 2018·Nucleic Acids Research·Ángel Cantero-Camacho, José Gallego
Jan 10, 2018·Frontiers in Molecular Biosciences·Li-Zhen SunShi-Jie Chen
Apr 4, 2019·Nucleic Acids Research·Jasmin ChahalSelena M Sagan
Nov 7, 2019·RNA·Jesús Castillo-MartínezJosé Gallego
Apr 2, 2020·International Journal of Molecular Sciences·Michael Niepmann, Gesche K Gerresheim
Aug 14, 2020·Nucleic Acids Research·Tamari Chkuaseli, K Andrew White
Feb 25, 2017·Scientific Reports·Cristina Romero-LópezAlfredo Berzal-Herranz
Feb 10, 2017·Nucleic Acids Research·Rosa Diaz-ToledanoEncarnacion Martinez-Salas
Mar 23, 2018·Frontiers in Microbiology·Guoli Shi, Tetsuro Suzuki
Jul 28, 2019·Nucleic Acids Research·Catherine KendallAndrew Tuplin
Feb 27, 2020·International Journal of Molecular Sciences·Cristina Romero-López, Alfredo Berzal-Herranz
Nov 23, 2017·Frontiers in Microbiology·Cristina Romero-López, Alfredo Berzal-Herranz
Mar 16, 2019·Pharmaceuticals·Alfredo Berzal-HerranzSara Ramos-Lorente
Aug 21, 2018·World Journal of Gastroenterology : WJG·Mariola Dutkiewicz, Jerzy Ciesiołka
Nov 2, 2018·Scientific Reports·Cristina Romero-LópezAlfredo Berzal-Herranz
Mar 30, 2018·Frontiers in Microbiology·Michael NiepmannOliver Rossbach
Apr 14, 2018·Chemical Reviews·Nicholas J BarrowsMariano A Garcia-Blanco
Aug 14, 2021·Proceedings of the National Academy of Sciences of the United States of America·Jasmin ChahalSelena M Sagan

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Datasets Mentioned

BETA
AF011753
SL9266

Methods Mentioned

BETA
dissection
NMR
electrophoresis
transfection
chemical modification
PCR
but

Software Mentioned

UNAfold
MFOLD
TotalLab
SHAPE

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