Mutational interference mapping experiment (MIME) for studying RNA structure and function

Smyth, Redmond P., Despons, Laurence, Huili, Gong, Bernacchi, Serena, Hijnen, Marcel, Mak, Johnson, Jossinet, Fabrice, Weixi, Li, Paillart, Jean-Christophe, von Kleist, Max and Marquet, Roland 2015, Mutational interference mapping experiment (MIME) for studying RNA structure and function, Nature methods, vol. 12, no. 9, pp. 866-872, doi: 10.1038/nmeth.3490.

Attached Files
Name Description MIMEType Size Downloads

Title Mutational interference mapping experiment (MIME) for studying RNA structure and function
Author(s) Smyth, Redmond P.
Despons, Laurence
Huili, Gong
Bernacchi, Serena
Hijnen, Marcel
Mak, JohnsonORCID iD for Mak, Johnson
Jossinet, Fabrice
Weixi, Li
Paillart, Jean-Christophe
von Kleist, Max
Marquet, Roland
Journal name Nature methods
Volume number 12
Issue number 9
Start page 866
End page 872
Total pages 7
Publisher Nature Publishing Group
Place of publication New York, NY
Publication date 2015-09
ISSN 1548-7105
Keyword(s) Science & Technology
Life Sciences & Biomedicine
Biochemical Research Methods
Biochemistry & Molecular Biology
Summary RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.
Language eng
DOI 10.1038/nmeth.3490
Field of Research 110804 Medical Virology
Socio Economic Objective 920109 Infectious Diseases
HERDC Research category C1 Refereed article in a scholarly journal
Grant ID NHMRC 1025273
NHMRC 543107
ARC FT100100297
Copyright notice ©2015, Nature Publishing Group
Persistent URL

Document type: Journal Article
Collection: School of Medicine
Connect to link resolver
Unless expressly stated otherwise, the copyright for items in DRO is owned by the author, with all rights reserved.

Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 12 times in TR Web of Science
Scopus Citation Count Cited 15 times in Scopus
Google Scholar Search Google Scholar
Access Statistics: 210 Abstract Views, 1 File Downloads  -  Detailed Statistics
Created: Thu, 22 Oct 2015, 10:08:13 EST

Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact