ArticleNucleic acids research2010
'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- A CsrA-Binding,Journal of bacteriology · 2019Article
- Pseudouridines on Trypanosoma brucei spliceosomal small nuclear RNAs and their implication for RNA and protein interactions.Nucleic acids research · 2019Article
- Small nucleolar RNAs controlling rRNA processing in Trypanosoma brucei.Nucleic acids research · 2019Article
- RNA interactomics: recent advances and remaining challenges.F1000Research · 2018Review
- Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution.Journal of molecular evolution · 2017Article
- Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation.ACS chemical biology · 2016Review
- RNAIII of the Staphylococcus aureus agr system activates global regulator MgrA by stabilizing mRNA.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The Streptococcus mutans irvA gene encodes a trans-acting riboregulatory mRNA.Molecular cell · 2015Article
- Genome-wide analysis of small nucleolar RNAs of Leishmania major reveals a rich repertoire of RNAs involved in modification and processing of rRNA.RNA biology · 2015Article
- The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability.Nucleic acids research · 2013Article
- RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs.Nucleic acids research · 2012Article
- Small nucleolar RNA interference in Trypanosoma brucei: mechanism and utilization for elucidating the function of snoRNAs.Nucleic acids research · 2010Article
- Residues in SRP9/14 essential for elongation arrest activity of the signal recognition particle define a positively charged functional domain on one side of the protein.RNA (New York, N.Y.) · 2010Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this study we describe a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed 'RNA walk'. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR or real-time PCR. Domains carrying the cross-linked adducts fail to efficiently amplify by PCR compared with non-cross-linked domains. This method was calibrated and used to study the interaction between a special tRNA-like molecule (sRNA-85) that is part of the trypanosome signal recognition particle (SRP) complex and the ribosome. Four contact sites between sRNA-85 and rRNA were identified by 'RNA walk' and were further fine-mapped by primer extension. Two of the contact sites are expected; one contact site mimics the interaction of the mammalian Alu domain of SRP with the ribosome and the other contact sites include a canonical tRNA interaction. The two other cross-linked sites could not be predicted. We propose that 'RNA walk, is a generic method to map target RNA small RNAs interactions in vivo.
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