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The technical support of Laura Barbado is acknowledged. This work was funded by Ministerio de Economia y Competitividad (BFU2017-84955-R) grant.

Analysis of institutional authors

Diaz-Lopez, IreneAuthorToribio, ReneAuthorVentoso, IvánAuthor

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November 23, 2020
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Mapping mRNA-18S rRNA Contacts Within Translation Initation Complex by Means of Reverse Transcriptase Termination Sites and RNAseq

Publicated to:Bio Protoc. 10 (16): e3713- - 2020-08-20 10(16), DOI: 10.21769/BioProtoc.3713

Authors: Diaz-Lopez, Irene; Toribio, Rene; Ventoso, Ivan;

Affiliations

‎ MRC Lab Mol Biol, Cambridge, England - Author
‎ Univ Autonoma Madrid UAM, Ctr Biol Mol Severo Ochoa CSIC UAM, Madrid, Spain - Author
‎ UPM INIA, Ctr Biotecnol & Genom Plantas, Madrid, Spain - Author

Abstract

The nucleotides involved in RNA-RNA interaction can be tagged by chemical- or UV-induced crosslinking, and further identified by classical or modern high throughput techniques. The contacts of mRNA with 18S rRNA that occur along the mRNA channel of 40S subunit have been mapped by site-specific UV crosslinking followed by reverse transcriptase termination sites (RTTS) using radioactive or fluorescent oligonucleotides. However, the sensitivity of this technique is restricted to the detection of those fragments that resulted from the most frequent crosslinkings. Here, we combined RTTS with RNAseq to map the mRNA-18S rRNA contacts with a much deeper resolution. Although aimed to detect the interaction of mRNA with the ES6S region of 18S rRNA, this technique can also be applied to map the interaction of mRNA with other non-coding RNA molecules (e.g., snRNAs, microRNAs and lncRNAs) during transcription, splicing or RNA-mediated postranscriptional regulation.

Keywords

reverse transcription stopribosomerna-rna interactionrnaseqsite-specific crosslinkingtranslation initiationMrnaReverse transcription stopRibosomeRna-rna interactionRnaseqSite-specific crosslinkingTranslation initiation

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Bio Protoc, Q4 Agency Scopus (SJR), its regional focus and specialization in Neuroscience (Miscellaneous), give it significant recognition in a specific niche of scientific knowledge at an international level.

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-22:

  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 2 (PlumX).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: United Kingdom.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (DIAZ LOPEZ, IRENE) .