Work

Bioinformatic tools for analysis of CLIP ribonucleoprotein data

Year: 2016

Type: review

Abstract: Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying. Here, we focus on state-of-the-art molecular biology techniques that employ crosslinking and immunoprecipitation (CLIP) of an RBP to study and map RNP interactions. We review the different software tools and databases available to analyze the most widely used CLIP methods, HITS-CLIP, PAR-CLIP, and iCLIP. WIREs RNA 2017, 8:e1404. doi: 10.1002/wrna.1404 For further resources related to this article, please visit the WIREs website.

Source: Wiley Interdisciplinary Reviews - RNA

DOI: 10.1002/wrna.1404

Authors: Supriyo De, Myriam Gorospe

Institutions: National Institutes of Health, National Institute on Aging

Language: English

Topic: RNA Research and Splicing

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Institutes of Health, National Institute on Aging

Award: Influence of Post-transcriptional Gene Regulation on Cell Senescence and Aging