Analysis of sequencing data for probing RNA secondary structures and protein–RNA binding in studying posttranscriptional regulations
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AbstractHigh-throughput sequencing has been used to study posttranscriptional regulations, where the identification of protein–RNA binding is a major and fast-developing sub-area, which is in turn benefited by the sequencing methods for whole-transcriptome probing of RNA secondary structures. In the study of RNA secondary structures using high-throughput sequencing, bases are modified or cleaved according to their structural features, which alter the resulting composition of sequencing reads. In the study of protein–RNA binding, methods have been proposed to immuno-precipitate (IP) protein-bound RNA transcripts in vitro or in vivo. By sequencing these transcripts, the protein–RNA interactions and the binding locations can be identified. For both types of data, read counts are affected by a combination of confounding factors, including expression levels of transcripts, sequence biases, mapping errors and the probing or IP efficiency of the experimental protocols. Careful processing of the sequencing data and proper extraction of important features are fundamentally important to a successful analysis. Here we review and compare different experimental methods for probing RNA secondary structures and binding sites of RNA-binding proteins (RBPs), and the computational methods proposed for analyzing the corresponding sequencing data. We suggest how these two types of data should be integrated to study the structural properties of RBP binding sites as a systematic way to better understand posttranscriptional regulations.
All Author(s) ListXihao Hu, Yang Wu, Zhi John Lu, Kevin Y. Yip
Journal nameBriefings in Bioinformatics
Year2016
Month11
Volume Number17
Issue Number6
Pages1032 - 1043
ISSN1467-5463
eISSN1477-4054
LanguagesEnglish-United Kingdom

Last updated on 2021-23-09 at 01:00