Bioinformatic tools for analysis of <scp>CLIP</scp> ribonucleoprotein data

De, Supriyo; Gorospe, Myriam

doi:10.1002/wrna.1404

Cited by 10 publications

(7 citation statements)

References 87 publications

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“…To enable researchers to implement both of these approaches, RBP-Maps can run in two modes: --peak mode (which takes a bigbed file that describes significantly enriched regions of CLIP signal identified from any standard CLIP analysis toolkit), and --density mode (which accepts read densities formatted as two standard bigwig files, one for each strand). Conversion of read density into computationally identified peaks or clusters, using one of a variety of peak-calling algorithms, is a standard step of CLIP analysis (De and Gorospe 2017). The use of peaks provides two appealing benefits for simplified creation of splicing maps.…”

Section: Reads Versus Peaksmentioning

confidence: 99%

RBP-Maps enables robust generation of splicing regulatory maps

Yee

Pratt

Graveley

et al. 2018

RNA

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Alternative splicing of pre-messenger RNA transcripts enables the generation of multiple protein isoforms from the same gene locus, providing a major source of protein diversity in mammalian genomes. RNA binding proteins (RBPs) bind to RNA to control splice site choice and define which exons are included in the resulting mature RNA transcript. However, depending on where the RBPs bind relative to splice sites, they can activate or repress splice site usage. To explore this positionspecific regulation, in vivo binding sites identified by methods such as cross-linking and immunoprecipitation (CLIP) are integrated with alternative splicing events identified by RNA-seq or microarray. Merging these data sets enables the generation of a "splicing map," where CLIP signal relative to a merged meta-exon provides a simple summary of the position-specific effect of binding on splicing regulation. Here, we provide RBP-Maps, a software tool to simplify generation of these maps and enable researchers to rapidly query regulatory patterns of an RBP of interest. Further, we discuss various alternative approaches to generate such splicing maps, focusing on how decisions in construction (such as the use of peak versus read density, or whole-reads versus only single-nucleotide candidate crosslink positions) can affect the interpretation of these maps using example eCLIP data from the 150 RBPs profiled by the ENCODE consortium.Receive free email alerts when new articles cite this article -sign up in the box at the http://rnajournal.cshlp.org/subscriptions go to: RNA To subscribe to

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Section: Reads Versus Peaksmentioning

confidence: 99%

RBP-Maps enables robust generation of splicing regulatory maps

Yee

Pratt

Graveley

et al. 2018

RNA

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“…Many tools were developed for CLIP-seq peak calling (38). A typical peak calling process can be divided into two tasks (39).…”

Section: Peak Callingmentioning

confidence: 99%

Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions

Chen

Castro

Liu

et al. 2019

Methods

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RNA-binding proteins are important players in post-transcriptional regulation, such as modulating mRNA splicing, translation, and degradation under diverse biological settings. Identifying and characterizing the RNA substrates is a critical step in deciphering the function and molecular mechanisms of the target RNA-binding proteins. High-throughput sequencing of the RNA fragments isolated by crosslinking immunoprecipitation (CLIP-seq) is one of the standard techniques to identify the in vivo transcriptome-wide binding sites of the target RNA-binding protein. This method is widely used in functional and mechanistic characterizations of RNAbinding proteins. In this review, we provide several practical considerations on performing and analyzing CLIP-seq experiments. Particularly, we focus on how to perform CLIP-seq experiments on endogenous RNA-binding proteins. In addition, we provide a practical summary on how to choose and use computational pipelines from an increasing number of computational methods and packages that are available for analyzing the sequencing datasets from the CLIP-seq experiments. We hope these practical considerations will facilitate experimental biologists in performing and analyzing CLIP-seq experiment to obtain biologically relevant mechanistic insights.

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“…The comprehensive list of available software and websites has been recently reviewed in Ref. [161]. However, we are still far from having a comprehensive understanding of mechanisms of RNA biogenesis and its relevance in physiological and pathological conditions.…”

Section: Micrornas (Mirnas)mentioning

confidence: 99%

Mammalian Cis-Acting RNA Sequence Elements

Louis¹,

Sagarsky²

2018

Gene Expression and Regulation in Mammalian Cells - Transcription From General Aspects

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Cis-acting regulatory sequence elements are sequences contained in the 3 0 and 5 0 untranslated region, introns, or coding regions of precursor RNAs and mature mRNAs that are selectively recognized by a complementary set of one or more trans-acting factors to regulate posttranscriptional gene expression. This chapter focuses on mammalian cis-acting regulatory elements that had been recently discovered in different regions: pre-processed and mature. The chapter begins with an overview of two large networks of mRNAs that contain conserved AU-rich elements (AREs) or GU-rich elements (GREs), and their role in mammalian cell physiology. Other, less conserved, cisacting elements and their functional role in different steps of RNA maturation and metabolism will be discussed. The molecular characteristics of pathological cis-acting sequences that rose from gene mutations or transcriptional aberrations are briefly outlined, with the proposed approach to restore normal gene expression. Concise models of the function of posttranscriptional regulatory networks within different cellular compartments conclude this chapter.

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Bioinformatic tools for analysis of CLIP ribonucleoprotein data

Cited by 10 publications

References 87 publications

RBP-Maps enables robust generation of splicing regulatory maps

RBP-Maps enables robust generation of splicing regulatory maps

Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions

Mammalian Cis-Acting RNA Sequence Elements

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