2016
DOI: 10.1016/j.molcel.2016.02.012
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Resources for the Comprehensive Discovery of Functional RNA Elements

Abstract: Summary Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated reposito… Show more

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Cited by 128 publications
(122 citation statements)
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“…First, we developed a list of 1787 human annotated RBPs by combining the list of 1072 by Sundararaman et al (Sundararaman et al, 2016) and 1542 by Gerstberger et al (Gerstberger et al, 2014) (Table S3). Next, we generated “neighborhoods” for all proteins in the human BioPlex PPI dataset, which consists of dozens of thousands of interactions (Huttlin et al, 2015).…”
Section: Resultsmentioning
confidence: 99%
“…First, we developed a list of 1787 human annotated RBPs by combining the list of 1072 by Sundararaman et al (Sundararaman et al, 2016) and 1542 by Gerstberger et al (Gerstberger et al, 2014) (Table S3). Next, we generated “neighborhoods” for all proteins in the human BioPlex PPI dataset, which consists of dozens of thousands of interactions (Huttlin et al, 2015).…”
Section: Resultsmentioning
confidence: 99%
“…Nearly 50% of these RBPs are involved in mRNA metabolism and intriguingly; they are amongst the most abundant RBPs in the cell. The Encyclopedia of DNA Elements (ENCODE) project is employing next-generation sequencing methods to generate detailed information about the extent and impact of individual RBPs on gene expression in model organisms and human cells [118]. Further intersection of these genomics and large-scale metabolomics datasets must probe which RBPs have direct roles in regulating energy homeostasis and beyond.…”
Section: Discussionmentioning
confidence: 99%
“…It should also be kept in mind that not only do RNAs fold into specific secondary and tertiary structures, but most RNAs are associated with RNA binding proteins in vivo. An exciting avenue of future analysis will be integrating large-scale RNA-protein interaction datasets, such as those being generated in the ENCODE project (Sundararaman et al, 2016; Van Nostrand et al, 2016), with these RNA structure datasets. Such analyses may be able to provide insight into the packaging and structure of RNPs in eukaryotic cells and therefore how RNP structure may impact function.…”
Section: New Methods To Identify Rna Pairs In Vivomentioning
confidence: 99%