A large-scale binding and functional map of human RNA-binding proteins
Eric L. Van Nostrand,Peter Freese,Gabriel A. Pratt,Xiaofeng Wang,Xintao Wei,Rui Xiao,Rui Xiao,Steven M. Blue,Jia-Yu Chen,Neal A.L. Cody,Daniel Dominguez,Sara Olson,Balaji Sundararaman,Lijun Zhan,Cassandra Bazile,Louis Philip Benoit Bouvrette,Julie Bergalet,Michael O. Duff,Keri E. Garcia,Chelsea Gelboin-Burkhart,Myles Hochman,Nicole J. Lambert,Hairi Li,Michael P. McGurk,Thai B. Nguyen,Tsultrim Palden,Ines Rabano,Shashank Sathe,Rebecca Stanton,Amanda Su,Ruth Wang,Brian A. Yee,Bing Zhou,Ashley L. Louie,Stefan Aigner,Xiang-Dong Fu,Eric Lécuyer,Eric Lécuyer,Christopher B. Burge,Brenton R. Graveley,Gene W. Yeo +40 more
TL;DR: The spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization are described.
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Abstract: Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
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