![]() ![]() ![]() ![]() b, Example IP–western image for DCP1B IP success in K562 cells during initial IP tests performed without enzymatic steps (left) and IP failure in K562 cells during eCLIP experiments (right). Inputs were taken by sampling 2% of one of the two biosamples before IP. A combination of five assays is used to produce a catalogue of RNA elements to which RNA-binding proteins bind in human cells.Įxperimental quality assessment of eCLIP assaysĪ, Model of ENCODE eCLIP experiments. 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. 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. 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 mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. 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. 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. Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. ![]()
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