A large-scale binding and functional map of human RNA-binding proteins

Abstract

Article Methods Cell lines Cell lines were purchased from ATCC and were not formally authenticated, but confirmation of expected gene expression patterns were performed for RNA-seq and eCLIP experiments. Cell lines were routinely tested for mycoplasma contamination (MycoAlert, Lonza).

Expanded encyclopaedias of DNA elements in the human and mouse genomes

“…The RNA sequences and structures recognized by RBPs are encoded by the underlying genomic sequence, and thus represent a class of functional sequence elements not previously explored by ENCODE (Table 1). Using an enhanced crosslinking and immunoprecipitation assay (eCLIP) 23 , we identified the binding sites for 150 RBPs in two extensively assayed ENCODE cell lines, K562 and HepG2, and further validated the RNA targets recognized by each RBP by knocking down the RBP and performing RNA-seq 9 Table 2). We also developed an in vitro binding assay and applied it to 78 RBPs, demonstrating that the binding sites of most RBPs in K562 or HepG2 cells are consistent with their in vitro RNA sequence specificity 24 Table 3).…”

“…Across multiple data types, the increase in the scale of experimental data has provided new insights into genome organization and function, and catalysed new capabilities for deriving biological understandings and principles, as illustrated below and detailed in accompanying papers [7][8][9][10][11][12][13][14][15][16] . In summary, we:…”

“…• Describe an expansive new genomic compartment of DNA elements that encode recognition sites for RNA-binding proteins, providing new insights into post-transcriptional regulation 9 . • Deeply map the co-occupancy patterns of human transcription factors in reference cell types and connect these with key biological features of promoters and distal enhancers 10 .…”

Perspectives on ENCODE

“…An important part of ENCODE 3 is that the regulatory mapping efforts have now been integrated and synthesized into the first version of an encyclopedia, highlighting a registry of 0.9 million cCREs in human and 0.3 million cCREs in mouse. Details can be found in the accompanying ENCODE paper 8 and companion papers in this issue and other journals [9][10][11][12][13][14] .…”

DDX5 promotes oncogene C3 and FABP1 expressions and drives intestinal inflammation and tumorigenesis

“…Mechanistically, DDX proteins have two major modes of action. First, they can directly bind to specific RNA substrates, use ATP hydrolysis energy to unwind RNA duplexes, facilitate RNA annealing, and/or organize RNA-protein complex assembly (30,31,32,33). Second, DDXs can partner with transcription factors to modulate gene transcription (24,30,34,35,36,37,38,39,40).…”