2020
DOI: 10.1038/s41586-020-2077-3
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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).

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Cited by 890 publications
(885 citation statements)
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References 60 publications
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“…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).…”
Section: Rna-binding Proteinsmentioning
confidence: 99%
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“…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).…”
Section: Rna-binding Proteinsmentioning
confidence: 99%
“…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:…”
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confidence: 99%
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“…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] .…”
mentioning
confidence: 99%
“…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).…”
Section: Introductionmentioning
confidence: 99%