A large-scale binding and functional map of human RNA-binding proteins
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Abstract
Many proteins regulate the expression of genes by binding to specific regions encoded in the genome 1 . 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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Linear sequence motifs alone are often insufficient to fully capture the binding specificities of RBPs, and other contextual features such as RNA secondary structure and surrounding base composition contribute to binding specificity.
“Previous studies have shown that linear sequence motifs alone are often insufficient to fully capture the binding specificities of RBPs, and other contextual features such as RNA secondary structure and surrounding base composition contribute to binding specificity (Dominguez et al. 2018; Nostrand et al. 2020).”
From ESRP2–microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation (2025) · cites this paper as Nostrand et al. 2020
The in vivo ESRP2-binding site determination with FLAG-ESRP2 eCLIP is accurate, as the identified UG-containing motifs match those identified in vitro by SELEX-seq and RNA bind-n-seq.
“Similar UG-containing sequence motifs for ESRP proteins have been identified in vitro by SELEX-seq (Dittmar et al. 2012) and RNA bind-n-seq (Nostrand et al. 2020), confirming the accuracy of our in vivo ESRP2-binding site determination with FLAG-ESRP2 eCLIP.”
From ESRP2–microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation (2025) · cites this paper as Nostrand et al. 2020
The ‘In vitro RBP binding motifs’ section reports using RNA Bind-N-Seq to identify motifs for many RBPs, and ‘In vitro specificity drives in vivo binding’ discusses comparisons with eCLIP. But searches for ESRP1, ESRP2 and UG-containing ESRP motifs found no passage identifying an ESRP motif or comparing it with FLAG-ESRP2 eCLIP, so our copy cannot verify the specific match claimed. (LLM, conf=0.72)
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- Authors
- Van Nostrand, E. L., Freese, P., Pratt, G. A., Wang, X., Wei, X., Xiao, R., Blue, S. M., Chen, J.-Y., Cody, N. A. L., Dominguez, D., Olson, S., Sundararaman, B., Zhan, L., Bazile, C., Bouvrette, L. P. B., Bergalet, J., Duff, M. O., Garcia, K. E., Gelboin-Burkhart, C., Hochman, M., Lambert, N. J., Li, H., McGurk, M. P., Nguyen, T. B., Palden, T., Rabano, I., Sathe, S., Stanton, R., Su, A., Wang, R., Yee, B. A., Zhou, B., Louie, A. L., Aigner, S., Fu, X.-D., Lécuyer, E., Burge, C. B., Graveley, B. R., & Yeo, G. W.
- Affiliations
- Massachusetts Institute of Technology (US)
- Montreal Clinical Research Institute (CA)
- UConn Health (US)
- University of California San Diego (US)
- Corresponding author
- Fu, Xiang-Dong
- Burge, Christopher B.
- Graveley, Brenton R.
- Yeo, Gene W.
- ORCID
- Van Nostrand, Eric L.
- Wang, Xiaofeng
- Xiao, Rui
- Blue, Steven M.
- Chen, Jia-Yu
- Olson, Sara
- Sundararaman, Balaji
- Zhan, Lijun
- Bazile, Cassandra
- Bouvrette, Louis Philip Benoit
- Duff, Michael O.
- Hochman, Myles
- McGurk, Michael P.
- Nguyen, Thai B.
- Rabano, Ines
- Sathe, Shashank
- Wang, Ruth
- Yee, Brian A.
- Zhou, Bing
- Aigner, Stefan
- Fu, Xiang-Dong
- Burge, Christopher B.
- Graveley, Brenton R.
- Yeo, Gene W.
- Venue
- Nature
- Published
- 2020-07-29
- Volume
- 583
- Issue
- 7818
- Pages
- 711-719
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7410833
- OpenAlex
- W3046003662
- Cited by
- 1,317
- References
- 94
- Citations by year
- 2026: 193 · 2025: 232 · 2024: 248 · 2023: 170 · 2022: 204 · 2021: 153 · 2020: 55 · 2019: 36 · 2018: 21 · 2017: 2 · 2016: 1 · 2012: 1
- FWCI
- 50.08
- Type
- journal article
- Language
- en
- Update notices
- correction (2021-01-05)
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Damon Runyon Cancer Research Foundation (DRG-2172-13)
- National Institutes of Health (HG009530)
- National Human Genome Research Institute (K99HG009530, R00HG009530, R01HG004659, HG009530, U41HG009889, U54HG007005)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- RNA-binding proteins, RBP binding sites, post-transcriptional regulation, splicing regulation, RNA stability, RNA localization, cleavage and polyadenylation, RNA editing, K562 cells, HepG2 cells, human transcriptome
- MeSH terms
- Base Sequence, Binding Sites, Cell Line, Chromatin, Female, Humans, Male, Protein Binding, RNA, Messenger, Substrate Specificity, RNA-Binding Proteins, Alternative Splicing, Databases, Genetic, Intracellular Space, Gene Knockdown Techniques, Transcriptome
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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