A large-scale binding and functional map of human RNA-binding proteins (2024)

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., ... Yeo, G. W. (2020). A large-scale binding and functional map of human RNA-binding proteins. Nature, 583(7818), 711-719. https://doi.org/10.1038/s41586-020-2077-3

Van Nostrand, Eric L. ; Freese, Peter ; Pratt, Gabriel A. et al. / A large-scale binding and functional map of human RNA-binding proteins. In: Nature. 2020 ; Vol. 583, No. 7818. pp. 711-719.

@article{a450c5426e3742a59aa88fea654d9180,

title = "A large-scale binding and functional map of human RNA-binding proteins",

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.",

author = "{Van Nostrand}, {Eric L.} and Peter Freese and Pratt, {Gabriel A.} and Xiaofeng Wang and Xintao Wei and Rui Xiao and Blue, {Steven M.} and Chen, {Jia Yu} and Cody, {Neal A.L.} and Daniel Dominguez and Sara Olson and Balaji Sundararaman and Lijun Zhan and Cassandra Bazile and Bouvrette, {Louis Philip Benoit} and Julie Bergalet and Duff, {Michael O.} and Garcia, {Keri E.} and Chelsea Gelboin-Burkhart and Myles Hochman and Lambert, {Nicole J.} and Hairi Li and McGurk, {Michael P.} and Nguyen, {Thai B.} and Tsultrim Palden and Ines Rabano and Shashank Sathe and Rebecca Stanton and Amanda Su and Ruth Wang and Yee, {Brian A.} and Bing Zhou and Louie, {Ashley L.} and Stefan Aigner and Fu, {Xiang Dong} and Eric L{\'e}cuyer and Burge, {Christopher B.} and Graveley, {Brenton R.} and Yeo, {Gene W.}",

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = jul,

day = "30",

doi = "10.1038/s41586-020-2077-3",

language = "English",

volume = "583",

pages = "711--719",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

number = "7818",

}

A large-scale binding and functional map of human RNA-binding proteins. / Van Nostrand, Eric L.; Freese, Peter; Pratt, Gabriel A. et al.
In: Nature, Vol. 583, No. 7818, 30.07.2020, p. 711-719.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - A large-scale binding and functional map of human RNA-binding proteins

AU - Van Nostrand, Eric L.

AU - Freese, Peter

AU - Pratt, Gabriel A.

AU - Wang, Xiaofeng

AU - Wei, Xintao

AU - Xiao, Rui

AU - Blue, Steven M.

AU - Chen, Jia Yu

AU - Cody, Neal A.L.

AU - Dominguez, Daniel

AU - Olson, Sara

AU - Sundararaman, Balaji

AU - Zhan, Lijun

AU - Bazile, Cassandra

AU - Bouvrette, Louis Philip Benoit

AU - Bergalet, Julie

AU - Duff, Michael O.

AU - Garcia, Keri E.

AU - Gelboin-Burkhart, Chelsea

AU - Hochman, Myles

AU - Lambert, Nicole J.

AU - Li, Hairi

AU - McGurk, Michael P.

AU - Nguyen, Thai B.

AU - Palden, Tsultrim

AU - Rabano, Ines

AU - Sathe, Shashank

AU - Stanton, Rebecca

AU - Su, Amanda

AU - Wang, Ruth

AU - Yee, Brian A.

AU - Zhou, Bing

AU - Louie, Ashley L.

AU - Aigner, Stefan

AU - Fu, Xiang Dong

AU - Lécuyer, Eric

AU - Burge, Christopher B.

AU - Graveley, Brenton R.

AU - Yeo, Gene W.

N1 - Publisher Copyright:© 2020, The Author(s).

PY - 2020/7/30

Y1 - 2020/7/30

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85088711364&partnerID=8YFLogxK

U2 - 10.1038/s41586-020-2077-3

DO - 10.1038/s41586-020-2077-3

M3 - Article

C2 - 32728246

AN - SCOPUS:85088711364

SN - 0028-0836

VL - 583

SP - 711

EP - 719

JO - Nature

JF - Nature

IS - 7818

ER -

Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R et al. A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020 Jul 30;583(7818):711-719. doi: 10.1038/s41586-020-2077-3