Open Access
Nature, volume 583, issue 7818, pages 711-719
A large-scale binding and functional map of human RNA-binding proteins
Van Nostrand Eric L.
1, 2
,
Freese Peter
3
,
Pratt Gabriel A
1, 2, 4
,
Wang Xiaofeng
5
,
Wei Xintao
6
,
Xiao Rui
1, 2, 7
,
Blue Steven M
1, 2
,
Chen Jia Yu
1, 2
,
Cody Neal A L
5
,
DOMÍNGUEZ DANIEL
8
,
Olson Sara
6
,
Sundararaman Balaji
1, 2
,
Zhan Lijun
6
,
Bazile Cassandra
8
,
Bouvrette Louis Philip Benoit
5, 9
,
Bergalet Julie
5
,
Duff Michael O
6
,
Garcia Keri E
1, 2
,
Gelboin Burkhart Chelsea
1, 2
,
Hochman Myles
8
,
Lambert Nicole J
8
,
Li Hairi
1, 2
,
Mcgurk Michael P
8
,
Nguyen Thai B.
1, 2
,
Palden Tsultrim
8, 10
,
Rabano Ines
1, 2
,
Sathe Shashank
1, 2
,
Stanton Rebecca
1, 2
,
Su Amanda
8
,
Wang Ruth
1, 2
,
Yee Brian A
1, 2
,
Zhou Bing
1, 2
,
Louie Ashley L
1, 2
,
Aigner Stefan
1, 2
,
Fu Xiang-Dong
1, 2
,
Lécuyer Éric
5, 9, 11
,
Burge Christopher B.
3, 8, 10
,
Graveley Brenton R
6
,
Yeo Gene W.
1, 2, 4
1
Institute for Genomic Medicine, University of California San Diego, La Jolla, USA
|
2
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, USA
|
3
4
Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, USA
|
5
Institut de recherches cliniques de Montréal (IRCM), Montreal, Canada
|
6
Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, USA
|
9
Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Canada
|
11
Division of Experimental Medicine, McGill University, Montreal, Canada
|
Publication type: Journal Article
Publication date: 2020-07-29
PubMed ID:
32728246
Multidisciplinary
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. A combination of five assays is used to produce a catalogue of RNA elements to which RNA-binding proteins bind in human cells.
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Van Nostrand E. L. et al. A large-scale binding and functional map of human RNA-binding proteins // Nature. 2020. Vol. 583. No. 7818. pp. 711-719.
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Van Nostrand E. L. et al. A large-scale binding and functional map of human RNA-binding proteins // Nature. 2020. Vol. 583. No. 7818. pp. 711-719.
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TY - JOUR
DO - 10.1038/s41586-020-2077-3
UR - https://doi.org/10.1038%2Fs41586-020-2077-3
TI - A large-scale binding and functional map of human RNA-binding proteins
T2 - Nature
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 - DOMÍNGUEZ, 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, Éric
AU - Burge, Christopher B.
AU - Graveley, Brenton R
AU - Yeo, Gene W.
PY - 2020
DA - 2020/07/29 00:00:00
PB - Springer Nature
SP - 711-719
IS - 7818
VL - 583
PMID - 32728246
SN - 0028-0836
SN - 1476-4687
ER -
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@article{2020_Van Nostrand,
author = {Eric L. Van Nostrand and Peter Freese and Gabriel A Pratt and Xiaofeng Wang and Xintao Wei and Rui Xiao and Steven M Blue and Jia Yu Chen and Neal A L Cody and DANIEL DOMÍNGUEZ and Sara Olson and Balaji Sundararaman and Lijun Zhan and Cassandra Bazile and Louis Philip Benoit Bouvrette and Julie Bergalet and Michael O Duff and Keri E Garcia and Chelsea Gelboin Burkhart and Myles Hochman and Nicole J Lambert and Hairi Li and Michael P Mcgurk and B. Nguyen Thai and Tsultrim Palden and Ines Rabano and Shashank Sathe and Rebecca Stanton and Amanda Su and Ruth Wang and Brian A Yee and Bing Zhou and Ashley L Louie and Stefan Aigner and Xiang-Dong Fu and Éric Lécuyer and Christopher B. Burge and Brenton R Graveley and Gene W. Yeo},
title = {A large-scale binding and functional map of human RNA-binding proteins},
journal = {Nature},
year = {2020},
volume = {583},
publisher = {Springer Nature},
month = {jul},
url = {https://doi.org/10.1038%2Fs41586-020-2077-3},
number = {7818},
pages = {711--719},
doi = {10.1038/s41586-020-2077-3}
}
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Van Nostrand, Eric L., et al. “A large-scale binding and functional map of human RNA-binding proteins.” Nature, vol. 583, no. 7818, Jul. 2020, pp. 711-719. https://doi.org/10.1038%2Fs41586-020-2077-3.