Nature, volume 582, issue 7812, pages 432-437
RIC-seq for global in situ profiling of RNA–RNA spatial interactions
Cai Zhaokui
1, 2
,
Cao Changchang
1
,
Lei Ji
1
,
Rong Ye
1, 2
,
Wang Di
1, 2
,
Xia Cong
3
,
Wang Sui
1, 2
,
Du Zongchang
1, 2
,
Hu Naijing
1, 2
,
YU XIAOHUA
1
,
Chen Juan
1
,
Wang Lei
1, 4
,
Yang Xianguang
3
,
He Shunmin
1
,
Xue Yuanchao
1, 2
1
Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
|
4
College of life sciences, Xinyang Normal University, Xinyang, China
|
Publication type: Journal Article
Publication date: 2020-05-06
Multidisciplinary
Abstract
Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA–RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans -interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L —a super-enhancer hub RNA—interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA. RNA in situ conformation sequencing (RIC-seq) enables the generation of three-dimensional interaction maps of RNA in cells, which sheds light on the interactions and regulatory functions of RNA.
Citations by journals
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1 publication, 0.6%
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1 publication, 0.6%
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1 publication, 0.6%
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Life
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1 publication, 0.6%
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Citations by publishers
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Springer Nature
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38 publications, 22.89%
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Elsevier
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31 publications, 18.67%
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17 publications, 10.24%
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Oxford University Press
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14 publications, 8.43%
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Frontiers Media S.A.
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12 publications, 7.23%
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Wiley
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Wiley
9 publications, 5.42%
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Portland Press
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7 publications, 4.22%
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American Society for Clinical Investigation
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2 publications, 1.2%
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Wolters Kluwer Health
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2 publications, 1.2%
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Cold Spring Harbor Laboratory
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2 publications, 1.2%
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Acta Naturae Ltd
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Acta Naturae Ltd, 2, 1.2%
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2 publications, 1.2%
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American Society of Plant Biologists
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American Society of Plant Biologists
1 publication, 0.6%
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BMJ
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BMJ
1 publication, 0.6%
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American Chemical Society (ACS)
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American Chemical Society (ACS)
1 publication, 0.6%
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Royal Society of Chemistry (RSC)
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1 publication, 0.6%
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Taylor & Francis
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Taylor & Francis
1 publication, 0.6%
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EMBO press
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EMBO press
1 publication, 0.6%
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American Physiological Society
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American Physiological Society
1 publication, 0.6%
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Annual Reviews
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Annual Reviews
1 publication, 0.6%
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Biophysical Society
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Biophysical Society
1 publication, 0.6%
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Public Library of Science (PLoS)
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Public Library of Science (PLoS)
1 publication, 0.6%
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PeerJ
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PeerJ
1 publication, 0.6%
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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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Cai Z. et al. RIC-seq for global in situ profiling of RNA–RNA spatial interactions // Nature. 2020. Vol. 582. No. 7812. pp. 432-437.
GOST all authors (up to 50)
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Cai Z., Cao C., Lei J., Rong Y., Wang D., Xia C., Wang S., Du Z., Hu N., YU X., Chen J., Wang L., Yang X., He S., Xue Y. RIC-seq for global in situ profiling of RNA–RNA spatial interactions // Nature. 2020. Vol. 582. No. 7812. pp. 432-437.
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TY - JOUR
DO - 10.1038/s41586-020-2249-1
UR - https://doi.org/10.1038%2Fs41586-020-2249-1
TI - RIC-seq for global in situ profiling of RNA–RNA spatial interactions
T2 - Nature
AU - Cai, Zhaokui
AU - Cao, Changchang
AU - Lei, Ji
AU - Rong, Ye
AU - Wang, Di
AU - Xia, Cong
AU - Wang, Sui
AU - Du, Zongchang
AU - Hu, Naijing
AU - YU, XIAOHUA
AU - Chen, Juan
AU - Wang, Lei
AU - Yang, Xianguang
AU - He, Shunmin
AU - Xue, Yuanchao
PY - 2020
DA - 2020/05/06 00:00:00
PB - Springer Nature
SP - 432-437
IS - 7812
VL - 582
SN - 0028-0836
SN - 1476-4687
ER -
Cite this
BibTex
Copy
@article{2020_Cai,
author = {Zhaokui Cai and Changchang Cao and Ji Lei and Ye Rong and Di Wang and Cong Xia and Sui Wang and Zongchang Du and Naijing Hu and XIAOHUA YU and Juan Chen and Lei Wang and Xianguang Yang and Shunmin He and Yuanchao Xue},
title = {RIC-seq for global in situ profiling of RNA–RNA spatial interactions},
journal = {Nature},
year = {2020},
volume = {582},
publisher = {Springer Nature},
month = {may},
url = {https://doi.org/10.1038%2Fs41586-020-2249-1},
number = {7812},
pages = {432--437},
doi = {10.1038/s41586-020-2249-1}
}
Cite this
MLA
Copy
Cai, Zhaokui, et al. “RIC-seq for global in situ profiling of RNA–RNA spatial interactions.” Nature, vol. 582, no. 7812, May. 2020, pp. 432-437. https://doi.org/10.1038%2Fs41586-020-2249-1.