RIC-seq for global in situ profiling of
RNA
-
RNA
spatial interactions
ABCD PBi
RIC-seq for global in situ profiling of
RNA
-
RNA
spatial interactions
Autor:
Cai, Zhaokui
;
Cao, Changchang
;
Ji, Lei
;
Ye, Rong
;
Wang, Di
;
Xia, Cong
;
Wang, Sui
;
Du, Zongchang
;
Hu, Naijing
;
Yu, Xiaohua
;
Chen, Juan
;
Wang, Lei
;
Yang, Xianguang
;
He, Shunmin
;
Xue, Yuanchao
Assuntos:
Analysis
;
Biological activity
;
Cell Line
;
Chromatin
;
Chromatin - genetics
;
Chromatin - metabolism
;
Chromosomes, Human - genetics
;
Coupling (molecular)
;
Enhancer Elements, Genetic - genetics
;
Enhancers
;
Gene sequencing
;
Genes, myc - genetics
;
Genes, rRNA - genetics
;
Heterogeneous-Nuclear Ribonucleoprotein K - metabolism
;
Humans
;
Identification and classification
;
Interactomes
;
Kinases
;
Monte Carlo simulation
;
Myc protein
;
Nucleic Acid Conformation
;
Promoter Regions, Genetic - genetics
;
Proteins
;
Reproducibility of Results
;
Ribonucleic acid
;
RNA
;
RNA
- chemistry
;
RNA
- genetics
;
RNA
sequencing
;
RNA
, Long Noncoding - chemistry
;
RNA
, Long Noncoding - genetics
;
RNA
-binding protein
;
Sequence Analysis,
RNA
- methods
;
Structure
;
Transcription
;
Transcription, Genetic
É parte de:
Nature (London), 2020-06, Vol.582 (7812), p.432-437
Notas:
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Descrição:
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.
Editor:
England: Nature Publishing Group
Idioma:
Inglês