Transcriptomics

Dataset Information

421

Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions


ABSTRACT: We show that N6-methyladenosine (m6A), the most abundant internal modification in mRNA/lncRNA with still poorly characterized function, alters RNA structure to facilitate the access of RBM for heterogeneous nuclear ribonucleoprotein C (hnRNP C). We term this mechanism m6A-switch. Through combining PAR-CLIP with Me-RIP, we identify 39,060 m6A-switches among hnRNP C binding sites transcriptome-wide. We show that m6A-methyltransferases METTL3 or METTL14 knockdown decreases hnRNP C binding at 16,582 m6A-switches. Taken together, 2,798 m6A-switches of high confidence are identified to mediate RNA-hnRNP C interactions and affect diverse biological processes including cell cycle regulation. These findings reveal the biological importance of m6A and provide insights into the sophisticated regulation of RNA-RBP interactions through m6A-induced RNA structural remodeling. Measure the m6A methylated hnRNP C binding sites transcriptome-wide by PARCLIP-MeRIP; measure the differential hnRNP C occupancies upon METTL3/METTL14 knockdown by PAR-CLIP; measure RNA abundance and splicing level changes upon HNRNPC, METTL3 and METTL14 knockdown

ORGANISM(S): Homo sapiens  

SUBMITTER: Tao Pan   C He  Q Dai  N Liu  T Pan  M Parisien 

PROVIDER: E-GEOD-56010 | ArrayExpress | 2015-02-27

SECONDARY ACCESSION(S): SRP040278GSE56010PRJNA242201

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions.

Liu Nian N   Dai Qing Q   Zheng Guanqun G   He Chuan C   Parisien Marc M   Pan Tao T  

Nature 20150201 7540


RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBMs). However, RBMs can be buried within their local RNA structures, thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs, but how m(6)A achieves its wide-ranging physiological role needs  ...[more]

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