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Series GSE56010 Query DataSets for GSE56010
Status Public on Feb 27, 2015
Title Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Other
Summary 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.
 
Overall design 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
 
Contributor(s) Liu N, Dai Q, He C, Parisien M, Pan T
Citation(s) 25719671
Submission date Mar 18, 2014
Last update date May 15, 2019
Contact name Tao Pan
E-mail(s) taopan@uchicago.edu
Phone (773) 702-4179
Organization name University of Chicago
Department Biochemistry and Molecular Biology
Street address 929 E. 57th Street
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (18)
GSM1350192 PARCLIP-MeRIP-Input-rep1
GSM1350193 PARCLIP-MeRIP-Input-rep2
GSM1350194 PARCLIP-MeRIP-IP-rep1
Relations
BioProject PRJNA242201
SRA SRP040278

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56010_Processed_location_m6A-switch_updated.xlsx 1.4 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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