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Series GSE49339 Query DataSets for GSE49339
Status Public on Nov 29, 2013
Title m6A-dependent regulation of messenger RNA stability
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNA of all higher eukaryotes. Here we present that m6A is selectively recognized by human YTH domain family (YTHDF2) protein to regulate mRNA degradation. By using crosslinking and immunoprecipitation, we have identified over 4000 substrate RNA of YTHDF2 with conserved core motif of G(m6A)C. We further estabilshed the role of YTHDF2 in RNA metabolism by a combination of ribosome profiling, RNA sequencing, m6A level quantification and cell-based imaging: the C-terminal domain of YTHDF2 selectively binds to m6A of mRNA and the N-terminal domain is responsive for localizing mRNA from translatable pool to processing body where mRNA decay occurs.
Overall design PAR-CLIP and RIP was used to identify YTHDF2 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF2 siRNA knock-down
Contributor(s) Wang X, Lu Z, Yue Y, Han D, Hon GC, Ren B, Pan T, He C
Citation(s) 23453015, 24284625
Submission date Jul 30, 2013
Last update date May 15, 2019
Contact name zhike lu
Organization name University of Chicago
Department department of chemistry
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (29)
GSM1197605 YTHDF2-PAR-CLIP-rep1 A1
GSM1197606 YTHDF2-PAR-CLIP-rep2 A2
GSM1197607 YTHDF2-PAR-CLIP-rep3 A3
BioProject PRJNA213675
SRA SRP028325

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Supplementary file Size Download File type/resource
GSE49339_A-PARCLIP.xlsx.gz 5.3 Mb (ftp)(http) XLSX
GSE49339_B-RIP.xlsx.gz 6.9 Mb (ftp)(http) XLSX
GSE49339_C-Ribosome_profiling.xlsx.gz 4.4 Mb (ftp)(http) XLSX
GSE49339_D-mRNA_lifetime-rep1.xlsx.gz 7.0 Mb (ftp)(http) XLSX
GSE49339_E-mRNA_Lifetime-rep2.xlsx.gz 7.1 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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