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Series GSE86214 Query DataSets for GSE86214
Status Public on Sep 15, 2016
Title YTHDF3 facilitates translation and decay of the N6-methyladenosine-modified RNA
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs), and plays important roles in cell differentiation and organism development. It regulates multiple steps throughout the RNA life cycle including RNA processing, translation, and metabolism, via the recognition by selective binding proteins. In cytoplasm, m6A binding protein YTHDF1 facilitates translation of m6A-modified mRNAs, and YTHDF2 accelerates the decay of m6A-modified transcripts. The biological function of YTHDF3, another cytoplasmic m6A binder of the YTH domain family, remains unknown. Here, we report that YTHDF3 promotes protein synthesis in synergy with YTHDF1, and affects methylated mRNA decay mediated by YTHDF2. Cells deficient in all of YTHDF proteins experience the most dramatic accumulation of the m6A-methylated transcripts. These results indicate that in cytoplasm, YTHDF proteins act in an integrated and cooperative network to accelerate metabolism of m6A-modified mRNAs. The combinative and dynamic nature of YTHDF proteins may collectively impact fundamental biological processes and diseases related to m6A RNA methylation.
 
Overall design We utilized PAR-CLIP triplicates and RIP replicates to identify binding sites and target transcripts of YTHDF3, and performed ribosome profling replicates to assess the consequences of YTHDF3 siRNA knock-down in HeLa cells.
 
Contributor(s) Shi H, Wang X, Lu Z, Zhao BS, Ma H, Hsu PJ, He C
Citation(s) 28106072
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM071440 Direct Oxidative Nucleic Acids Demethylation: Chemistry and Mechanism of Direct DNA Repair Proteins UNIVERSITY OF CHICAGO HE
R01 GM113194 Recognition and mechanism of N6-methyl adenosine modifications UNIVERSITY OF CHICAGO HE
Submission date Aug 30, 2016
Last update date May 15, 2019
Contact name Chuan He
E-mail(s) chuanhe@uchicago.edu
Phone 773-702-5061
Organization name The University of Chicago
Department Department of Chemistry
Street address 929 E 57th St., GCIS E319
City Chicago
State/province ILLINOIS
ZIP/Postal code 60637
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (25)
GSM2424844 YTHDF3-PAR-CLIP-repl.1
GSM2424845 YTHDF3-PAR-CLIP-repl.2
GSM2424846 YTHDF3-PAR-CLIP-repl.3
Relations
BioProject PRJNA340948
SRA SRP083699

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE86214_YTHDF3_PAR-CLIP.xlsx 62.6 Mb (ftp)(http) XLSX
GSE86214_YTHDF3_RIP.xlsx 1.2 Mb (ftp)(http) XLSX
GSE86214_siYTHDF3_RiboProfile.xlsx 2.2 Mb (ftp)(http) XLSX
GSE86214_siYTHDF3_YTHDF12RIP.xlsx 3.0 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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