PXD036032 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins Revealed Potential Crosstalk between N6-Methyladenosine and Other RNA Modifications |
Description | N⁶-methyladenosine (m6A) and its reader, writer, and eraser (RWE) proteins assume crucial roles in regulating the splicing, stability, and translation of mRNA. To our knowledge, no systematic investigations have been conducted about the crosstalk between m6A and other modified nucleosides in RNA. Herein, we modified our recently established liquid chromatography-parallel-reaction monitoring (LC-PRM) method by incorporating stable isotope-labeled (SIL) peptides as internal or surrogate standards for profiling epitranscriptomic RWE proteins. We were able to detect reproducibly a total of 114 RWE proteins in HEK293T cells with the genes encoding m6A eraser proteins (i.e., ALKBH5, FTO) and the catalytic subunit of the major m6A writer complex (i.e., METTL3) being individually ablated. Notably, eight proteins were altered by more than 1.5-fold in the opposite directions in HEK293T cells depleted of METTL3 and ALKBH5. Analysis of published m6A mapping results revealed the presence of m6A in the corresponding mRNAs of four of these proteins. Together, we integrated SIL peptides into our LC-PRM method for quantifying epitranscriptomic RWE proteins, and our work revealed potential crosstalks between m6A and other epitranscriptomic modifications. Our modified LC-PRM method with the use of SIL peptides should be applicable for high-throughput profiling of epitranscriptomic RWE proteins in other cell types and in tissues. |
HostingRepository | PRIDE |
AnnounceDate | 2022-09-24 |
AnnouncementXML | Submission_2022-09-24_11:03:46.972.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Tianyu Qi |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-08-12 13:25:55 | ID requested | |
⏵ 1 | 2022-09-24 11:03:47 | announced | |
Publication List
Qi TF, Liu X, Tang F, Yin J, Yu K, Wang Y, Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Using Stable Isotope-Labeled Peptides. Anal Chem, 94(37):12559-12564(2022) [pubmed] |
Keyword List
submitter keyword: LC-PRM, N6-Methyladenosine, Epitranscriptomic Reader, Writer and Eraser Proteins |
Contact List
Yinsheng Wang |
contact affiliation | Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521, United States |
contact email | Yinsheng.Wang@ucr.edu |
lab head | |
Tianyu Qi |
contact affiliation | UC RIVERSIDE |
contact email | tqi001@ucr.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD036032
- Label: PRIDE project
- Name: Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins Revealed Potential Crosstalk between N6-Methyladenosine and Other RNA Modifications