PXD036032

PXD036032 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-12 13:25:55	ID requested
⏵ 1	2022-09-24 11:03:47	announced

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]

submitter keyword: LC-PRM, N6-Methyladenosine, Epitranscriptomic Reader, Writer and Eraser Proteins

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

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PRIDE project URI

• PRIDE
  1. PXD036032
     1. Label: PRIDE project
     2. Name: Targeted Quantitative Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins Revealed Potential Crosstalk between N6-Methyladenosine and Other RNA Modifications