TY - JOUR
T1 - YTHDF2 Recognition of N1-Methyladenosine (m1A)-Modified RNA Is Associated with Transcript Destabilization
AU - Seo, Kyung W.
AU - Kleiner, Ralph E.
N1 - Funding Information:
We thank T. Srikumar and the Princeton University Mass Spectrometry and Proteomics Core Facility for performing proteomics analysis. We thank W. Wang and R. Leach at the Princeton University Genomics Core Facility for performing Illumina sequencing and associated data analysis. We thank J. Dragon for experimental assistance. This research was supported by the NIH (R01 GM132189 to R.E.K.), the Sidney Kimmel Foundation (Sidney Kimmel Scholar Award to R.E.K.), the Damon Runyon Cancer Research Foundation (DFS #21-16 to R.E.K.), and the Alfred P. Sloan Foundation (Sloan Foundation Research Fellowship to R.E.K.). K.W.S. was supported by a generous gift from the Edward C. Taylor Third Year Graduate Fellowship in Chemistry. All authors thank Princeton University for financial support.
Publisher Copyright:
Copyright © 2019 American Chemical Society.
PY - 2020/1/17
Y1 - 2020/1/17
N2 - Epitranscriptomic modifications play an important role in RNA function and can impact gene expression. Here, we apply a chemical proteomics approach to investigate readers of N1-methyladenosine (m1A), a poorly characterized modification on mammalian mRNA. We find that YTHDF proteins, known m6A readers, recognize m1A-modified sequences in a methylation-specific manner. We characterize binding of recombinant YTHDF1/2 proteins to m1A-modified oligonucleotides to demonstrate that these interactions can exhibit comparable affinity to m6A-recognition events and occur in diverse sequence contexts. Further, we demonstrate YTHDF2 interacts specifically with endogenously modified m1A transcripts. Finally, we deplete cellular YTHDF2 to show that the abundance of m1A-modified transcripts is increased in its absence. Similarly, increasing m1A levels through depletion of ALKBH3, an m1A eraser protein, destabilizes known m1A-containing RNAs. Our results shed light on the function of m1A on mRNA and provide a mechanistic framework to further evaluate the role of m1A in biological processes.
AB - Epitranscriptomic modifications play an important role in RNA function and can impact gene expression. Here, we apply a chemical proteomics approach to investigate readers of N1-methyladenosine (m1A), a poorly characterized modification on mammalian mRNA. We find that YTHDF proteins, known m6A readers, recognize m1A-modified sequences in a methylation-specific manner. We characterize binding of recombinant YTHDF1/2 proteins to m1A-modified oligonucleotides to demonstrate that these interactions can exhibit comparable affinity to m6A-recognition events and occur in diverse sequence contexts. Further, we demonstrate YTHDF2 interacts specifically with endogenously modified m1A transcripts. Finally, we deplete cellular YTHDF2 to show that the abundance of m1A-modified transcripts is increased in its absence. Similarly, increasing m1A levels through depletion of ALKBH3, an m1A eraser protein, destabilizes known m1A-containing RNAs. Our results shed light on the function of m1A on mRNA and provide a mechanistic framework to further evaluate the role of m1A in biological processes.
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U2 - 10.1021/acschembio.9b00655
DO - 10.1021/acschembio.9b00655
M3 - Article
C2 - 31815430
AN - SCOPUS:85076635251
SN - 1554-8929
VL - 15
SP - 132
EP - 139
JO - ACS chemical biology
JF - ACS chemical biology
IS - 1
ER -