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10.1002/anie.201900901
Angewandte Chemie International Edition
COMMUNICATION
Identification of Flavin Mononucleotide as Cell-Active Artificial
N6-Methyladenosine RNA Demethylase
Li-Jun Xie,†[a],[d] Xiao-Ti Yang,†[b],[d] Rui-Li Wang,[a],[d] Hou-Ping Cheng,[a],[d] Zhi-Yan Li,[a] Li Liu,[a],[d]
Lanqun Mao,[b],[d] Ming Wang,*[b],[d] and Liang Cheng*[a],[c],[d]
In Memory of Professor Ronald Breslow (1931-2017)
Abstract: N6-Methyladenosine (m6A) represents a common and
highly dynamic modification in eukaryotic RNA that affects various
cellular pathways. Natural dioxygenases such as FTO and ALKBH5
are enzymes that demethylate m6A residues in mRNA. Herein, the
first identification of a small-molecule modulator that functions as an
artificial m6A demethylase was reported. Flavin mononucleotide
(FMN), the metabolite produced by riboflavin kinase, undergoes
substantial photochemical demethylation of m6A residues of RNA in
dioxygenases bind to and oxidizes m6A to generate N6-
hydroxymethyladenosine (hm6A) and N6-formyladenosine (f6A)
as intermediates.6 These modifications are relatively unstable
under physiological conditions and partially decompose to
adenosine (A),4a-b completing the demethylation process.
Although the mechanism and function of dioxygenases-
mediated RNA demethylation have been extensively studied
(Scheme 1B, upper),7 the corresponding biomimetic approach
using small organic molecules that may regulate such important
biological processes, i.e., the chemical demethylation of m6A, is
nearly blank8 (Scheme 1B, lower). Thus, one of the challenges
here is the design of such a functional small molecule, either by
gaining inspiration from nature or by creating a new structure
type not based on proteins at all. These purposeful chemical
motifs, if capable of influencing those modifications in genomic
nucleic acids, could potentially be used as structure-specific
probes (artificial enzymes)9 or pharmaceuticals that regulate
RNA functions by controlling genetic information expression.
live cells. This study provides
a new perspective to the
understanding of demethylation of m6A residues in mRNA and sheds
light on the development of powerful small molecules as RNA
demethylases and new probes for use in RNA biology.
N6-Methyladensoine (m6A), the most abundant internal
modification in RNAs, significantly impacts cellular biological
functions, and thus is associated with numerous diseases in
human. Research on m6A contributes considerably to the
advancement in modern chemistry, biology, and medicine.1-2
The past decade has witnessed the blooming of mechanistic
studies in the related adenosine methylation (“writer”),
recognition (“reader”), and also the active demethylation
pathways (“eraser”)3 (Scheme 1A). Recent studies have
reported the discovery of two members of the superfamily of iron
α-ketoglutarate (KG) dependent dioxygenases, namely, fat mass
and obesity-associated protein (FTO)4 and α-KG-dependent
dioxygenase alkB homolog
5
(ALKBH5)5, as selective
demethylases capable of regulating gene expression and cell
fate by oxidative removal of the methyl group in m6A-containing
substrates. Detailed mechanistic studies indicated that these
[a]
L.-J. Xie, R.-L. Wang, H.-P. Cheng, Z.-Y. Li, Prof. Dr. L. Liu, Prof. Dr.
L. Cheng
Scheme 1. Dynamic m6A modification on RNAs. (A) The reversible
methylation and demethylation of m6A on RNAs. (B) Oxidative demethylation
of m6A RNAs by enzymatic (FTO) and chemical (FMN, this work) pathways.
Beijing National Laboratory for Molecular Sciences (BNLMS), CAS
Key Laboratory of Molecular Recognition and Function, CAS
Research/Education Center for Excellence in Molecular Sciences
Institute of Chemistry, Chinese Academy of Sciences
Beijing 100190, China
Recently,
we
developed
a
selective
photochemical
E-mail: chengl@iccas.ac.cn
demethylation of m6A at nucleoside level, indicating that the
regulation of m6A modification by external small organic
molecules is possible.8b We found that by using prudently
selected chemical oxidant (Selectfluor), an exogenous
photosensitizer molecule, riboflavin10 would selectively
recognize and activate the modified nucleoside, thereby allowing
oxidation of m6A with high efficacy. A similar conclusion was
also obtained using a basic approach with endogenously
generated hydrogen peroxide (H2O2).8a In this study, we
describe a visible-light induced oxidation of m6A RNA in live cells
under atmospheric O2 by applying the biocompatible metabolite,
namely, flavin mononucleotide (FMN),11 as an efficient
photosensitizer.12 Our result will create opportunities for
[b]
X.-T. Yang, Prof. Dr. L. Mao, Prof. Dr. M. Wang
BNLMS, CAS Key Laboratory of Analytical Chemistry for Living
Biosystems
Institute of Chemistry, Chinese Academy of Sciences
E-mail: mingwang@iccas.ac.cn
[c]
[d]
Prof. Dr. L. Cheng
Key Lab of Functional Molecular Engineering of Guangdong
Province (South China University of Technology)
Guangzhou 510640, China
L.-J. Xie, X.-T. Yang, R.-L. Wang, H.-P. Cheng, Prof. Dr. L. Liu, Prof.
Dr. L. Mao, Prof. Dr. M. Wang, Prof. Dr. L. Cheng
University of Chinese Academy of Sciences
Beijing 100049, China
† These authors contributed equally to this work.
Supporting information for this article is given via a link at the end of
the document.
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