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Abstract | Cellular RNAs carry diverse chemical modifications that used to be regarded as
static and having minor roles in fine-tuning structural and functional properties of RNAs.
In this Review, we focus on reversible methylation through the most prevalent mammalian
mRNA internal modification, N6-methyladenosine (m6A). Recent studies have discovered
protein writers, erasers and readers of this RNA chemical mark, as well as its dynamic
deposition on mRNA and other types of nuclear RNA. These findings strongly indicate
dynamic regulatory roles that are analogous to the well-known reversible epigenetic
modifications of DNA and histone proteins. This reversible RNA methylation adds a new
dimension to the developing picture of post-transcriptional regulation of gene expression.
Epigenetic modifications
Reversible chemical
modifications on DNA and
histones that regulate gene
expression independently of the
genome sequences and that are
heritable through cell division.
In the central dogma of molecular biology, genetic information flows from DNA to RNA and then to protein.
Reversible epigenetic modifications occur on genomic
DNA15 and histone proteins69 to substantially regulate
gene expression that defines cell status and that affects
cell differentiation and development (FIG.1). Although
both DNA and proteins are subject to reversible chemical tuning, as we pointed out in 2010, a similar process
on mRNA or other forms of RNA as the third component of the central dogma had been missing 10. RNA has
crucial roles in biological systems not only by passing
genetic information from DNA to protein but also by
regulating various biological processes. The diverse
functions of RNA are accompanied by more than 100
chemical modifications1114, although the functions of
most of these RNA modifications have remained a mystery. Most RNA species were thought to be short lived,
and RNA modifications were considered to be static and
unalterable after their covalent attachment. The central role of RNA in gene expression and the intrinsic
chemical reversibility of certain types of RNA methylation prompted us to raise the question of reversible
RNA modifications in gene expression regulation10. In
this Review, we discuss how, only in the past 23years,
N6-methyladenosine (m6A) has been discovered as the
first example of reversible RNA methylation15,16. We
describe the transcriptome-wide distribution of m6A
in mammalian systems17,18, the identification of protein writers, erasers and readers for this dynamic RNA
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Methyltransferase
An enzyme that transfers a
methyl group to its substrate.
Most methyltransferases use
S-adenosyl-l-methionine (SAM)
as the methyl donor.
High-performance liquid
chromatography coupled
with triple-quadrupole
tandem mass spectrometry
(HPLCQqQMS/MS). A liquid
chromatography method
coupled with triple-quadrupole
tandem mass spectrometry,
which can quantitatively and
simultaneously monitor
multiple molecular species
according to their
fragmentation patterns.
Central dogma
Chemical modications
DNA replication
Reversible
DNA methylation
m5C
hm5C
DNA
Transcription
?
?
RNA
Reversible
RNA methylation
m6A
hm6A
Translation
Protein
Reversible histone
methylation or
acetylation
Me
Ac
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a
Me
A
mRNA
Me
An
Fragmentation
to ~100 nucleotides
A
Me
A
Me
A
A
Immunoprecipitation
with m6A-specic
antibodies
Input control
Me
Me
Me
Signal
m6A peak
Signal
m6A peak
Input signal
Locus
Locus
b
m6A abundance
mRNA
5 transcription
start site
Long exon
Stop codon
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m6A RNA
immunoprecipitation
An immunoprecipitation
method to selectively enrich
for N6-methyladenosine
(m6A)-containing RNA using
an m6A-targeted antibody.
Nuclear speckles
Nuclear domains located in
the interchromatin regions
of the nucleoplasm and
enriched with pre-mRNA
processing factors.
DPAW
b Consensus motif
SAM-binding
S. cerevisiae Ime4
METTL14
DPPW
SAM-binding
Human METTL3
Coiled-coil
EPPL
SAM-binding
Human METTL14
G-rich
METTL3
c
E. coli AlkB
Coiled-coil
Human ALKBH5
(PARCLIP). A biochemical
method that takes advantage
of incorporated photoreactive
ribonucleoside analogues to
identify the binding sites of
RNA-binding proteins in cells.
Human FTO
A-rich
C-terminal domain
WTAP
Extra
loop
METTL3 METTL14
+ other
factors?
H
WTAP
N H
N
N
H
C H
H
N
N
ALKBH5
m6A reader
Functions
m6A
FTO
H
FTO
N C
N
H
OH
N C H
H
N
f6A
hm6A
Readers?
Figure 3 | Reversible m6A methylation of mRNA and other types of nuclear RNA. The N6-methyladenosine (m6A)
Nature Reviews | Genetics
modification is installed by a hetero complex of two methyltransferases METTL3METTL14, assisted by Wilms
tumour1associating protein (WTAP), and can be demethylated by the -ketoglutarate (-KG)-dependent
dioxygenases FTO and ALKBH5. a | Saccharomyces cerevisiae inducer of meiosis4 (Ime4), and human METTL3 and
METTL14 contain the S-adenosyl-l-methionine (SAM)-dependent methyltransferase domain for m6A methylation. The
(D/E)P(P/A)(W/L) active site and the SAM-binding motif are conserved. b | Photoactivatable ribonucleoside-enhanced
crosslinking and immunoprecipitation (PARCLIP) reveals that the binding sites of METTL14 and METTL3 on mRNA
resemble the consensus sequence of m6A in mammalian mRNA. The sequence bound by WTAP moderately overlaps
with those bound by METTL14 and METTL3. c | Mammalian FTO and ALKBH5 contain the active site motif HXDXnH
(where X denotes any amino acid) for Fe(ii) binding, RXXXXXR for both -KG binding and substrate recognition, and an
extra loop that leads to preferential binding of single-stranded over double-stranded nucleic acids68,121,122. Relative to
Escherichia coli AlkB, mammalian ALKBH5 has an aminoterminal alaninerich sequence and a potential coiled-coil
structure that could be important for its localization. FTO contains an extra carboxyterminal domain with a novel fold,
possibly to engage in additional proteinprotein interactions. d | Methylation and demethylation of m6A on RNA are
shown. Whereas ALKBH5 catalyses the direct removal of m6A, FTO can oxidize m6A to N6-hydroxymethyladenosine
(hm6A) and N6-formyladenosine (f6A) sequentially; hm6A and f6A are moderately stable (with half-lives of ~3hours under
physiological conditions) and can be hydrolysed to adenine.
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question: why is the m6A methyltransferase complex
composed of two active components, both of which bind
to the methyl donor S-adenosyl-l-methionine (SAM)?
The hetero complex may allow the selective tuning
of methylation activity through post-translational
modification of each component in order to affect different substrate transcripts, thus having an influence
on different biological pathways. A heterodimer of two
methyltransferase components is required for optimal
activities of several other known RNA methyltransferase complexs4346. Typically, one subunit has a SAMbinding pocket, and the other non-catalytic subunit
either stabilizes the catalytic subunit or enhances its
activity by forming a continuous substrate-binding surface. However, both METTL3 and METTL14 are active.
A crystal structure of this complex will be helpful in
uncovering the synergy between the two enzymes and
the properties associated with each active component.
Demethylase
An enzyme that removes a
methyl group from its substrate.
WTAP is the third crucial component of the m6A methyltransferase complex invivo. Yeast two-hybrid screens have
identified FKBP12interacting protein of 37kDa (FIP37;
also known as AT3g54170) in Arabidopsis thaliana47 and
Mum2 in yeast as the partner proteins of the METTL3
homologues in these organisms48. These two proteins
are homologues of the Wilms tumour 1associating protein (WTAP) in humans. WTAP was initially identified
as a splicing factor that binds to the Wilms tumour1
(WT1) protein49, and it is essential for cell cycle progression and early mammalian embryonic development. We
found that knockdown of WTAP leads to a decrease in
the total m6A level in HeLa and 293FT cells40. WTAP
interacts with both METTL3 and METTL14, and colocalizes with the METTL3METTL14 heterodimer in
nuclear speckles to participate in m6A RNA methylation
(FIG.3d). In fact, knockdown of WTAP leads to the largest
decrease in m6A levels in these cell lines, which indicates
that WTAP has important roles in cellular m6A deposition. A PARCLIP assay revealed that WTAP shares
a similar binding sequence of GACU; that is, the sequence
bound by WTAP moderately overlaps with the GGAC
sequence bound by both METTL3 and METTL14
(FIG.3b). As identified by PARCLIP, these targets have
a ~50% overlap with m6A-containing transcripts, which
further indicates that METTL3, METTL14 and WTAP
form the core of the major cellular writer complex of m6A
(REF.40). A large proportion of the binding sites of these
three proteins are found in introns (2934%), which further implies that methylation occurs cotranscriptionally
either before or at the same time as splicing. As WTAP
has been thought to be a splicing factor, a recent study
indicates that the knockdown of WTAP or METTL3
yields different isoforms of m6A-containing transcripts,
which suggests that methylation could affect splicing 50.
How does WTAP enhance the methylation activity
of METTL3 and METTL14 invivo (FIG.3d)? Potentially,
WTAP may help to recruit METTL3 and METTL14 to
their target mRNAs. WTAP has also been shown to be
essential for the nuclear speckle localization of METTL3
and METTL14, which could affect the methylation
efficiency of these proteins50. WTAP, which is known
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development: Fto-knockout mice shows increased postnatal lethality and growth retardation59, and a homozygous lossoffunction mutation (Arg316Gln) in the FTO
protein in humans leads to postnatal retardation, as well
as multiple dysmorphisms and malformations61.
FTO is a member of the Fe(ii) and -ketoglutaratedependent AlkB family of proteins that catalyse oxidative
demethylation 58 ; close homologues participate in
epigenetic regulation, such as oxidative DNA demethylation6264 and histone demethylation8. FTO was originally shown to demethylate N3-methylthymidine in
single-stranded DNA58 and N3-methyluridine in singlestranded RNA65 invitro; however, the function of FTO
invivo remained unknown until we discovered that
FTO efficiently demethylates m6A in both RNA and
DNA invitro15. Further experiments showed that silencing of FTO in HeLa and 293FT cells increased total m6A
levels in polyadenylated RNA, and overexpression of
FTO decreased m6A levels on RNA15. FTO is expressed in
dot-like patterns in the nucleoplasm and partially colocalizes with nuclear speckles. These cell-based results,
together with observations that most mammalian cells
and tissues contain very low levels (a few parts per million)
of m6A on genomic DNA, led us to conclude that m6A
on nuclear RNA (including mRNA, lncRNA and possibly other types of RNA) is the main substrate of FTO.
Recent work showed that m6A on three mRNA species
could be demethylated by FTO invivo, and this function
seems to affect neuronal activities66. FTO may also act
as a nutrient sensor, which could modulate its demethylation activities67. It should be noted that although
FTO works preferentially on single-stranded RNA
and DNA, it can still exhibit demethylation activity,
albeit low, towards double-stranded RNA andDNA15.
The crystal structure of the FTO protein reveals
an active domain that is similar to those of other proteins of the AlkB family 68 (FIG.3c). FTO also contains a
Cterminal domain with a novel fold that is distinct from
other proteins of this family. This Cterminal domain
may engage in additional proteinprotein or protein
RNA interactions to affect the function of FTO. The
discovery of FTO as an m6A demethylase strongly suggests functional roles for m6A in human developmental
regulation; however, to achieve the end goal of uncovering the underlying mechanism, a considerable amount
of future work is required to identify the physiological
RNA targets of FTO and to elucidate the functional
consequences of such demethylation.
Oxidative demethylation
A chemical reaction in which
the CH bond of a methyl
group attached to a nitrogen or
an oxygen atom is oxidized to
OH by demethylases, and the
intermediate decomposes to
release the methyl group as
formaldehyde.
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Box 1 | RNA modifications
Cellular RNA species contain more than 100 chemical modifications with
diverse properties. Chemical modifications of RNA can occur on the N1,
N3, N7 and C8 atoms in both adenine and guanine; C2 and N6 in adenine;
N2 and O6 in guanine; N1, O2, N3 and C5 in cytosine and uracil; N4 in
cytosine and O4 in uracil; as well as on 2O of the ribose backbone and the
OH group of the phosphate backbone (see the figure, part a). These
modifications can modulate hydrophobicity, steric and electrostatic
effects, and hydrogen-bonding abilities of RNA bases and backbones.
Methylation or other forms of alkylation on nitrogen or oxygen atoms can
be removed through either an oxidative or a nucleophilic substitution
mechanism. The oxidative demethylation (see the figure, part b) is best
exemplified by Fe(ii) and -ketoglutarate-dependent dioxygenase
enzymes, which use Fe(ii) as a catalytic centre, O2 as an oxidant and
a
NH2
N
NH2
Ribose
NH
N
Ribose
A
HC
(e.g. f6A)
NH
NH2
(e.g. Adenine)
Ribose O
Base
OH
Ribose
Ribose
Phosphate
RNA backbone
OH
(Formic acid)
Oxidation
CH3
H2C
OH
(e.g. m6A)
(e.g. hm6A)
Oxidation
N CH3
H
N
(e.g. Adenine)
+
OH
O
CH3
CH2
N H
:Nu
CH3
Nu
CH3
(Formaldyhyde)
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a
S. cerevisiae Mrb1
YTH domain
S. pombe Mmi1
YTH domain
Human YTHDF1
P/Q/N-rich
YTH domain
Human YTHDF2
P/Q/N-rich
YTH domain
Human YTHDF3
P/Q/N-rich
YTH domain
600
Non-m6A
m6A
500
400
300
200
100
0
3
12
15
18
Translation
P/Q/Nrich
?
Me
An
m7Gppp
RNA
Transcription
YTHDF2 YTH
Me
m7Gppp
An
?
DNA
Localization
(strorage or transport)
Degradation
Figure 4 | Functions of the reader (that is, effector) proteins of m6A. a | The
6
Nature
ReviewsHuman
| Genetics
characterized YTHDF proteins serve as N6-methyladenosine (m
A) readers.
YTHDF13 proteins contain a carboxyterminal YTH RNA-binding domain and an
aminoterminal P/Q/N-rich region. The YTH domain protein is conserved in the fission
yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae.
b | The m6A modification is enriched in mRNAs with shorter half-lives in general,
which supports the proposed main role of m6A in regulating mRNA stability. c | The
m6A-specific RNA-binding proteins are engaged in post-transcriptional regulation
of gene expression. YTHDF2 regulates the methylation (me)-dependent RNA
degradation. Other reader proteins may exist and affect RNA splicing, storage,
trafficking and translation. Data in part b courtesy of X.Wang, laboratory of C.H.
Ribosome profiling
Qualitative and quantitative
sequencing of the RNA attached
to ribosomes as a signature of
genes that are expressed.
Processing bodies
(P-bodies). Distinct foci in the
cytoplasm that are enriched
with RNA degradation factors.
contain adenine, hm6A or f 6A, or that have m6A in nonconsensus sequences have decreased binding affinity.
The enrichment of m6A in RNA immunoprecipitated
with YTHDF13 further supports the role of YTHDF
proteins as m6A-specific RNA-binding proteins.
RNA immunoprecipitation and PARCLIP experiments revealed mostly mRNA as targets of YTHDF2,
in addition to some lncRNA targets. The binding sites
localize around stop codons and at 3UTRs with a
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distributed in the 3UTRs of mRNA transcripts a
region bound by numerous RNA-binding proteins that
regulate mRNA metabolism and translation. It is possible that certain anti-reading mechanisms exist to regulate the fate of methylated mRNA. m6A is also known to
protect RNA from recognition by cellular innate immunity proteins. Toll-like receptor 3 (TLR3) and TLR7 recognize unmodified double-stranded and single-stranded
RNA as invasive RNA species and selectively target them
for degradation88,89. The incorporation of m6A and other
RNA modifications in transfected exogenous RNA can
reduce the recognition by innate immune systems to
prevent unnecessary degradation, which increases
their expression. An anti-reading mechanism possibly
operates in this process.
Indirect reading. Certain RNA modifications, such as
pseudouridine (), are known to cause secondary and
tertiary structural changes90. The m6A modification
reduces the base-pairing energy of A:U only marginally 35, but this difference may shift the equilibrium of
certain secondary and tertiary structures of RNA. The
altered structures could have an effect on the binding
of specific proteins, leading to indirect reading and
regulation. In a recent study of HuR (also known as
ELAVL1) a well-known RNA-binding protein that
affects the stability of many mRNA transcripts in mammalian cells9196 the m6A modification affected the
ability of HuR to bind to different RNA probes invitro42.
In this particular case, the RNA structure altered by
methylation might indirectly contribute to the accessibility of the cognate HuR-binding site. However,
the consensus sequence recognized by HuR invivo is
different from the m6A-containing sequence91,92. The
extent and details of the cellular connection between
HuR and m6A still need to be further investigated.
So far, no cellular example is known for this indirect
reading mechanism.
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to reduced nuclear retention time16, although it is not
clear whether m6A has a direct cis role in modulating the
export specifically of m6A-containing RNA molecules or
whether it is an indirect consequence of perturbation to
the RNA export machinery.
The m6A RNA modification is involved in priming
yeast cells to bipotential states and meiosis during nitrogen starvation. Through carefully monitoring methylation profiles at different stages, a recent study suggests
that methylation is important for the kinetic control
of RNAs during the meiotic prophase32. Although no
marked change in half-lives has been observed for the
m6A-containing RNAs, the accessibility of these RNAs
to translation may be modulated through interactions with potential reader proteins. Analogous to the
proposed function of m6A in accelerating both RNA
export and degradation in mammalian cells, m6A may
ensure faster turnover of the RNA transcripts that
are important during the meiotic prophase but that are
harmful and need to be degraded after the exit from
prophase. This example suggests that m6A could globally ensure fast kinetic responses by redirecting RNA
to different organelles and by quickly decreasing the
expression of related proteins. A similar mechanism
could also affect eukaryotic mitosis.
Similarly, another study in mESCs revealed that the
m6A methylation accelerates transcript decay, which
is consistent with the main role that we propose for
m6A, and affects stem cell maintenance and differentiation42. Interestingly, when compared with pluripotency-related genes, developmental regulators were
significantly enriched among target genes of METTL3
and METTL14 in mESCs. In particular, m6A destabilizes developmental regulator transcripts, which may
suggest that methylation is important for maintenance
and differentiation of mESCs. Temporal and spatial
regulation of mRNA is known to have crucial roles in
embryonic development. Post-fertilization, maternal
mRNA needs to be degraded in a programmed manner.
The methylation on mRNA could affect this process
through altering the localization and half-lives of target mRNA transcripts. Such methylation could mark
specific sets of RNA species and therefore differentiate
between maternal and zygotic mRNA in a kinetic manner. Heritable information could perhaps be passed
down to generations of cells through orchestrated RNA
methylation and demethylation activities.
Advantage and specificity of the m6A-based regulation. The first m6A reader protein to be characterized is
known to affect more than 3,000 different mRNA transcripts76. We propose that the reversible RNA methylation pathway, in general, has evolved to affect processes
that involve changes in the expression of large groups of
genes. This property is intimately related to the potential advantages of reversible methylation at the RNA
level. Besides providing increased complexity to the
regulatory network, this mechanism may allow rapid
responses to signalling and stimuli when the expression of a group of proteins (which can range from tens
to thousands) needs to be adjusted in a rapid manner;
when the response at the DNA level (that is, transcription) could be too slow; and when the response at
the protein level may require specific interactions or
modifications to tens to thousands of proteins, which
is difficult to achieve. Reversible methylation or other
forms of modifications on mRNA provides the best
option. A specific sequence that can undergo reversible modification, and thus be subjected to regulation,
can be readily included in a group of mRNA transcripts
(for example, at their 3UTRs) and lncRNAs in order
to affect RNA stability, localization and translatability,
as shown in the example ofYTHDF2.
Perspectives
In summary, reversible RNA methylation shares many
of the same characteristics as epigenetic DNA and histone modifications. Expression levels and potentially
post-translational modifications of writers, erasers
and readers can constantly sculpt the RNA methylome (FIG.5), which might in turn affect the eventual
protein expression. Therefore, the reversible chemical
tagging that dynamically controls the outcome of gene
expression occurs in all three main components of the
central dogma. Whereas epigenetic DNA and histone
modifications affect mostly transcriptional events,
reversible RNA methylation mainly has an impact on
regulation of post-transcriptional gene expression and
could directly affect protein production. Indeed, recent
research indicates that cellular protein levels are not
necessarily correlated with the mRNA levels105,106, which
emphasizes the importance of post-transcriptional
regulation of gene expression. Owing to the shared
use of reversible chemical tagging for dynamic gene
expression control, reversible RNA methylation has
been compared with epigenetic DNA and histone
modifications10,107. To also be a true epigenetic mark,
m6A would need to be heritable through cell division;
although this has not yet been demonstrated, such
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METTL14
METTL3
WTAP
Histone modication
RNA polymerase II
An
m7Gppp
Nuclear retention
Nuclear
speckle
ALKBH5
FTO foci
Translation
FTO
m7Gppp
6
Me m A
An
m7Gppp
An
Me
m7Gppp
An
m7Gppp
An
Storage or
transport
Me
m7Gppp
6
Me m A
An
Export
YTHDF2
Translation
Me
m7Gppp
An
m7Gppp
An
m7Gppp
Me
An
m7Gppp
An
m7Gppp
An
Ribosome
Me
m
7Gppp
Me
Translating pool
An
ppp
Me
An
An
Me
Me
Me
m 7G
Me
Translatable pool
Me
m 7Gpp
Me
Me
An
Stress granule
ppp
Me
mG
m 7Gppp
Me
Me
An
mRNA decay
P-body
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a possibility is conceivable through direct passage
of writer, reader and eraser proteins or methylated
RNA between generations of cells, which is a research
direction that needs to be further explored.
Many challenges lie ahead. It will be important to
clearly define the spatiotemporal properties of m6A
in terms of tissue specificity and in response to external and internal cues. The top priority is to elucidate
the involvement of m6A in RNA degradation, transport, storage, translation and splicing. The first steps
to achieve this goal will involve identifying and elucidating the functions of m6A reader proteins. Some
additional questions are: what is the interplay between
methyltransferases and demethylases that orchestrate
the methylation status of individual sites? How is
methylation and demethylation selectivity achieved?
Is the methylation coupled with transcription, and do
the two processes have mutual interactions? From yeast
to humans, how do the functions of m6A relate to cell
phenotypes and cell behaviour? Could some of the
processes be targeted to regulate biological functions
or to treat human diseases? Further research will answer
some of these questions and reveal fundamental aspects
of m6A biology.
Suzuki,M.M. & Bird,A. DNA methylation landscapes:
provocative insights from epigenomics. Nature Rev.
Genet. 9, 465476 (2008).
2. Kohli,R.M. & Zhang,Y. TET enzymes, TDG and the
dynamics of DNA demethylation. Nature 502,
472479 (2013).
3. Jones,P.A. Functions of DNA methylation: islands,
start sites, gene bodies and beyond. Nature Rev.
Genet. 13, 484492 (2012).
4. Branco,M.R., Ficz,G. & Reik,W. Uncovering the role
of 5hydroxymethylcytosine in the epigenome. Nature
Rev. Genet. 13, 713 (2012).
5. Bhutani,N., Burns,D.M. & Blau,H.M. DNA
demethylation dynamics. Cell 146, 866872 (2011).
6. Strahl,B.D. & Allis,C.D. The language of covalent
histone modifications. Nature 403, 4145 (2000).
7. Shi,Y. Histone lysine demethylases: emerging roles in
development, physiology and disease. Nature Rev.
Genet. 8, 829833 (2007).
8. Klose,R.J., Kallin,E.M. & Zhang,Y. JmjC-domaincontaining proteins and histone demethylation.
Nature Rev. Genet. 7, 715727 (2006).
9. Bird,A. Molecular biology. Methylation talk between
histones and DNA. Science. 294, 21132115 (2001).
10. He,C. Grand challenge commentary: RNA epigenetics?
Nature Chem. Biol. 6, 863865 (2010).
11. Grosjean,H. & Benne,R. Modification and Editing
of RNA (American Society for Microbiology Press,
1998).
12. Grosjean,H.Fine-Tuning of RNA Functions by
Modication and Editing (Springer-Verlag, 2005).
13. Machnicka,M.A. etal. MODOMICS: a database
of RNA modification pathways 2013 update.
Nucleic Acids Res. 41, D262D267 (2013).
14. Motorin,Y. & Helm,M. RNA nucleotide methylation.
Wiley Interdiscip. Rev. RNA 2, 611631 (2011).
15. Jia,G. etal. N6methyladenosine in nuclear RNA is a
major substrate of the obesity-associated FTO.
Nature Chem. Biol. 7, 885887 (2011).
This work describes a major breakthrough of
discovering the first m6A RNA demethylase FTO,
which highlights the possible biological function
of m6A.
16. Zheng,G. etal. ALKBH5 is a mammalian RNA
demethylase that impacts RNA metabolism and
mouse fertility. Mol. Cell 49, 1829 (2013).
This study discovered the second mammalian m6A
demethylase ALKBH5 that affects mouse
spermatogenesis.
17. Dominissini,D. etal. Topology of the human and
mouse m6A RNA methylomes revealed by m6A-seq.
Nature 485, 201206 (2012).
1.
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REVIEWS
42. Wang,Y. etal. N6-methyladenosine modification
destabilizes developmental regulators in embryonic
stem cells. Nature Cell Biol. 16, 191198 (2014).
This study discovered that the m6A modification
on mRNA affects embryonic cell differentiation.
43. Alexandrov,A., Martzen,M.R. & Phizicky,E.M.
Two proteins that form a complex are required for
7methylguanosine modification of yeast tRNA.
RNA 8, 12531266 (2002).
44. Chujo,T. & Suzuki,T. Trmt61B is a methyltransferase
responsible for 1methyladenosine at position 58 of
human mitochondrial tRNAs. RNA 18, 22692276
(2012).
45. Ozanick,S., Krecic,A., Andersland,J. &
Anderson,J.T. The bipartite structure of the
tRNA m1A58 methyltransferase from S.cerevisiae
is conserved in humans. RNA 11, 12811290
(2005).
46. Leulliot,N. etal. Structure of the yeast tRNA m7G
methylation complex. Structure 16, 5261 (2008).
47. Zhong,S. etal. MTA is an Arabidopsis messenger
RNA adenosine methylase and interacts with a
homolog of a sex-specific splicing factor. Plant Cell 20,
12781288 (2008).
48. Agarwala,S.D., Blitzblau,H.G., Hochwagen,A. &
Fink,G.R. RNA methylation by the MIS complex
regulates a cell fate decision in yeast. PLoS Genet. 8,
e1002732 (2012).
49. Little,N.A., Hastie,N.D. & Davies,R.C. Identification
of WTAP, a novel Wilms tumour 1associating protein.
Hum. Mol. Genet. 9, 22312239 (2000).
50. Ping,X.L. etal. Mammalian WTAP is a regulatory
subunit of the RNA N6methyladenosine
methyltransferase. Cell Res. 24, 177189 (2014).
51. Horiuchi,K. etal. Identification of Wilms
Tumor1associating protein complex and its role in
alternative splicing and the cell cycle. J.Biol. Chem.
288, 3329233302 (2013).
52. Bodi,Z. etal. Adenosine methylation in Arabidopsis
mRNA is associated with the 3 end and reduced
levels cause developmental defects. Front. Plant Sci.
3, 48 (2012).
53. Hongay,C.F. & Orr-Weaver,T.L. Drosophila Inducer of
MEiosis 4 (IME4) is required for Notch signaling
during oogenesis. Proc. Natl Acad. Sci. USA 108,
1485514860 (2011).
54. Peters,T., Ausmeier,K. & Ruther,U. Cloning of Fatso
(Fto), a novel gene deleted by the Fused toes (Ft)
mouse mutation. Mamm. Genome 10, 983986
(1999).
55. Dina,C. etal. Variation in FTO contributes to
childhood obesity and severe adult obesity. Nature
Genet. 39, 724726 (2007).
56. Frayling,T.M. etal. A common variant in the FTO
gene is associated with body mass index and
predisposes to childhood and adult obesity. Science
316, 889894 (2007).
57. Scuteri,A. etal. Genome-wide association scan
shows genetic variants in the FTO gene are
associated with obesity-related traits. PLoS Genet. 3,
e115 (2007).
58. Gerken,T. etal. The obesity-associated FTO gene
encodes a 2oxoglutarate-dependent nucleic acid
demethylase. Science 318, 14691472 (2007).
59. Fischer,J. etal. Inactivation of the Fto gene protects
from obesity. Nature 458, 894898 (2009).
60. Church,C. etal. Overexpression of Fto leads to
increased food intake and results in obesity. Nature
Genet. 42, 10861092 (2010).
61. Boissel,S. etal. Lossoffunction mutation in the
dioxygenase-encoding FTO gene causes severe growth
retardation and multiple malformations. Am. J.Hum.
Genet. 85, 106111 (2009).
62. He,Y.F. etal. Tet-mediated formation of
5carboxylcytosine and its excision by TDG in
mammalian DNA. Science 333, 13031307
(2011).
63. Ito,S. etal. Tet proteins can convert 5methylcytosine
to 5formylcytosine and 5carboxylcytosine. Science
333, 13001303 (2011).
64. Tahiliani,M. etal. Conversion of 5methylcytosine to
5hydroxymethylcytosine in mammalian DNA by MLL
partner TET1. Science 324, 930935 (2009).
65. Jia,G. etal. Oxidative demethylation of
3methylthymine and 3methyluracil in single-stranded
DNA and RNA by mouse and human FTO. FEBS Lett.
582, 33133319 (2008).
66. Hess,M.E. etal. The fat mass and obesity associated
gene (Fto) regulates activity of the dopaminergic
midbrain circuitry. Nature Neurosci. 16, 10421048
(2013).
REVIEWS
119. Fu,Y. etal. The AlkB domain of mammalian ABH8
catalyzes hydroxylation of
5methoxycarbonylmethyluridine at the wobble
position of tRNA. Angew. Chem. Int. Ed Engl. 49,
88858888 (2010).
120. van den Born,E. etal. ALKBH8mediated formation
of a novel diastereomeric pair of wobble nucleosides
in mammalian tRNA. Nature Commun. 2, 172
(2011).
121. Aik, W. et al. Structure of human RNA
N6-methyladenine demethylase ALKBH5 provides
insights into its mechanisms of nucleic acid recognition
and demethylation. Nucleic Acids Res. http://dx.doi.
org/10.1093/nar/gku085 (2014).
Acknowledgements
FURTHER INFORMATION
Modomics a database of RNA modification pathways:
http://modomics.genesilico.pl/
Three-dimensional ribosomal modification maps database:
http://people.biochem.umass.edu/fournierlab/3dmodmap/
main.php
tRNAmod prediction of tRNA modifications: http://crdd.
osdd.net/raghava/trnamod/
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