dynamic rna modifications in disease
TRANSCRIPT
Dynamic RNA modifications in diseaseArne Klungland1,2 and John Arne Dahl1,3
Available online at www.sciencedirect.com
ScienceDirect
While the presence of 6-methyladenosine (m6A) modifications
in mRNA was noted several decades ago, the first enzyme
reversing this modification was identified very recently. Today
we know of two methyltransferases introducing m6A in
mRNA — METTL3 and METTL14 — and two demethylases
that remove it have been identified — FTO (ALKBH9) and
ALKBH5. The conserved role of m6A seems to relate to
meiosis, and mice lacking ALKBH5 are infertile. While loss-of-
function mutation in FTO causes a recessive lethal syndrome,
sequence variants in introns of the FTO gene are associated
with obesity and type 2 diabetes.
Addresses1 Clinic for Diagnostics and Intervention and Institute of Medical
Microbiology, Oslo University Hospital, Rikshospitalet, Sognsvannsveien
20, 0027 Oslo, Norway2 Institute of Basic Medical Sciences, University of Oslo, 0315 Oslo,
Norway
Corresponding author: Klungland, Arne ([email protected])3Current address: Ludwig Institute for Cancer Research, La Jolla, CA
92093, USA.
Current Opinion in Genetics & Development 2014, 26:47–52
This review comes from a themed issue on Molecular and genetic
bases of disease
Edited by Cynthia T McMurray and Jan Vijg
http://dx.doi.org/10.1016/j.gde.2014.05.006
0959-437X # 2014 Published by Elsevier Ltd. All right reserved.
IntroductionA broad repertoire of modifications is known to underlie
the adaptable coding and structural function of proteins,
DNA and various RNA species. Methylations of mam-
malian DNA and histone residues are known to impact
regulation of transcription and the discoveries of
demethylases that remove methylation in DNA and
histones provide a basis for the understanding of dynamic
regulation of mammalian gene expression. The discovery
of these demethylases has led to significant progress in
the understanding of methyl marks in gene regulation and
the role of dynamic regulation in numerous diseases [1–6]. In mRNA, the m6A modification is particularly inter-
esting since it is the most abundant internal modification
and each mRNA contains on average from three to five
m6A modifications [7]. In prokaryotes, the m6A base
modification in DNA is a well-known epigenetic mark
www.sciencedirect.com
that influences many cellular processes [8], while m6A
seems to be absent from mammalian DNA. Early reports
indicate that the m6A modification in mRNA is installed
by a single methyltransferase complex with METTL3
(MT-A70) as the critical S-adenosyl-L-methionine
(SAM)-binding component [9–11]. The sequence speci-
ficity of this methyltransferase is not absolute, however,
m6A is only found on the degenerate consensus sequence
RR-m6A-CH (R = purine, H = C, A or U), yet, only a
fraction of consensus sequences is methylated [12,13].
Recently, two laboratories used a novel antibody-based
approach for methylated RNA immunoprecipitation com-
bined with massively parallel sequencing [14��,15��].These comprehensive analyses of mRNA methylation
revealed a distinct pattern of the m6A topology.
While 5-methylcytosine (5mC), and products thereof,
represent the key base modifications in DNA; cellular
RNAs, such as mRNA, tRNA, rRNA, and snRNA, have
long been known to contain more than 100 structurally
different base modifications [16]. Indeed, ALKBH8 was
previously shown to be required for the biogenesis of
multiple tRNA wobble uridine modifications [17–20].
The exact function of many of these RNA modifications
remains elusive, yet some are directly linked with human
diseases [21–23]; reviewed in [24]. It has been speculated
that some RNA modifications could be dynamic and have
regulatory roles analogous to modifications of proteins and
DNA [25]. Recently the m6A modification in mRNA was
given increased attention after it was demonstrated to be
a dynamic mark. This modification also exists in other
RNA species like tRNA [26] and rRNA [27].
Studies in model organisms, as well as in humans, points
toward important roles of m6A in cellular homeostasis.
Additionally, inactivation of enzymes required for
m6A demethylation cause obvious pathologies in mice
and men. In this short review, we will describe novel
findings on the dynamics of m6A and its role in disease
(Figure 1).
Topology of 6-methyladenosine (m6A) in mRNAAlthough the abundance of m6A in mRNA has been
known for a long time, a method for globally identifying
the m6A sites was only established recently. In 2012, two
independent laboratories reported on the distribution of
m6A in mRNA [14��,15��]. Both these studies developed
an antibody-based method for enrichment of m6A sites
combined with high throughput sequencing. More than
7000 human genes were recognized as m6A containing,
and m6A sites are particularly enriched around stop
codons. Sites were also found at 30 UTRs and within
Current Opinion in Genetics & Development 2014, 26:47–52
48 Molecular and genetic bases of disease
Figure 1
N
N
NN
N
N
NN
HN
HN
RNA
RNA
RNA
RNA
O
OO
N N
NN
RNA
OH
RNA
OO
O
OO
OO
CHH
OH
OH
FTO loss-of-function in humans cause severe growthretardation and multiple malformations [55].
MUTANT AND POLYMORPHIC VARIANTS OF m6ADEMETHYLASES
MUTANT ORGANISMS FOR COMPONENTS OF THE m6A METHYLTRANSFERASE COMPLEX
CH3
NH2
CH2OH
m6Adenosine
hm6Adenosine
Adenosine
Hydroxylases(demethylases)
FTO andALKBH5
+O2,Fe(II)/α-KG
Methyltransferase complexMETTL3,METTL14,
WTAP, and more+
S-Adenosy-L-methionine
Formaldehyde
ALKBH5 inactivation in mice causes female and male infertility and increased amount of internal m6A modifications in mRNA [29].
Polymorphic variants in the human FTO gene and FTO overexpression in mice leads to obesity, [52-54, 57].
IME4 is required for sporulation in S. Cerevisiae and induction of sporulation leads to appearence of m6A in yeast mRNA [47].
IME4 is expressed in testes and ovaries of D. Melanogaster and is required for viability. Hypomorphic IME4 alleles reveal critical functions in oogenesis [49].
MTA is required for the developing embryo of Arabidopsis. MTA expression strongly correlates with dividing tissues, particularly in reproductive organs [48].
WTAP, a subunit of the mammalian methyltransferase complex, is required for differentiation of endoderm and mesoderm in the mosue embryo and WTAPmutant embryos dies at day 6.5 - 10.5 [50-51].
FTO inactivation in mice leads to growth retardation, infertility and protects from obesity [56].
Current Opinion in Genetics & Development
Methylation and demethylation of 6-methyladenosine (m6A) in mRNA. Methylation of internal adenosines in mRNA is most likely catalyzed by a single
methyltransferase complex of which METTL3 is the S-adenosyl-L-methionine (SAM)-binding component. FTO and ALKBH5 catalyze the oxidative
demethylation of m6A in mRNA with hydroxymethyladenosine (hm6A) as a predictable unstable intermediate. FTO and ALKBH5 are iron(II)/a-KG-
dependent dioxygenases, which use their iron(II) center and the a-KG cofactor to activate dioxygen. The unstable oxidized intermediate, hm6A, then
spontaneously releases formaldehyde, resulting in the removal of the methyl group from adenine. The phenotypes of mutant organisms lacking genes
required for m6A dynamics are specified.
long internal exons. Importantly, m6A sites were found to
be highly conserved between humans and mice. These
data strongly support a fundamental regulatory role of
m6A. More recently, a high-resolution map of m6A modi-
fications in meiotic yeast transcripts was obtained [28��].These results reveal a dynamically regulated mRNA
methylome in yeast meiosis, and this study is of particular
interest for mammalian studies where the enzymatic
reversion of m6A to adenosine (A) seems to be essential
for successful spermatogenesis and oogenesis [29��]. Cur-
rently, several protocols are being developed for the
identification of m6A in the transcriptome [30,31].
Current Opinion in Genetics & Development 2014, 26:47–52
Writers and erasers of 6-methyladenosine(m6A) in mRNAThe m6A modification in mammalian mRNA is most
likely installed by a single methyltransferase complex
and METTL3 (MT-A70) was early identified as the
candidate S-adenosyl-L-methionine (SAM)-binding com-
ponent of this complex [9]. Recently, affinity purification
of tagged-METTL3 led to the identification of
METTL14, thus suggesting that the methyltransferase
complex contains two active methyltransferase subunits
[32��]. At the same time, two other publications described
the identification of the METTL14 methyltransferase by
www.sciencedirect.com
Dynamic RNA modifications in disease Klungland and Dahl 49
sequence homology search [33��,34�]. The METTL3 and
METTL14 methyltransferases are not well character-
ized, though it seems that they have overlapping func-
tions and downregulation of METTL3 and METTL14 in
stem cells led to similar phenotypes. WTAP has been
identified as a third member of the methyltransferase
complex and is required for the localization of METTL3
and METTL14 to nuclear speckles and downregulation
of WTAP affects the cellular m6A level [32��,33��]. The
mammalian methyltransferase complex probably con-
tains numerous essential proteins yet to be identified.
In 2011, it was reported that the fat mass and obesity-
associated FTO protein catalyzes the removal of m6A
from RNA in vitro and in vivo [35��]. This was the first
example of reversible RNA methylation. The oxidation
of m6A by FTO has later been described in more detail.
FTO also generates the two additional intermediate
modifications, 6-hydroxymethyladenosine (hm6A) and
6-formyladenosine (f6A), and, importantly, both of these
products have been identified in vivo [36]. FTO is a
distantly related member of the mammalian AlkB family
and is also identified as ALKBH9. ALKBH5 was reported
as a second m6A demethylase and a lack of ALKBH5 in
mice lead to a remarkable upregulation of m6A in mRNA
in vivo [29��]. In contrast, the role of FTO in demethylat-
ing m6A in vivo has not been firmly established and FTO
has the ability to demethylate several modifications in
single-stranded DNA and RNA in vitro [37,38].
A few reports on the structure of m6A demethylases,
FTO and ALKBH5 have been published and they all
identify a loop that confers single-stranded RNA or DNA
selectivity [39�,40–42]. While the structure of FTO is in a
complex with the mononucleotide 3-methyltymine
(m3T) no structures have yet been obtained with
RNA-oligoes containing the relevant modified base.
Readers of 6-methyladenosine (m6A) in mRNA6-Methyladenosine appears to have biochemical proper-
ties similar to adenosine. Thus, it seems likely that the
role of m6A is executed through proteins and other RNAs
that bind at specific m6A sites. A breakthrough in this
direction was the discovery of the selective recognition of
m6A by the human YTH domain family 2 (YTHDF2)
protein [43��]. YTHDF2 regulates mRNA degradation
and has over 3000 cellular RNA targets, including
mRNAs and non-coding RNAs. The RNA-Binding
Protein DataBase (RBPDB) includes 422 human proteins
[44]. While some of these have sequence specificities
excluding them from being specific for m6A recognition,
others might well require m6A for selective binding [45].
Indeed, there is a good overlap between m6A peaks in the
untranslated 30 region of mRNAs and known regions for
RNA regulatory elements [15��]. Also, it might well be
that m6A affects the binding of miRNA [46].
www.sciencedirect.com
Mutant organisms and diseaseEarly studies in yeast failed to identify m6A in mRNA.
However, the IME4 (Inducer of MEiosis 4) gene of
S. cerevisiae is very similar to the mammalian m6A methyl-
transferase subunit and the amount of IME4 mRNA is
greatly elevated during sporulation and in the stationary
phase [47]. With this information, an increased level of
m6A was detected in both vegetative and sporulating
yeast cells [47]. Mutations in the catalytic domain of
IME4 cause defective sporulation. Similarly, studies of
the METTL3 homolog in Arabidopsis and Drosophilamutants point toward a conserved role for m6A in game-
togenesis [48,49] Unlike yeast, the m6A methyltransfer-
ases in Arabidopsis and Drosophila are required for
viability. No reports on the mutating of the two putative
mammalian m6A methyltransferases, METTL3 and
METTL14, have been published. WTAP, one of the
other subunits of the methyltransferase complex, is
required for differentiation of endoderm and mesoderm
in the mouse embryo and the WTAP mutant embryos die
between day 6.5 and day 10.5 [50,51].
Obesity and type 2 diabetes obviously depends upon
environmental and social factors such as inactive daily
life and unhealthy diet. On the other hand, some genetic
variants clearly increase the risk of weight gain and in
2007 several genome wide association studies (GWAS)
identified an association with common variants of the
FTO gene and childhood and adult obesity [52–54]. While
variants of several genes have been found to increase
weight gain, the variant most strongly associated with
obesity is found in intron 1 of the FTO gene. Despite
extensive efforts, the possible role of the FTO protein
and m6A dynamics in obesity remains elusive. In con-
trast, loss-of-function mutation in the FTO gene is
responsible for a recessive lethal syndrome [55]. Charac-
teristics of affected individuals include postnatal growth
retardation, microcephaly, psychomotor delay, brain def-
icits and cardiac defects [55]. These findings point
toward an essential role of FTO and m6A dynamics for
normal development of the human brain and the cardi-
ovascular system.
In mice, loss of the FTO gene causes postnatal growth
retardation whereas FTO overexpression leads to
increased food intake and obesity [56,57]. Most studies
in mice have been done on gene-targeted mutants,
which might be less informative for obesity. Yet, it has
been shown that FTO demethylate specific mRNAs that
regulates the activity of dopaminergic midbrain circuitry
[58]. In another study, FTO was found to have a role in
cellular sensing of amino acids and it was proposed that
FTO might influence the body mass index by cellular
nutrient sensing [59]. In a most recent study on FTO,
however, obesity variants within the FTO gene are
reported to form long-range functional connections
with the homeobox gene IRX3 [60��]. IRX3 is located
Current Opinion in Genetics & Development 2014, 26:47–52
50 Molecular and genetic bases of disease
downstream from FTO and is, together with FTO and
four other genes, within the 1.6 Mb region that if deleted
causes the fused toes (Ft) mutation [61]. The body
weight of IRX3 deficient mice is reduced by 25–30%
mostly through loss off fat mass and an increase in
metabolic rate. Additionally, it was previously shown
that obesity associated variants located in FTO introns
contain conserved noncoding sequences overlapping
with regulatory elements of transcription factors and
that irx3a knockdown in zebrafish suggests a direct role
of IRX3 for both obesity and type 2 diabetes [62]. These
studies indicate that the FTO protein itself is not linked
to obesity in humans.
Finally, in an exciting study, it is reported that m6A
mRNA methylation affects the mammalian circadian
clock and that specific inhibition of m6A methylation
cause an elongation of the circadian period [63��]. There
is considerable epidemiological evidence, although com-
plex, for an association of circadian disruption and human
diseases such as obesity, diabetes and cancer [64]. Thus,
mutant organisms of m6A writers and readers should be
characterized for possible circadian disruption and disease
association.
Conclusions and future prospectsDespite the recent focus on m6A and the identification of
its dynamic appearance, studies on m6A are still in their
infancy. The highly regulated and sequence specific meth-
ylation of adenosine in mRNA points to the important
regulatory roles of m6A. This speculation is further sub-
stantiated by the severe phenotype of organisms, including
mice, lacking the proteins required for m6A metabolism.
Future, and probably present, studies on dynamic RNA
modifications would have the following focuses.
� Only three proteins of the mammalian methyltrans-
ferase complex have been identified. Several other
proteins of the complex exist and should be identified
along with other proteins that might specifically
interact with m6A modifications and shed light on
the highly controlled and sequence specific methyla-
tion of mRNA.
� At present, a simple and truly single-nucleotide
resolution strategy for identifying m6A in the tran-
scriptome is missing. Improved methodology would
allow for detailed analysis of reversible m6A sites in
development and disease.
� The fundamental role of m6A during meiosis is
revealed, yet, the detailed understanding of m6A
dynamics during meiosis is completely lacking. Mature
eggs and sperm are very rare in animal models for m6A
demethylases and discourage further analysis. Single-
cell analysis on immature cells could provide insight
into the specific regulation of m6A in mammalian
meiosis.
Current Opinion in Genetics & Development 2014, 26:47–52
� The structures of the writers and erasers of m6A, in a
complex with RNA substrate, are lacking despite
substantial efforts in several laboratories. Thus,
detailed information on the structure-function relation-
ship of the writers and readers of m6A should be
pursued.
� It is reasonable to speculate that other dynamic
modifications of RNA bases exist. Mutant organisms
lacking methyl transferases for protein-methylation,
DNA-methylation or RNA-methylation can generally
be characterized by identifying the missing methyl
group, and the methyl group can be added in vitro by
the addition of the recombinant enzyme. It is more
difficult to study the reversal of dynamic modifications
where a fine tuned balance might only be slightly
distorted, and thus, the characterization of demethy-
lases is lagging behind. The identification of reversible
modifications in short-lived RNA species is another
challenge. Nevertheless, future work should aim at
identifying other reversible modifications in RNA and
initially the focus could be on relatively stable and
abundant RNAs such as tRNAs and ribosomal RNAs.
AcknowledgementsWe acknowledge the generous support from the Norwegian ResearchCouncil, The Norwegian Cancer Society and Oslo University Hospital. Thisproject is also supported by the Norwegian-Polish collaborative grant.
References and recommended readingPapers of particular interest, published within the period of review,have been highlighted as:
� of special interest�� of outstanding interest
1. Tsukada Y, Fang J, Erdjument-Bromage H, Warren ME,Borchers CH, Tempst P, Zhang Y: Histone demethylation by afamily of JmjC domain-containing proteins. Nature 2006,439:811-816.
2. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z,Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, He C, Xu GL: Tet-mediated formation of 5-carboxylcytosine and its excision byTDG in mammalian DNA. Science 2011, 333:1303-1307.
3. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C,Zhang Y: Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011,333:1300-1303.
4. Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA,Casero RA, Shi Y: Histone demethylation mediated by thenuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953.
5. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y,Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A: Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalianDNA by MLL partner TET1. Science 2009, 324:930-935.
6. Jaenisch R, Bird A: Epigenetic regulation of gene expression:how the genome integrates intrinsic and environmentalsignals. Nat Genet 2003, 33(Suppl):245-254.
7. Tuck MT: The formation of internal 6-methyladenine residuesin eucaryotic messenger RNA. Int J Biochem 1992, 24:379-386.
8. Wion D, Casadesus J: N6-methyl-adenine: an epigenetic signalfor DNA–protein interactions. Nat Rev Microbiol 2006, 4:183-192.
9. Bokar JA, Shambaugh ME, Polayes D, Matera AG, Rottman M:Purification and cDNA cloning of the AdoMet-binding subunit
www.sciencedirect.com
Dynamic RNA modifications in disease Klungland and Dahl 51
of the human mRNA (N6-adenosine)-methyltransferase. RNA1997, 3:1233-1247.
10. Bodi Z, Button JD, Grierson D, Fray RG: Yeast targets for mRNAmethylation. Nucleic Acids Res 2010, 38:5327-5335.
11. Wei CM, Gershowitz A, Moss B: 50-Terminal and internalmethylated nucleotide sequences in HeLa cell mRNA.Biochemistry 1976, 15:397-401.
12. Harper JE, Miceli SM, Roberts RJ, Manley JL: Sequencespecificity of the human mRNA N6-adenosine methylase invitro. Nucleic Acids Res 1990, 18:5735-5741.
13. Schibler U, Kelley DE, Perry RP: Comparison of methylatedsequences in messenger RNA and heterogeneous nuclearRNA from mouse L cells. J Mol Biol 1977, 115:695-714.
14.��
Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE,Jaffrey SR: Comprehensive analysis of mRNA methylationreveals enrichment in 30 UTRs and near stop codons. Cell 2012,149:1635-1646.
This study, together with Ref. [15��], developed a novel method forportraying the distribution of m6A in the mammalian transcriptome.
15.��
Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J,Amariglio N, Kupiec M, Sorek R, Rechavi G: Topology of thehuman and mouse m6A RNA methylomes revealed by m6A-seq. Nature 2012, 485:201-206.
This study, together with Ref. [14��], developed a novel method forportraying the distribution of m6A in the mammalian transcriptome.
16. Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA,Zhang X, Vendeix FA, Fabris D, Agris PF: The RNA ModificationDatabase, RNAMDB: 2011 update. Nucleic Acids Res 2011,39:D195-D201.
17. Songe-Moller L, van den Born E, Leihne V, Vagbo CB,Kristoffersen T, Krokan HE, Kirpekar F, Falnes PO, Klungland A:Mammalian ALKBH8 possesses tRNA methyltransferaseactivity required for the biogenesis of multiple wobble uridinemodifications implicated in translational decoding. Mol CellBiol 2010, 30:1814-1827.
18. Fu D, Brophy JA, Chan CT, Atmore KA, Begley U, Paules RS,Dedon PC, Begley TJ, Samson LD: Human AlkB homolog ABH8Is a tRNA methyltransferase required for wobble uridinemodification and DNA damage survival. Mol Cell Biol 2010,30:2449-2459.
19. Fu Y, Dai Q, Zhang W, Ren J, Pan T, He C: The AlkB domain ofmammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position oftRNA. Angew Chem Int Ed Engl 2010, 49:8885-8888.
20. van den Born E, Vagbo CB, Songe-Moller L, Leihne V, Lien GF,Leszczynska G, Malkiewicz A, Krokan HE, Kirpekar F, Klungland A,Falnes PO: ALKBH8-mediated formation of a noveldiastereomeric pair of wobble nucleosides in mammaliantRNA. Nat Commun 2011, 2:172.
21. Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K: Taurine as aconstituent of mitochondrial tRNAs: new insights into thefunctions of taurine and human mitochondrial diseases. EMBOJ 2002, 21:6581-6589.
22. Kirino Y, Yasukawa T, Ohta S, Akira S, Ishihara K, Watanabe K,Suzuki T: Codon-specific translational defect caused by awobble modification deficiency in mutant tRNA from a humanmitochondrial disease. Proc Natl Acad Sci U S A 2004,101:15070-15075.
23. Wei FY, Suzuki T, Watanabe S, Kimura S, Kaitsuka T, Fujimura A,Matsui H, Atta M, Michiue H, Fontecave M, Yamagata K, Suzuki T,Tomizawa K: Deficit of tRNA(Lys) modification by Cdkal1causes the development of type 2 diabetes in mice. J Clin Invest2011, 121:3598-3608.
24. Carell T, Brandmayr C, Hienzsch A, Muller M, Pearson D, Reiter V,Thoma I, Thumbs P, Wagner M: Structure and function ofnoncanonical nucleobases. Angew Chem Int Ed Engl 2012,51:7110-7131.
25. He C: Grand challenge commentary: RNA epigenetics? NatChem Biol 2010, 6:863-865.
www.sciencedirect.com
26. Saneyoshi M, Harada F, Nishimura S: Isolation andcharacterization of N6-methyladenosine from Escherichia colivaline transfer RNA. Biochim Biophys Acta 1969, 190:264-273.
27. Iwanami Y, Brown GM: Methylated bases of ribosomalribonucleic acid from HeLa cells. Arch Biochem Biophys 1968,126:8-15.
28.��
Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P,Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA,Lander ES, Fink GR, Regev A: High-resolution mapping revealsa conserved, widespread, dynamic mRNA methylationprogram in yeast meiosis. Cell 2013, 155:1409-1421.
Methylation of adenosine to m6A in mRNA is particularly important formeiosis and this is the first publication mapping the dynamic of m6Amethylation during meiosis.
29.��
Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ,Vagbo CB, Shi Y, Wang WL, Song SH, Lu Z, Bosmans RP, Dai Q,Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K,Fu Y, Jia G, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG, He C:ALKBH5 is a mammalian RNA demethylase that impacts RNAmetabolism and mouse fertility. Mol Cell 2013, 49:18-29.
The second m6A demethylase is identified in this study and a functionalrole for m6A dynamics in mammalian mRNA is also discovered.
30. Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M,Amariglio N, Rechavi G: Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturingand massively parallel sequencing. Nat Protoc 2013, 8:176-189.
31. Liu N, Parisien M, Dai Q, Zheng G, He C, Pan T: Probing N6-methyladenosine RNA modification status at single nucleotideresolution in mRNA and long noncoding RNA. RNA 2013,19:1848-1856.
32.��
Ping XL, Sun BF, Wang L, Xiao W, Yang X, Wang WJ, Adhikari S,Shi Y, Lv Y, Chen YS, Zhao X, Li A, Yang Y, Dahal U, Lou XM, Liu X,Huang J, Yuan WP, Zhu XF, Cheng T, Zhao YL, Wang X, RendtlewDanielsen JM, Liu F, Yang YG: Mammalian WTAP is a regulatorysubunit of the RNA N6-methyladenosine methyltransferase.Cell Res 2014, 24:177-189.
Functional interactions with METTL3 identify WTAP and METTL14 ascrucial subunits of the mammalian m6A-methylase complex.
33.��
Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L, Jia G, Yu M, Lu Z,Deng X, Dai Q, Chen W, He C: A METTL3-METTL14 complexmediates mammalian nuclear RNA N6-adenosine methylation.Nat Chem Biol 2014, 10:93-95.
This work uncovers components of the m6A RNA methyltransferasecomplex and reveals a negative correlation between the m6A level inmRNA and gene expression.
34.�
Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC: N6-methyladenosine modification destabilizes developmentalregulators in embryonic stem cells. Nat Cell Biol 2014, 16:191-198.
This work revealed that m6A modifications in mRNA affect differentiationof embryonic stem cells.
35.��
Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, Yi C, Lindahl T, Pan T,Yang YG, He C: N6-methyladenosine in nuclear RNA is a majorsubstrate of the obesity-associated FTO. Nat Chem Biol 2011,7:885-887.
A breakthrough study that for the first time identifies a m6A demethylase.
36. Fu Y, Jia G, Pang X, Wang RN, Wang X, Li CJ, Smemo S, Dai Q,Bailey KA, Nobrega MA, Han KL, Cui Q, He C: FTO-mediatedformation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat Commun 2013,4:1798.
37. Gerken T, Girard CA, Tung YC, Webby CJ, Saudek V,Hewitson KS, Yeo GS, McDonough MA, Cunliffe S, McNeill LA,Galvanovskis J, Rorsman P, Robins P, Prieur X, Coll AP, Ma M,Jovanovic Z, Farooqi IS, Sedgwick B, Barroso I, Lindahl T,Ponting CP, Ashcroft FM, O’Rahilly S, Schofield CJ: The obesity-associated FTO gene encodes a 2-oxoglutarate-dependentnucleic acid demethylase. Science 2007, 318:1469-1472.
38. Jia G, Yang CG, Yang S, Jian X, Yi C, Zhou Z, He C: Oxidativedemethylation of 3-methylthymine and 3-methyluracil insingle-stranded DNA and RNA by mouse and human FTO.FEBS Lett 2008, 582:3313-3319.
Current Opinion in Genetics & Development 2014, 26:47–52
52 Molecular and genetic bases of disease
39.�
Han Z, Niu T, Chang J, Lei X, Zhao M, Wang Q, Cheng W, Wang J,Feng Y, Chai J: Crystal structure of the FTO protein revealsbasis for its substrate specificity. Nature 2010, 464:1205-1209.
The first structure analysis that unravel the single-strand specificity of am6A demethylase.
40. Feng C, Liu Y, Wang G, Deng Z, Zhang Q, Wu W, Tong Y, Cheng C,Chen Z: Crystal structures of human RNA demethylase Alkbh5reveal basis for substrate recognition. J Biol Chem 2014.
41. Chen W, Zhang L, Zheng G, Fu Y, Ji Q, Liu F, Chen H, He C: Crystalstructure of the RNA demethylase ALKBH5 from zebrafish.FEBS Lett 2014, 588:892-898.
42. Aik W, Scotti JS, Choi H, Gong L, Demetriades M, Schofield CJ,McDonough MA: Structure of human RNA N6-methyladeninedemethylase ALKBH5 provides insights into its mechanismsof nucleic acid recognition and demethylation. Nucleic AcidsRes 2014.
43.��
Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M,Dai Q, Jia G, Ren B, Pan T, He C: N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 2014,505:117-120.
A ground breaking paper with the first identification of an m6A readerprotein.
44. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR: RBPDB: adatabase of RNA-binding specificities. Nucleic Acids Res 2011,39:D301-D308.
45. Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X,Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M,Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B,Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F,Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW,Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD,Hughes TR: A compendium of RNA-binding motifs fordecoding gene regulation. Nature 2013, 499:172-177.
46. Niu Y, Zhao X, Wu YS, Li MM, Wang XJ, Yang YG: N6-methyl-adenosine (m6A) in RNA: an old modification with a novelepigenetic function. Genom Proteom Bioinform 2013, 11:8-17.
47. Clancy MJ, Shambaugh ME, Timpte CS, Bokar JA: Induction ofsporulation in Saccharomyces cerevisiae leads to theformation of N6-methyladenosine in mRNA: a potentialmechanism for the activity of the IME4 gene. Nucleic Acids Res2002, 30:4509-4518.
48. Zhong S, Li H, Bodi Z, Button J, Vespa L, Herzog M, Fray RG: MTAis an Arabidopsis messenger RNA adenosine methylase andinteracts with a homolog of a sex-specific splicing factor. PlantCell 2008, 20:1278-1288.
49. Hongay CF, Orr-Weaver TL: Drosophila Inducer of MEiosis 4(IME4) is required for Notch signaling during oogenesis. ProcNatl Acad Sci U S A 2011, 108:14855-14860.
50. Horiuchi K, Umetani M, Minami T, Okayama H, Takada S,Yamamoto M, Aburatani H, Reid PC, Housman DE, Hamakubo T,Kodama T: Wilms’ tumor 1-associating protein regulates G2/Mtransition through stabilization of cyclin A2 mRNA. Proc NatlAcad Sci U S A 2006, 103:17278-17283.
51. Fukusumi Y, Naruse C, Asano M: Wtap is required fordifferentiation of endoderm and mesoderm in the mouseembryo. Dev Dyn 2008, 237:618-629.
52. Dina C, Meyre D, Gallina S, Durand E, Korner A, Jacobson P,Carlsson LM, Kiess W, Vatin V, Lecoeur C, Delplanque J, Vaillant E,Pattou F, Ruiz J, Weill J, Levy-Marchal C, Horber F, Potoczna N,Hercberg S, Le SC, Bougneres P, Kovacs P, Marre M, Balkau B,Cauchi S, Chevre JC, Froguel P: Variation in FTO contributes tochildhood obesity and severe adult obesity. Nat Genet 2007,39:724-726.
53. Frayling TM, Timpson NJ, Weedon MN, Zeggini E, Freathy RM,Lindgren CM, Perry JR, Elliott KS, Lango H, Rayner NW, Shields B,Harries LW, Barrett JC, Ellard S, Groves CJ, Knight B, Patch AM,
Current Opinion in Genetics & Development 2014, 26:47–52
Ness AR, Ebrahim S, Lawlor DA, Ring SM, Ben-Shlomo Y,Jarvelin MR, Sovio U, Bennett AJ, Melzer D, Ferrucci L, Loos RJ,Barroso I, Wareham NJ, Karpe F, Owen KR, Cardon LR, Walker M,Hitman GA, Palmer CN, Doney AS, Morris AD, Smith GD,Hattersley AT, McCarthy MI: A common variant in the FTO geneis associated with body mass index and predisposes tochildhood and adult obesity. Science 2007, 316:889-894.
54. Scuteri A, Sanna S, Chen WM, Uda M, Albai G, Strait J, Najjar S,Nagaraja R, Orru M, Usala G, Dei M, Lai S, Maschio A, Busonero F,Mulas A, Ehret GB, Fink AA, Weder AB, Cooper RS, Galan P,Chakravarti A, Schlessinger D, Cao A, Lakatta E, Abecasis GR:Genome-wide association scan shows genetic variants in theFTO gene are associated with obesity-related traits. PLoSGenet 2007, 3:e115.
55. Boissel S, Reish O, Proulx K, Kawagoe-Takaki H, Sedgwick B,Yeo GS, Meyre D, Golzio C, Molinari F, Kadhom N, Etchevers HC,Saudek V, Farooqi IS, Froguel P, Lindahl T, O’Rahilly S, Munnich A,Colleaux L: Loss-of-function mutation in the dioxygenase-encoding FTO gene causes severe growth retardation andmultiple malformations. Am J Hum Genet 2009, 85:106-111.
56. Fischer J, Koch L, Emmerling C, Vierkotten J, Peters T, Bruning JC,Ruther U: Inactivation of the Fto gene protects from obesity.Nature 2009, 458:894-898.
57. Church C, Moir L, McMurray F, Girard C, Banks GT, Teboul L,Wells S, Bruning JC, Nolan PM, Ashcroft FM, Cox RD:Overexpression of Fto leads to increased food intake andresults in obesity. Nat Genet 2010, 42:1086-1090.
58. Hess ME, Hess S, Meyer KD, Verhagen LA, Koch L, Bronneke HS,Dietrich MO, Jordan SD, Saletore Y, Elemento O, Belgardt BF,Franz T, Horvath TL, Ruther U, Jaffrey SR, Kloppenburg P,Bruning JC: The fat mass and obesity associated gene (Fto)regulates activity of the dopaminergic midbrain circuitry. NatNeurosci 2013, 16:1042-1048.
59. Gulati P, Cheung MK, Antrobus R, Church CD, Harding HP,Tung YC, Rimmington D, Ma M, Ron D, Lehner PJ, Ashcroft FM,Cox RD, Coll AP, O’Rahilly S, Yeo GS: Role for the obesity-related FTO gene in the cellular sensing of amino acids. ProcNatl Acad Sci U S A 2013, 110:2557-2562.
60.��
Smemo S, Tena JJ, Kim KH, Gamazon ER, Sakabe NJ, Gomez-Marin C, Aneas I, Credidio FL, Sobreira DR, Wasserman NF,Lee JH, Puviindran V, Tam D, Shen M, Son JE, Vakili NA, Sung HK,Naranjo S, Acemel RD, Manzanares M, Nagy A, Cox NJ, Hui CC,Gomez-Skarmeta JL, Nobrega MA: Obesity-associated variantswithin FTO form long-range functional connections with IRX3.Nature 2014, 507:371-375.
This study identifies a long-range connection of FTO-obesity variants withIRX3 and question a direct role for the FTO protein in obesity.
61. Peters T, Ausmeier K, Dildrop R, Ruther U: The mouse Fusedtoes (Ft) mutation is the result of a 1.6-Mb deletion includingthe entire Iroquois B gene cluster. Mamm Genome 2002,13:186-188.
62. Ragvin A, Moro E, Fredman D, Navratilova P, Drivenes O,Engstrom PG, Alonso ME, de la Calle ME, Gomez Skarmeta JL,Tavares MJ, Casares F, Manzanares M, van H, Molven V,Njolstad A, Argenton PR, Lenhard F, Becker TS: B: Long-rangegene regulation links genomic type 2 diabetes and obesity riskregions to HHEX, SOX4, and IRX3. Proc Natl Acad Sci U S A2010, 107:775-780.
63.��
Fustin JM, Doi M, Yamaguchi Y, Hida H, Nishimura S, Yoshida M,Isagawa T, Morioka MS, Kakeya H, Manabe I, Okamura H: RNA-methylation-dependent RNA processing controls the speed ofthe circadian clock. Cell 2013, 155:793-806.
This report shows that the period of the circadian clock is inverselyproportional to the methylation potential and that METTL3 knockdownresults in circadian period elongation.
64. Zelinski EL, Deibel SH, McDonald RJ: The trouble with circadianclock dysfunction: multiple deleterious effects on the brainand body. Neurosci Biobehav Rev 2014, 40:80-101.
www.sciencedirect.com