RNA modification types. 5 capping 3 poly(a) tailing Splicing Chemical modification editing

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2 RNA modification types 5 capping 3 poly(a) tailing Splicing Chemical modification editing

3 >150 RNA modifications

4 Purine nucleotide modifications (A and G) Machnicka, M.A. NAR 2013

5 Pyrimidine nucleotide modifications (C and U) Machnicka, M.A. NAR 2013

6 trna modifications

7 mrna modifications Cell 2017

8 S4U protect cell against UV stress E. coli Absorbance in near-uv

9 Queuosine is a guanosine analogue conserved in various species trna-guanine transglycosylase First position of anticodon Evolutionary conserved Prevent stop codon read-through Lung cancer cells: high Q deficiency

10 Pseudouridine (Y) is a the fifth base 1957 C-glycoside rotation isomer of uridine Change RNA structure UAG UAA UGA stop codon YAG YAA YGA non-stop codon trnas, rrnas, spliceosomal snrnas, But not in mrnas. about 100 ψ's in mammalian rrnas and over 20 ψ's in vertebrate spliceosomal snrnas play a role in ribosome biogenesis and in protein synthesis.

11 2 -O-methylation on RNA Plant HEN1 methylase discrimination of self and nonself mrna protect the 3 end of mirna against poly(u) degradation

12 The history of the research on m6a in mrna

13 m 6 A: the most prevalent RNA modification m 6 A on nuclear RNA including mrna, lncrna m 6 A also exists in various classes of RNA in eukaryotes, bacteria and archaea, including rrna, trna and snrna 50% mrna of S. cerevisiae contains m 6 A during meiosis. 3 5 m 6 A sites per mrna ; m6a sites in >7000 mrna (3 UTR) and 300 ncrna transcripts (NEAT1, TUG1, MALAT1) (A/G)(G>A)m 6 AC(U/A/C): G(m 6 A)C (70%) or A(m 6 A)C (30%)

14 m 6 A Functions Development Yeast: Appearance during meosis (Schwartz, et al. Cell 2013) Plant: MTA (METTL3 homologue) depletion - delayed embryogenesis (Zhong et al. Plant Cell 2008) Fly: IME4 (METTL3 homologue) knock out - embryonic lethality (Clancy et al. NAR 2002) Zebra fish: METTL3 and WTAP knock down development defect (Ping et al. Cell Research 2014) Mouse: FTO and ALKBH5 knock out adipo-tissue and testis defects, respectively (Fischer et al. Nature 2009; Zheng et al., Mol Cell 2013) Biological effect Regulation of circadian rhythms (Hastings et al Cell 2013) FTO: susceptibility gene of obesity and type-ii-diabetes (Vogan Nature Genetics, 2014) WTAP and m6a binding protein YTHDF2: leukemia susceptibility gene (Banasal et al. Leukemia 2014, Nguyen et al. Gene, Chromosomes & Cancer 2006) Molecular and Cellular function Cell pluripotency (Geula et al. Science 2015; Chen et al. Cell Stem Cell; Batista et al. Cell Stem Cell 2014) RNA stability (Wang et al. Nature 2014); mrna splicing; exonic splicing; intronic splicing

15 The transcriptome landscape of m 6 A Dominissini et al. Nature 2012

16 m 6 A in RNA splicing

17 m6a writers METTL3 (MT-A70) and METTL14 form a heterodimer, colocalize in nuclear speckles Y2H identified plant FIP37 and yeast Mum2 as a partner proteins of METTL3: WTAP (splicing factor) WTAP helps L3/L14 to target mrna, and speckle localization.

18 m 6 A methyltransferase complex Ping et al., Cell Res, 2014

19 Heterotrimer m6a writer is conserved a1/a2 complex RME2 WTAP METLL3 MET LL14 Danio rerio mammals MUM2 IME4 SLZ1 Ime1 MTA FIP37 Arabidopisis Nutrient starvation nucleolus meiosis IME4 FL(2)D Drosophila

20 Chuan He m 6 A erasers

21 ALKBH5: Dioxygenase AlkB Homologue 5 Mol Cell, 2013

22 FTO: Fat mass and obesity-associated protein

23 ALKBH family proteins In mice, primary oxidative demethylase for repairing m1a and m3c lesions in DNA Mitochondria

24 ALKBH8

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26 m 6 A Readers

27 YTHDF1 Function Wang et al. Cell 2015

28 YTHDF2

29 YTHDC1 Xiao et al. Mol Cell, 2015

30 HNRNPA2B1 Alarcon et al., Cell, 2015

31 m 5 C widely existed Motorin et al. NAR 2009

32 m 5 C in RNA trna; rrna 10,000 mrna ncrna mrna in untranslated region around argonaute binding sites; Several genes bearing m 5 C are enzymes involved in energy and lipid metabolism NOP2, NSun3, NSun5-7 mouse embryogenesis

33 m 5 C methyltransferase NSun2 Hussain et al. Cell Reports, 2013 Blanco et al. PLos Genet, 2011

34 m 5 C demethylase? Fu et al. JACS 2014

35 The functions of RNA methylation

36 retention export storage stress granule decay

37 The functions of RNA methylation

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39 RNA category

40 200nts RNA category

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42 Identification of circrnas 陈玲玲

43 Back-splicing for circrnas

44 The competition of RNA pairing for splicing or back-splicing

45 The competition of RNA pairing for splicing or back-splicing

46 The competition of RNA pairing for splicing or back-splicing

47 The competition of RNA pairing for splicing or back-splicing

48 Possible mechanisms for alternative circularization Alu elements

49 Possible mechanisms for alternative circularization

50 Possible mechanisms for alternative circularization

51 Summary of circrnas certain cell lines or upregulated during neural development in flies the processing of circrnas is not only catalyzed by canonical spliceosomal machinery, but also regulated as canonical splicing by both cis-elements and trans-factors Negative correlation between editing level in flanking introns by ADAR1 and circrna expression in neural tissues in flies and mammals Some abundant circrnas form specific particles in both neural cell bodies and dendrites What is the functions of circrna? How and when circrna produced?

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