N6-methyladenosine (m6A) and N6,2'-O-dimethyladenosine (m6Am) are two abundant modifications found in mRNAs and ncRNAs that can regulate multiple aspects of RNA biology. They function mainly by regulating interactions with specific RNA-binding proteins. Both modifications are linked to development, disease and stress response. To date, three methyltransferases and two demethylases have been identified that modify adenosines in mammalian mRNAs. Here, we present a comprehensive analysis of the interactomes of these enzymes. PCIF1 protein network comprises mostly factors involved in nascent RNA synthesis by RNA polymerase II, whereas ALKBH5 is closely linked with most aspects of pre-mRNA processing and mRNA export to the cytoplasm. METTL16 resides in subcellular compartments co-inhabited by several other RNA modifiers and processing factors. FTO interactome positions this demethylase at a crossroad between RNA transcription, RNA processing and DNA replication and repair. Altogether, these enzymes share limited spatial interactomes, pointing to specific molecular mechanisms of their regulation.

Central European Institute of Technology Masaryk University Brno 62500 Czech Republic

Institute of Biotechnology and HiLIFE Helsinki Institute of Life Science University of Helsinki Helsinki 00014 Finland

Zobrazit více v PubMed

Dominissini D., Moshitch-Moshkovitz S., Schwartz S., Salmon-Divon M., Ungar L., Osenberg S., Cesarkas K., Jacob-Hirsch J., Amariglio N., Kupiec M.et al. .. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012; 485:201–206. PubMed

Meyer K.D., Saletore Y., Zumbo P., Elemento O., Mason C.E., Jaffrey S.R.. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell. 2012; 149:1635–1646. PubMed PMC

Covelo-Molares H., Bartosovic M., Vanacova S.. RNA methylation in nuclear pre-mRNA processing. Wiley Interdiscip. Rev. RNA. 2018; 9:e1489. PubMed PMC

Shi H., Wei J., He C.. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol. Cell. 2019; 74:640–650. PubMed PMC

Mendel M., Chen K.M., Homolka D., Gos P., Pandey R.R., McCarthy A.A., Pillai R.S.. Methylation of structured RNA by the m(6)A writer METTL16 is essential for mouse embryonic development. Mol. Cell. 2018; 71:986–1000. PubMed PMC

Doxtader K.A., Wang P., Scarborough A.M., Seo D., Conrad N.K., Nam Y.. Structural basis for regulation of METTL16, an S-adenosylmethionine homeostasis factor. Mol. Cell. 2018; 71:1001–1011. PubMed PMC

Ruszkowska A., Ruszkowski M., Dauter Z., Brown J.A.. Structural insights into the RNA methyltransferase domain of METTL16. Sci. Rep. 2018; 8:5311. PubMed PMC

Liu J., Yue Y., Han D., Wang X., Fu Y., Zhang L., Jia G., Yu M., Lu Z., Deng X.et al. .. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 2014; 10:93–95. PubMed PMC

Patil D.P., Chen C.K., Pickering B.F., Chow A., Jackson C., Guttman M., Jaffrey S.R.. m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature. 2016; 537:369–373. PubMed PMC

Schwartz S., Mumbach M.R., Jovanovic M., Wang T., Maciag K., Bushkin G.G., Mertins P., Ter-Ovanesyan D., Habib N., Cacchiarelli D.et al. .. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Rep. 2014; 8:284–296. PubMed PMC

Yue Y., Liu J., Cui X., Cao J., Luo G., Zhang Z., Cheng T., Gao M., Shu X., Ma H.et al. .. VIRMA mediates preferential m(6)A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation. Cell Discov. 2018; 4:10. PubMed PMC

Ruzicka K., Zhang M., Campilho A., Bodi Z., Kashif M., Saleh M., Eeckhout D., El-Showk S., Li H., Zhong S.et al. .. Identification of factors required for m6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. The New Phytologist. 2017; 215:157–172. PubMed PMC

Knuckles P., Lence T., Haussmann I.U., Jacob D., Kreim N., Carl S.H., Masiello I., Hares T., Villasenor R., Hess D.et al. .. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m(6)A machinery component Wtap/Fl(2)d. Genes Dev. 2018; 32:415–429. PubMed PMC

Ping X.L., Sun B.F., Wang L., Xiao W., Yang X., Wang W.J., Adhikari S., Shi Y., Lv Y., Chen Y.S.et al. .. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 2014; 24:177–189. PubMed PMC

Bawankar P., Lence T., Paolantoni C., Haussmann I.U., Kazlauskiene M., Jacob D., Heidelberger J.B., Richter F.M., Nallasivan M.P., Morin V.et al. .. Hakai is required for stabilization of core components of the m(6)A mRNA methylation machinery. Nat. Commun. 2021; 12:3778. PubMed PMC

Wang Y., Zhang L., Ren H., Ma L., Guo J., Mao D., Lu Z., Lu L., Yan D.. Role of Hakai in m(6)A modification pathway in Drosophila. Nat. Commun. 2021; 12:2159. PubMed PMC

Harper J.E., Miceli S.M., Roberts R.J., Manley J.L.. Sequence specificity of the human mRNA N6-adenosine methylase in vitro. Nucleic Acids Res. 1990; 18:5735–5741. PubMed PMC

Akichika S., Hirano S., Shichino Y., Suzuki T., Nishimasu H., Ishitani R., Sugita A., Hirose Y., Iwasaki S., Nureki O.et al. .. Cap-specific terminal N (6)-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science. 2019; 363:eaav0080. PubMed

Kruse S., Zhong S., Bodi Z., Button J., Alcocer M.J., Hayes C.J., Fray R.. A novel synthesis and detection method for cap-associated adenosine modifications in mouse mRNA. Sci. Rep. 2011; 1:126. PubMed PMC

Mauer J., Luo X., Blanjoie A., Jiao X., Grozhik A.V., Patil D.P., Linder B., Pickering B.F., Vasseur J.J., Chen Q.et al. .. Reversible methylation of m6Am in the 5′ cap controls mRNA stability. Nature. 2017; 541:371–375. PubMed PMC

Fan H., Sakuraba K., Komuro A., Kato S., Harada F., Hirose Y.. PCIF1, a novel human WW domain-containing protein, interacts with the phosphorylated RNA polymerase II. Biochem. Biophys. Res. Commun. 2003; 301:378–385. PubMed

Jia G., Yang C.G., Yang S., Jian X., Yi C., Zhou Z., He C.. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 2008; 582:3313–3319. PubMed PMC

Zheng G., Dahl J.A., Niu Y., Fedorcsak P., Huang C.M., Li C.J., Vagbo C.B., Shi Y., Wang W.L., Song S.H.et al. .. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell. 2013; 49:18–29. PubMed PMC

Tung Y.C., Gulati P., Liu C.H., Rimmington D., Dennis R., Ma M., Saudek V., O’Rahilly S., Coll A.P., Yeo G.S.. FTO is necessary for the induction of leptin resistance by high-fat feeding. Mol. Metab. 2015; 4:287–298. PubMed PMC

Lin L., Hales C.M., Garber K., Jin P.. Fat mass and obesity-associated (FTO) protein interacts with CaMKII and modulates the activity of CREB signaling pathway. Hum. Mol. Genet. 2014; 23:3299–3306. PubMed PMC

Ontiveros R.J., Shen H., Stoute J., Yanas A., Cui Y., Zhang Y., Liu K.F.. Coordination of mRNA and tRNA methylations by TRMT10A. PNAS. 2020; 117:201913448. PubMed PMC

Zheng Q., Hou J., Zhou Y., Li Z., Cao X.. The RNA helicase DDX46 inhibits innate immunity by entrapping m6A-demethylated antiviral transcripts in the nucleus. Nat. Immunol. 2017; 18:1094–1103. PubMed

Shah A., Rashid F., Awan H.M., Hu S., Wang X., Chen L., Shan G.. The DEAD-box RNA helicase DDX3 interacts with m(6)A RNA demethylase ALKBH5. Stem Cells Int. 2017; 2017:8596135. PubMed PMC

Baltz A.G., Munschauer M., Schwanhausser B., Vasile A., Murakawa Y., Schueler M., Youngs N., Penfold-Brown D., Drew K., Milek M.et al. .. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell. 2012; 46:674–690. PubMed

Bartosovic M., Molares H.C., Gregorova P., Hrossova D., Kudla G., Vanacova S.. N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing. Nucleic Acids Res. 2017; 45:11356–11370. PubMed PMC

Ke S., Pandya-Jones A., Saito Y., Fak J.J., Vagbo C.B., Geula S., Hanna J.H., Black D.L., Darnell J.E. Jr, Darnell R.B.. m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev. 2017; 31:990–1006. PubMed PMC

Knuckles P., Carl S.H., Musheev M., Niehrs C., Wenger A., Buhler M.. RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding. Nat. Struct. Mol. Biol. 2017; 24:561–569. PubMed

Slobodin B., Han R., Calderone V., Vrielink J.A., Loayza-Puch F., Elkon R., Agami R.. Transcription impacts the efficiency of mRNA translation via co-transcriptional N6-adenosine methylation. Cell. 2017; 169:326–337. PubMed PMC

Huang H., Weng H., Zhou K., Wu T., Zhao B.S., Sun M., Chen Z., Deng X., Xiao G., Auer F.et al. .. Histone H3 trimethylation at lysine 36 guides m(6)A RNA modification co-transcriptionally. Nature. 2019; 567:414–419. PubMed PMC

Zhang S., Zhao B.S., Zhou A., Lin K., Zheng S., Lu Z., Chen Y., Sulman E.P., Xie K., Bogler O.et al. .. m6A demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer Cell. 2017; 31:591–606. PubMed PMC

Li Y., Xia L., Tan K., Ye X., Zuo Z., Li M., Xiao R., Wang Z., Liu X., Deng M.et al. .. N(6)-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2. Nat. Genet. 2020; 52:870–877. PubMed

Roux K.J., Kim D.I., Raida M., Burke B.. A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J. Cell Biol. 2012; 196:801–810. PubMed PMC

Liu X., Salokas K., Tamene F., Jiu Y., Weldatsadik R.G., Ohman T., Varjosalo M.. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat. Commun. 2018; 9:1188. PubMed PMC

Kim D.I., Birendra K.C., Zhu W., Motamedchaboki K., Doye V., Roux K.J.. Probing nuclear pore complex architecture with proximity-dependent biotinylation. PNAS. 2014; 111:E2453–E2461. PubMed PMC

Schweingruber C., Soffientini P., Ruepp M.D., Bachi A., Muhlemann O.. Identification of Interactions in the NMD Complex Using Proximity-Dependent Biotinylation (BioID). PLoS One. 2016; 11:e0150239. PubMed PMC

Roux K.J., Kim D.I., Burke B.. bioid: a screen for protein-protein interactions. Curr. Protoc. Protein Sci. 2013; 74:19.23.11–19.23.14. PubMed

Choi H., Larsen B., Lin Z.Y., Breitkreutz A., Mellacheruvu D., Fermin D., Qin Z.S., Tyers M., Gingras A.C., Nesvizhskii A.I.. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nat. Methods. 2011; 8:70–73. PubMed PMC

Hirose Y., Iwamoto Y., Sakuraba K., Yunokuchi I., Harada F., Ohkuma Y.. Human phosphorylated CTD-interacting protein, PCIF1, negatively modulates gene expression by RNA polymerase II. Biochem. Biophys. Res. Commun. 2008; 369:449–455. PubMed

Warda A.S., Kretschmer J., Hackert P., Lenz C., Urlaub H., Hobartner C., Sloan K.E., Bohnsack M.T.. Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep. 2017; 18:2004–2014. PubMed PMC

Wei J., Liu F., Lu Z., Fei Q., Ai Y., He P.C., Shi H., Cui X., Su R., Klungland A.et al. .. Differential m(6)A, m(6)Am, and m(1)A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. Mol. Cell. 2018; 71:973–985. PubMed PMC

Xu W., Li J., He C., Wen J., Ma H., Rong B., Diao J., Wang L., Wang J., Wu F.et al. .. METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature. 2021; 591:317–321. PubMed

Choe J., Lin S., Zhang W., Liu Q., Wang L., Ramirez-Moya J., Du P., Kim W., Tang S., Sliz P.et al. .. mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis. Nature. 2018; 561:556–560. PubMed PMC

Lesbirel S., Viphakone N., Parker M., Parker J., Heath C., Sudbery I., Wilson S.A.. The m(6)A-methylase complex recruits TREX and regulates mRNA export. Sci. Rep. 2018; 8:13827. PubMed PMC

Kisseleva T., Bhattacharya S., Braunstein J., Schindler C.W.. Signaling through the JAK/STAT pathway, recent advances and future challenges. Gene. 2002; 285:1–24. PubMed

Bertero A., Brown S., Madrigal P., Osnato A., Ortmann D., Yiangou L., Kadiwala J., Hubner N.C., de Los Mozos I.R., Sadee C.et al. .. The SMAD2/3 interactome reveals that TGFbeta controls m(6)A mRNA methylation in pluripotency. Nature. 2018; 555:256–259. PubMed PMC

Pendleton K.E., Chen B., Liu K., Hunter O.V., Xie Y., Tu B.P., Conrad N.K.. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell. 2017; 169:824–835. PubMed PMC

Jeronimo C., Forget D., Bouchard A., Li Q., Chua G., Poitras C., Therien C., Bergeron D., Bourassa S., Greenblatt J.et al. .. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol. Cell. 2007; 27:262–274. PubMed PMC

He N., Jahchan N.S., Hong E., Li Q., Bayfield M.A., Maraia R.J., Luo K., Zhou Q.. A La-related protein modulates 7SK snRNP integrity to suppress P-TEFb-dependent transcriptional elongation and tumorigenesis. Mol. Cell. 2008; 29:588–599. PubMed PMC

Krueger B.J., Jeronimo C., Roy B.B., Bouchard A., Barrandon C., Byers S.A., Searcey C.E., Cooper J.J., Bensaude O., Cohen E.A.et al. .. LARP7 is a stable component of the 7SK snRNP while P-TEFb, HEXIM1 and hnRNP A1 are reversibly associated. Nucleic Acids Res. 2008; 36:2219–2229. PubMed PMC

Markert A., Grimm M., Martinez J., Wiesner J., Meyerhans A., Meyuhas O., Sickmann A., Fischer U.. The La-related protein LARP7 is a component of the 7SK ribonucleoprotein and affects transcription of cellular and viral polymerase II genes. EMBO Rep. 2008; 9:569–575. PubMed PMC

Pham V.V., Salguero C., Khan S.N., Meagher J.L., Brown W.C., Humbert N., de Rocquigny H., Smith J.L., D'Souza V.M. HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry. Nat. Commun. 2018; 9:4266. PubMed PMC

Brown J.A., Kinzig C.G., DeGregorio S.J., Steitz J.A.. Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA. PNAS. 2016; 113:14013–14018. PubMed PMC

Hussain S., Sajini A.A., Blanco S., Dietmann S., Lombard P., Sugimoto Y., Paramor M., Gleeson J.G., Odom D.T., Ule J.et al. .. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 2013; 4:255–261. PubMed PMC

Sajini A.A., Choudhury N.R., Wagner R.E., Bornelov S., Selmi T., Spanos C., Dietmann S., Rappsilber J., Michlewski G., Frye M.. Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat. Commun. 2019; 10:2550. PubMed PMC

Kurimoto R., Chiba T., Ito Y., Matsushima T., Yano Y., Miyata K., Yashiro Y., Suzuki T., Tomita K., Asahara H.. The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA. EMBO J. 2020; 39:e104708. PubMed PMC

Nance D.J., Satterwhite E.R., Bhaskar B., Misra S., Carraway K.R., Mansfield K.D.. Characterization of METTL16 as a cytoplasmic RNA binding protein. PLoS One. 2020; 15:e0227647. PubMed PMC

van Tran N., Ernst F.G.M., Hawley B.R., Zorbas C., Ulryck N., Hackert P., Bohnsack K.E., Bohnsack M.T., Jaffrey S.R., Graille M.et al. .. The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res. 2019; 47:7719–7733. PubMed PMC

Ma H., Wang X., Cai J., Dai Q., Natchiar S.K., Lv R., Chen K., Lu Z., Chen H., Shi Y.G.et al. .. N(6-)Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat. Chem. Biol. 2019; 15:88–94. PubMed PMC

Boulias K., Toczydlowska-Socha D., Hawley B.R., Liberman N., Takashima K., Zaccara S., Guez T., Vasseur J.J., Debart F., Aravind L.et al. .. Identification of the m(6)Am methyltransferase PCIF1 reveals the location and functions of m(6)Am in the transcriptome. Mol. Cell. 2019; 75:631–643. PubMed PMC

Sendinc E., Valle-Garcia D., Dhall A., Chen H., Henriques T., Navarrete-Perea J., Sheng W., Gygi S.P., Adelman K., Shi Y.. PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression. Mol. Cell. 2019; 75:620–630. PubMed PMC

Sun H., Zhang M., Li K., Bai D., Yi C.. Cap-specific, terminal N(6)-methylation by a mammalian m(6)Am methyltransferase. Cell Res. 2019; 29:80–82. PubMed PMC

Martinez-Rucobo F.W., Kohler R., van de Waterbeemd M., Heck A.J., Hemann M., Herzog F., Stark H., Cramer P.. Molecular basis of transcription-coupled pre-mRNA capping. Mol. Cell. 2015; 58:1079–1089. PubMed

Andrs M., Hasanova Z., Oravetzova A., Dobrovolna J., Janscak P.. RECQ5: a mysterious helicase at the interface of DNA replication and transcription. Genes. 2020; 11:232. PubMed PMC

Kassube S.A., Jinek M., Fang J., Tsutakawa S., Nogales E.. Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nat. Struct. Mol. Biol. 2013; 20:892–899. PubMed PMC

Aygun O., Xu X., Liu Y., Takahashi H., Kong S.E., Conaway R.C., Conaway J.W., Svejstrup J.Q.. Direct inhibition of RNA polymerase II transcription by RECQL5. J. Biol. Chem. 2009; 284:23197–23203. PubMed PMC

Rougvie A.E., Lis J.T.. The RNA polymerase II molecule at the 5′ end of the uninduced hsp70 gene of D. melanogaster is transcriptionally engaged. Cell. 1988; 54:795–804. PubMed

Core L.J., Waterfall J.J., Lis J.T.. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008; 322:1845–1848. PubMed PMC

Fustin J.M., Doi M., Yamaguchi Y., Hida H., Nishimura S., Yoshida M., Isagawa T., Morioka M.S., Kakeya H., Manabe I.et al. .. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell. 2013; 155:793–806. PubMed

Mauer J., Sindelar M., Despic V., Guez T., Hawley B.R., Vasseur J.J., Rentmeister A., Gross S.S., Pellizzoni L., Debart F.et al. .. FTO controls reversible m(6)Am RNA methylation during snRNA biogenesis. Nat. Chem. Biol. 2019; 15:340–347. PubMed PMC

Egloff S., Zaborowska J., Laitem C., Kiss T., Murphy S.. Ser7 phosphorylation of the CTD recruits the RPAP2 Ser5 phosphatase to snRNA genes. Mol. Cell. 2012; 45:111–122. PubMed PMC

Smith E.R., Lin C., Garrett A.S., Thornton J., Mohaghegh N., Hu D., Jackson J., Saraf A., Swanson S.K., Seidel C.et al. .. The little elongation complex regulates small nuclear RNA transcription. Mol. Cell. 2011; 44:954–965. PubMed PMC

Yamamoto J., Hagiwara Y., Chiba K., Isobe T., Narita T., Handa H., Yamaguchi Y.. DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes. Nat. Commun. 2014; 5:4263. PubMed

Hu X., Chen L.F.. Pinning down the transcription: a role for peptidyl-prolyl cis-trans isomerase Pin1 in gene expression. Front. Cell Dev. Biol. 2020; 8:179. PubMed PMC

Pandey R.R., Delfino E., Homolka D., Roithova A., Chen K.M., Li L., Franco G., Vagbo C.B., Taillebourg E., Fauvarque M.O.et al. .. The mammalian Cap-specific m(6)Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues. Cell Rep. 2020; 32:108038. PubMed

Zhang F., Yu X.. WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. Mol. Cell. 2011; 41:384–397. PubMed PMC

Gregersen L.H., Mitter R., Ugalde A.P., Nojima T., Proudfoot N.J., Agami R., Stewart A., Svejstrup J.Q.. SCAF4 and SCAF8, mRNA anti-terminator proteins. Cell. 2019; 177:1797–1813. PubMed PMC

Licatalosi D.D., Geiger G., Minet M., Schroeder S., Cilli K., McNeil J.B., Bentley D.L.. Functional interaction of yeast pre-mRNA 3′ end processing factors with RNA polymerase II. Mol. Cell. 2002; 9:1101–1111. PubMed

Ni Z., Xu C., Guo X., Hunter G.O., Kuznetsova O.V., Tempel W., Marcon E., Zhong G., Guo H., Kuo W.W.et al. .. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Nat. Struct. Mol. Biol. 2014; 21:686–695. PubMed PMC

Jia G., Fu Y., Zhao X., Dai Q., Zheng G., Yang Y., Yi C., Lindahl T., Pan T., Yang Y.G.et al. .. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 2011; 7:885–887. PubMed PMC

Li Y., Wu K., Quan W., Yu L., Chen S., Cheng C., Wu Q., Zhao S., Zhang Y., Zhou L.. The dynamics of FTO binding and demethylation from the m(6)A motifs. RNA Biology. 2019; 16:1179–1189. PubMed PMC

Zhao X., Yang Y., Sun B.F., Shi Y., Yang X., Xiao W., Hao Y.J., Ping X.L., Chen Y.S., Wang W.J.et al. .. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014; 24:1403–1419. PubMed PMC

Laggerbauer B., Liu S., Makarov E., Vornlocher H.P., Makarova O., Ingelfinger D., Achsel T., Luhrmann R.. The human U5 snRNP 52K protein (CD2BP2) interacts with U5-102K (hPrp6), a U4/U6.U5 tri-snRNP bridging protein, but dissociates upon tri-snRNP formation. RNA. 2005; 11:598–608. PubMed PMC

Liu Y.C., Chen H.C., Wu N.Y., Cheng S.C.. A novel splicing factor, Yju2, is associated with NTC and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing. Mol. Cell. Biol. 2007; 27:5403–5413. PubMed PMC

Chen W., Shulha H.P., Ashar-Patel A., Yan J., Green K.M., Query C.C., Rhind N., Weng Z., Moore M.J.. Endogenous U2.U5.U6 snRNA complexes in S. pombe are intron lariat spliceosomes. RNA. 2014; 20:308–320. PubMed PMC

Koh C.W.Q., Goh Y.T., Goh W.S.S.. Atlas of quantitative single-base-resolution N(6)-methyl-adenine methylomes. Nat. Commun. 2019; 10:5636. PubMed PMC

Xiang Y., Laurent B., Hsu C.H., Nachtergaele S., Lu Z., Sheng W., Xu C., Chen H., Ouyang J., Wang S.et al. .. RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature. 2017; 543:573–576. PubMed PMC

Abakir A., Giles T.C., Cristini A., Foster J.M., Dai N., Starczak M., Rubio-Roldan A., Li M., Eleftheriou M., Crutchley J.et al. .. N(6)-methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat. Genet. 2020; 52:48–55. PubMed PMC

Zhang C., Chen L., Peng D., Jiang A., He Y., Zeng Y., Xie C., Zhou H., Luo X., Liu H.et al. .. METTL3 and N6-methyladenosine promote homologous recombination-mediated repair of DSBs by modulating DNA-RNA hybrid accumulation. Mol. Cell. 2020; 79:425–442. PubMed

Schubert L., Ho T., Hoffmann S., Haahr P., Guerillon C., Mailand N.. RADX interacts with single-stranded DNA to promote replication fork stability. EMBO Rep. 2017; 18:1991–2003. PubMed PMC

Dungrawala H., Bhat K.P., Le Meur R., Chazin W.J., Ding X., Sharan S.K., Wessel S.R., Sathe A.A., Zhao R., Cortez D.. RADX promotes genome stability and modulates chemosensitivity by regulating RAD51 at replication forks. Mol. Cell. 2017; 67:374–386. PubMed PMC

Ma C., Chang M., Lv H., Zhang Z.W., Zhang W., He X., Wu G., Zhao S., Zhang Y., Wang D.et al. .. RNA m(6)A methylation participates in regulation of postnatal development of the mouse cerebellum. Genome Biol. 2018; 19:68. PubMed PMC

Tang C., Klukovich R., Peng H., Wang Z., Yu T., Zhang Y., Zheng H., Klungland A., Yan W.. ALKBH5-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells. PNAS. 2018; 115:E325–E333. PubMed PMC

Spector D.L., Lamond A.I.. Nuclear speckles. Cold Spring Harb. Perspect. Biol. 2011; 3:a000646. PubMed PMC

Boehm V., Gehring N.H.. Exon junction complexes: supervising the gene expression assembly line. Trends Genet.: TIG. 2016; 32:724–735. PubMed

Steckelberg A.L., Boehm V., Gromadzka A.M., Gehring N.H.. CWC22 connects pre-mRNA splicing and exon junction complex assembly. Cell Rep. 2012; 2:454–461. PubMed

Barbosa I., Haque N., Fiorini F., Barrandon C., Tomasetto C., Blanchette M., Le Hir H.. Human CWC22 escorts the helicase eIF4AIII to spliceosomes and promotes exon junction complex assembly. Nat. Struct. Mol. Biol. 2012; 19:983–990. PubMed

Alexandrov A., Colognori D., Shu M.D., Steitz J.A.. Human spliceosomal protein CWC22 plays a role in coupling splicing to exon junction complex deposition and nonsense-mediated decay. PNAS. 2012; 109:21313–21318. PubMed PMC

Murachelli A.G., Ebert J., Basquin C., Le Hir H., Conti E.. The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex. Nat. Struct. Mol. Biol. 2012; 19:378–386. PubMed

Masuda S., Das R., Cheng H., Hurt E., Dorman N., Reed R.. Recruitment of the human TREX complex to mRNA during splicing. Genes Dev. 2005; 19:1512–1517. PubMed PMC

Kiesler E., Miralles F., Visa N.. HEL/UAP56 binds cotranscriptionally to the Balbiani ring pre-mRNA in an intron-independent manner and accompanies the BR mRNP to the nuclear pore. Current Biology : CB. 2002; 12:859–862. PubMed

Xiao W., Adhikari S., Dahal U., Chen Y.S., Hao Y.J., Sun B.F., Sun H.Y., Li A., Ping X.L., Lai W.Y.et al. .. Nuclear m(6)A reader YTHDC1 regulates mRNA splicing. Mol. Cell. 2016; 61:507–519. PubMed

Roundtree I.A., Luo G.Z., Zhang Z., Wang X., Zhou T., Cui Y., Sha J., Huang X., Guerrero L., Xie P.et al. .. YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs. eLife. 2017; 6:e31311. PubMed PMC

Morris K.J., Corbett A.H.. The polyadenosine RNA-binding protein ZC3H14 interacts with the THO complex and coordinately regulates the processing of neuronal transcripts. Nucleic Acids Res. 2018; 46:6561–6575. PubMed PMC

Yang X., Yang Y., Sun B.F., Chen Y.S., Xu J.W., Lai W.Y., Li A., Wang X., Bhattarai D.P., Xiao W.et al. .. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 2017; 27:606–625. PubMed PMC

Li Q., Li X., Tang H., Jiang B., Dou Y., Gorospe M., Wang W.. NSUN2-mediated m5C methylation and METTL3/METTL14-mediated m6A methylation cooperatively enhance p21 translation. J. Cell. Biochem. 2017; 118:2587–2598. PubMed PMC

Perez-Riverol Y., Csordas A., Bai J., Bernal-Llinares M., Hewapathirana S., Kundu D.J., Inuganti A., Griss J., Mayer G., Eisenacher M.et al. .. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019; 47:D442–D450. PubMed PMC

Saitoh N., Spahr C.S., Patterson S.D., Bubulya P., Neuwald A.F., Spector D.L.. Proteomic analysis of interchromatin granule clusters. Mol. Biol. Cell. 2004; 15:3876–3890. PubMed PMC

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to interferon induction