Localization of METTL16 at the Nuclear Periphery and the Nucleolus Is Cell Cycle-Specific and METTL16 Interacts with Several Nucleolar Proteins

. 2021 Jul 08 ; 11 (7) : . [epub] 20210708

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid34357041

Grantová podpora
68081707 Internal support of the Institute of Biophysics of the Czech Academy of Sciences

METTL16 methyltransferase is responsible for the methylation of N6-adenosine (m6A) in several RNAs. In mouse cells, we showed that the nuclear distribution of METTL16 is cell cycle-specific. In the G1/S phases, METTL16 accumulates to the nucleolus, while in the G2 phase, the level of METTL16 increases in the nucleoplasm. In metaphase and anaphase, there is a very low pool of the METTL16 protein, but in telophase, residual METTL16 appears to be associated with the newly formed nuclear lamina. In A-type lamin-depleted cells, we observed a reduction of METTL16 when compared with the wild-type counterpart. However, METTL16 does not interact with A-type and B-type lamins, but interacts with Lamin B Receptor (LBR) and Lap2α. Additionally, Lap2α depletion caused METTL16 downregulation in the nuclear pool. Furthermore, METTL16 interacted with DDB2, a key protein of the nucleotide excision repair (NER), and also with nucleolar proteins, including TCOF, NOLC1, and UBF1/2, but not fibrillarin. From this view, the METTL16 protein may also regulate the transcription of ribosomal genes because we observed that the high level of m6A in 18S rRNA appeared in cells with upregulated METTL16.

Zobrazit více v PubMed

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. doi: 10.1038/nchembio.1432. PubMed DOI 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 N6-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science. 2019;363:doi10–1126. doi: 10.1126/science.aav0080. PubMed DOI

Ma H., Wang X., Cai J., Dai Q., Natchiar S.K., Lv R., Chen K., Lu Z., Chen H., Shi Y.G., et al. N6--Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat. Chem. Biol. 2019;15:88–94. doi: 10.1038/s41589-018-0184-3. PubMed DOI 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. doi: 10.1093/nar/gkz619. PubMed DOI PMC

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. doi: 10.15252/embr.201744940. PubMed DOI 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. doi: 10.1038/nchembio.687. PubMed DOI 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. doi: 10.1016/j.molcel.2012.10.015. PubMed DOI PMC

Xiang Y., Laurent B., Hsu C.H., Nachtergaele S., Luc 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. doi: 10.1038/nature21671. PubMed DOI PMC

Yue Y., Liu J., He C. RNA N6-Methyladenosine methylation in post-transcriptional geneexpression regulation. Genes Dev. 2015;29:1343–1355. doi: 10.1101/gad.262766.115. PubMed DOI PMC

Ruszkowska A. METTL16, methyltransferase-like protein 16: Current insights into structure and function. Int. Mol. Sci. 2021;22:2176. doi: 10.3390/ijms22042176. PubMed DOI PMC

Ruszkowska A., Ruszkowski M., Dauter Z., Brown J.A. Structural insights into the RNA methyltransferase domain of METTL16. Sci. Rep. 2018;8:5311. doi: 10.1038/s41598-018-23608-8. PubMed DOI 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.e14. doi: 10.1016/j.cell.2017.05.003. PubMed DOI PMC

Shima H., Matsumoto M., Ishigami Y., Ebina M., Muto A., Sato Y., Kumagai S., Ochiai K., Suzuki T., Igarashi K. S-Adenosylmethionine synthesis is regulated by selective N6-adenosine methylation and mRNA degradation Involving METTL16 and YTHDC1. Cell Rep. 2017;21:3354–3363. doi: 10.1016/j.celrep.2017.11.092. PubMed DOI

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 non-coding RNA. Proc. Natl. Acad. Sci. USA. 2016;113:14013–14018. doi: 10.1073/pnas.1614759113. PubMed DOI PMC

Koh C.W.Q., Goh Y.T., Goh W.S.S. Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes. Nat. Commun. 2019;10:5636. doi: 10.1038/s41467-019-13561-z. PubMed DOI PMC

Lence T., Paolantoni C., Worpenberg L., Roignant J.Y. Mechanistic insights into m6A RNA enzymes. Biochim. Biophys. Acta Gene Regul. Mech. 2019;1862:222–229. doi: 10.1016/j.bbagrm.2018.10.014. PubMed DOI

Mendel M., Chen K.M., Homolka D., Gos P., Pandey R.R., McCarthy A.A., Pillai R.S. Methylation of structured RNA by the m6A writer METTL16 Is essential for mouse embryonic development. Mol. Cell. 2018;71:986–1000.e11. doi: 10.1016/j.molcel.2018.08.004. PubMed DOI PMC

Dorsett M., Schedl T. A role for dynein in the inhibition of germ cell proliferative fate. Mol. Cell. Biol. 2009;29:6128–6139. doi: 10.1128/MCB.00815-09. PubMed DOI PMC

Svobodova Kovarikova A., Stixova L., Kovarik A., Komurkova D., Legartova S., Fagherazzi P., Bartova E. N6-Adenosine methylation in RNA and a reduced m3G/TMG Level in Non-Coding RNAs Appear at Microirradiation-Induced DNA Lesions. Cells. 2020;9:360. doi: 10.3390/cells9020360. PubMed DOI PMC

Naetar N., Korbei B., Kozlov S., Kerenyi M.A., Dorner D., Kral R., Gotic I., Fuchs P., Cohen T.V., Bittner R., et al. Loss of nucleoplasmic LAP2alpha-lamin A complexes causes erythroid and epidermal progenitor hyperproliferation. Nat. Cell. Biol. 2008;10:1341–1348. doi: 10.1038/ncb1793. PubMed DOI

Lukasova E., Kovarik A., Bacikova A., Falk M., Kozubek S. Loss of lamin B receptor is necessary to induce cellular senescence. Biochem. J. 2017;474:281–300. doi: 10.1042/BCJ20160459. PubMed DOI

Stixova L., Komurkova D., Svobodova Kovarikova A., Bartova E. UVA irradiation strengthened an interaction between UBF1/2 proteins and H4K20 di-/tri-methylation. Chromosome Res. 2019;27:41–55. doi: 10.1007/s10577-018-9596-x. PubMed DOI

Vecera J., Bartova E., Krejci J., Legartova S., Komurkova D., Ruda-Kucerova J., Stark T., Drazanova E., Kasparek T., Sulcova A., et al. HDAC1 and HDAC3 underlie dynamic H3K9 acetylation during embryonic neurogenesis and in schizophrenia-like animals. J. Cell. Physiol. 2018;233:530–548. doi: 10.1002/jcp.25914. PubMed DOI PMC

Horakova A.H., Bartova E., Galiova G., Uhlirova R., Matula P., Kozubek S. SUV39h-independent association of HP1 beta with fibrillarin-positive nucleolar regions. Chromosoma. 2010;119:227–241. doi: 10.1007/s00412-009-0252-2. PubMed DOI

Santoro R., Grummt I. Epigenetic mechanism of rRNA gene silencing: Temporal order of NoRC-mediated histone modification, chromatin remodeling, and DNA methylation. Mol. Cell. Biol. 2005;25:2539–2546. doi: 10.1128/MCB.25.7.2539-2546.2005. PubMed DOI 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. doi: 10.1371/journal.pone.0227647. PubMed DOI PMC

Maiser A., Dillinger S., Langst G., Schermelleh L., Leonhardt H., Nemeth A. Super-resolution in situ analysis of active ribosomal DNA chromatin organization in the nucleolus. Sci. Rep. 2020;10:7462. doi: 10.1038/s41598-020-64589-x. PubMed DOI 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.e4. doi: 10.1016/j.molcel.2018.07.025. PubMed DOI PMC

Xiang S., Gao M., Cao J., Shu X., Cheng M., Wang F., Deng T., Liu J. Precise identification of an RNA methyltransferase’s substrate modification site. Chem. Commun. 2021;57:2499–2502. doi: 10.1039/D0CC08260K. PubMed DOI

Mikutis S., Gu M., Sendinc E., Hazemi M.E., Kiely-Collins H., Aspris D., Vassiliou G.S., Shi Y., Tzelepis K., Bernardes G.J.L. meCLICK-Seq, a substrate-hijacking and RNA degradation strategy for the Study of RNA methylation. ACS Central Sci. 2020;6:2196–2208. doi: 10.1021/acscentsci.0c01094. PubMed DOI PMC

Li K., Luo H., Luo H., Zhu X. Clinical and prognostic pan-cancer analysis of m6A RNA methylation regulators in four types of endocrine system tumors. Aging. 2020;12:23931–23944. doi: 10.18632/aging.104064. PubMed DOI PMC

Wang S., Fan X., Zhu J., Xu D., Li R., Chen R., Hu J., Shen Y., Hao J., Wang K., et al. The differentiation of colorectal cancer is closely relevant to m6A modification. Biochem. Biophys. Res. Commun. 2021;546:65–73. doi: 10.1016/j.bbrc.2021.02.001. PubMed DOI

Arcidiacono O.A., Krejci J., Bartova E. The distinct function and localization of METTL3/METTL14 and METTL16 enzymes in cardiomyocytes. Int. J. Mol. Sci. 2020;21:8139. doi: 10.3390/ijms21218139. PubMed DOI PMC

Zhang J. Brothers in arms: Emerging roles of RNA epigenetics in DNA damage repair. Cell. Biosci. 2017;7:24. doi: 10.1186/s13578-017-0151-9. PubMed DOI PMC

Herrmann F., Pably P., Eckerich C., Bedford M.T., Fackelmayer F.O. Human protein arginine methyltransferases in vivo—distinct properties of eight canonical members of the PRMT family. J. Cell Sci. 2009;122:667–677. doi: 10.1242/jcs.039933. PubMed DOI

Zhang J., Ao Y., Zhang Z., Mo Y., Peng L., Jiang Y., Wang Z., Liu B. Lamin A safeguards the m6A methylase METTL14 nuclear speckle reservoir to prevent cellular senescence. Aging Cell. 2020;19:e13215. doi: 10.1111/acel.13215. PubMed DOI PMC

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

PARP-dependent and NAT10-independent acetylation of N4-cytidine in RNA appears in UV-damaged chromatin

. 2023 Jun 15 ; 16 (1) : 26. [epub] 20230615

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...