The DNA damage response is mediated by both DNA repair proteins and epigenetic markers. Here, we observe that N6-methyladenosine (m6A), a mark of the epitranscriptome, was common in RNAs accumulated at UV-damaged chromatin; however, inhibitors of RNA polymerases I and II did not affect the m6A RNA level at the irradiated genomic regions. After genome injury, m6A RNAs either diffused to the damaged chromatin or appeared at the lesions enzymatically. DNA damage did not change the levels of METTL3 and METTL14 methyltransferases. In a subset of irradiated cells, only the METTL16 enzyme, responsible for m6A in non-coding RNAs as well as for splicing regulation, was recruited to microirradiated sites. Importantly, the levels of the studied splicing factors were not changed by UVA light. Overall, if the appearance of m6A RNAs at DNA lesions is regulated enzymatically, this process must be mediated via the coregulatory function of METTL-like enzymes. This event is additionally accompanied by radiation-induced depletion of 2,2,7-methylguanosine (m3G/TMG) in RNA. Moreover, UV-irradiation also decreases the global cellular level of N1-methyladenosine (m1A) in RNAs. Based on these results, we prefer a model in which m6A RNAs rapidly respond to radiation-induced stress and diffuse to the damaged sites. The level of both (m1A) RNAs and m3G/TMG in RNAs is reduced as a consequence of DNA damage, recognized by the nucleotide excision repair mechanism.

Department of Experimental Biology Faculty of Science Masaryk University Kamenice 753 5 625 00 Brno Czech Republic

Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 612 00 Brno Czech Republic

Erratum v

Cells. 2024 Nov 04;13(21):1817. doi: 10.3390/cells13211817. PubMed

Zobrazit více v PubMed

Boccaletto P., Machnicka M.A., Purta E., Piatkowski P., Baginski B., Wirecki T.K., De Crecy-Lagard V., Ross R., Limbach P.A., Kotter A., et al. Modomics: A Database of Rna Modification Pathways. 2017 Update. Nucleic Acids Res. 2018;46:D303–D307. doi: 10.1093/nar/gkx1030. PubMed DOI PMC

Wang X., Feng J., Xue Y., Zeyuan G., Zhang D., Liu Z., Gong Z., Wang Q., Huang J., Tang C., et al. Structural Basis of N6-Adenosine Methylation by the Mettl3–Mettl14 Complex. Nature. 2016:534. doi: 10.1038/nature18298. PubMed DOI

Delatte B., Wang F., Ngoc L.V., Collignon E., Bonvin E., Deplus R., Calonne E., Hassabi B., Putmans P., Awe S., et al. RNA Biochemistry. Transcriptome-Wide Distribution and Function of RNA Hydroxymethylcytosine. Science. 2016;351:282–285. doi: 10.1126/science.aac5253. PubMed DOI

Squires J.E., Patel H.R., Nousch M., Sibbritt T., Humphreys D.T., Parker B.J., Suter C.M., Preiss T. Widespread Occurrence of 5-Methylcytosine in Human Coding and Non-Coding Rna. Nucleic Acids Res. 2012;40:5023–5033. doi: 10.1093/nar/gks144. PubMed DOI PMC

Yang Y., Fan X., Mao M., Song X., Wu P., Zhang Y., Jin Y., Yang Y., Chen L.L., Wang Y., et al. Extensive Translation of Circular Rnas Driven by N(6)-Methyladenosine. Cell Res. 2017;27:626–641. doi: 10.1038/cr.2017.31. PubMed DOI PMC

Sharma E., Sterne-Weiler T., O’hanlon D., Blencowe B.J. Global Mapping of Human Rna-Rna Interactions. Mol. Cell. 2016;62:618–626. doi: 10.1016/j.molcel.2016.04.030. PubMed DOI

Chimnaronk S., Suzuki T., Manita T., Ikeuchi Y., Yao M., Suzuki T., Tanaka I. Rna Helicase Module in an Acetyltransferase That Modifies a Specific Trna Anticodon. EMBO J. 2009;28:1362–1373. doi: 10.1038/emboj.2009.69. PubMed DOI PMC

Ito S., Shen L., Dai Q., Wu S.C., Collins L.B., Swenberg J.A., He C., Zhang Y. Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine. Science. 2011;333:1300–1303. doi: 10.1126/science.1210597. PubMed DOI PMC

Schwartz S., Agarwala S.D., Mumbach M.R., Jovanovic M., Mertins P., Shishkin A., Tabach Y., Mikkelsen T.S., Satija R., Ruvkun G., et al. High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic Mrna Methylation Program in Yeast Meiosis. Cell. 2013;155:1409–1421. doi: 10.1016/j.cell.2013.10.047. PubMed DOI PMC

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. doi: 10.1016/j.cell.2012.05.003. PubMed DOI PMC

Luo G.Z., Macqueen A., Zheng G., Duan H., Dore L.C., Lu Z., Liu J., Chen K., Jia G., Bergelson J., et al. Unique Features of the M6a Methylome in Arabidopsis Thaliana. Nat. Commun. 2014;5:5630. doi: 10.1038/ncomms6630. PubMed DOI PMC

Wang Y., Li Y., Toth J.I., Petroski M.D., Zhang Z., Zhao J.C. N6-Methyladenosine Modification Destabilizes Developmental Regulators in Embryonic Stem Cells. Nat. Cell Biol. 2014;16:191–198. doi: 10.1038/ncb2902. PubMed DOI PMC

Liu N., Dai Q., Zheng G., He C., Parisien M., Pan T. N(6)-Methyladenosine-Dependent Rna Structural Switches Regulate Rna-Protein Interactions. Nature. 2015;518:560–564. doi: 10.1038/nature14234. PubMed DOI PMC

Alarcon C.R., Goodarzi H., Lee H., Liu X., Tavazoie S., Tavazoie S.F. Hnrnpa2b1 Is a Mediator of M(6)a-Dependent Nuclear Rna Processing Events. Cell. 2015;162:1299–1308. doi: 10.1016/j.cell.2015.08.011. PubMed DOI PMC

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. doi: 10.1038/nature11112. PubMed DOI

Bokar J.A., Shambaugh M.E., Polayes D., Matera A.G., Rottman F.M. Purification and Cdna Cloning of the Adomet-Binding Subunit of the Human mRNA (N6-Adenosine)-Methyltransferase. RNA. 1997;3:1233–1247. 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. doi: 10.1038/nchembio.1432. PubMed DOI PMC

Wang P., Doxtader K.A., Nam Y. Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases. Mol. Cell. 2016;63:306–317. doi: 10.1016/j.molcel.2016.05.041. PubMed DOI PMC

Dahal U., Le K., Gupta M. Rna M6a Methyltransferase Mettl3 Regulates Invasiveness of Melanoma Cells by Matrix Metallopeptidase 2. Melanoma Res. 2019;29:382–389. doi: 10.1097/CMR.0000000000000580. PubMed DOI

Pendleton K.E., Chen B., Liu K., Hunter O.V., Xie Y., Tu B.P., Conrad N.K. The U6 Snrna M(6)a Methyltransferase Mettl16 Regulates Sam Synthetase Intron Retention. Cell. 2017;169:824–835. doi: 10.1016/j.cell.2017.05.003. 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. doi: 10.1016/j.molcel.2018.07.025. PubMed DOI 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 M(6)a Methylation Regulates the Ultraviolet-Induced DNA Damage Response. Nature. 2017;543:573–576. doi: 10.1038/nature21671. PubMed DOI PMC

Scharf S., Zech J., Bursen A., Schraets D., Oliver P.L., Kliem S., Pfitzner E., Gillert E., Dingermann T., Marschalek R. Transcription Linked to Recombination: A Gene-Internal Promoter Coincides with the Recombination Hot Spot Ii of the Human Mll Gene. Oncogene. 2007;26:1361–1371. doi: 10.1038/sj.onc.1209948. PubMed DOI

Hanawalt P.C., Spivak G. Transcription-Coupled DNA Repair: Two Decades of Progress and Surprises. Nat. Rev. Mol. Cell Biol. 2008;9:958–970. doi: 10.1038/nrm2549. PubMed DOI

Gillet L.C., Scharer O.D. Molecular Mechanisms of Mammalian Global Genome Nucleotide Excision Repair. Chem. Rev. 2006;106:253–276. doi: 10.1021/cr040483f. PubMed DOI

Latypov V.F., Tubbs J.L., Watson A.J., Marriott A.S., Mcgown G., Thorncroft M., Wilkinson O.J., Senthong P., Butt A., Arvai A.S., et al. Atl1 Regulates Choice between Global Genome and Transcription-Coupled Repair of O(6)-Alkylguanines. Mol. Cell. 2012;47:50–60. doi: 10.1016/j.molcel.2012.04.028. PubMed DOI PMC

Tubbs J.L., Latypov V., Kanugula S., Butt A., Melikishvili M., Kraehenbuehl R., Fleck O., Marriott A., Watson A.J., Verbeek B., et al. Flipping of Alkylated DNA Damage Bridges Base and Nucleotide Excision Repair. Nature. 2009;459:808–813. doi: 10.1038/nature08076. PubMed DOI PMC

Scharer O.D. Nucleotide Excision Repair in Eukaryotes. Cold Spring Harb. Perspect Biol. 2013;5:a012609. doi: 10.1101/cshperspect.a012609. 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

Zhao B.S., Wang X., Beadell A.V., Lu Z., Shi H., Kuuspalu A., Ho R.K., He C. M(6)a-Dependent Maternal Mrna Clearance Facilitates Zebrafish Maternal-to-Zygotic Transition. Nature. 2017;542:475–478. doi: 10.1038/nature21355. PubMed DOI PMC

Wei C.M., Gershowitz A., Moss B. Methylated Nucleotides Block 5’ Terminus of Hela Cell Messenger RNA. Cell. 1975;4:379–386. doi: 10.1016/0092-8674(75)90158-0. PubMed DOI

Desrosiers R., Friderici K., Rottman F. Identification of Methylated Nucleosides in Messenger Rna from Novikoff Hepatoma Cells. Proc. Natl. Acad. Sci. 1974;71:3971–3975. doi: 10.1073/pnas.71.10.3971. PubMed DOI 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. doi: 10.1038/cr.2014.3. PubMed DOI PMC

Liao S., Sun H., Xu C. Yth Domain: A Family of N(6)-Methyladenosine (M(6)a) Readers. Genom. Proteom. Bioinform. 2018;16:99–107. doi: 10.1016/j.gpb.2018.04.002. PubMed DOI PMC

Chen J., Du B. Novel Positioning from Obesity to Cancer: Fto, an M(6)a Rna Demethylase, Regulates Tumour Progression. J. Cancer Res. Clin. Oncol. 2019;145:19–29. doi: 10.1007/s00432-018-2796-0. PubMed DOI PMC

Huang J., Yin P. Structural Insights into N(6)-Methyladenosine (M(6)a) Modification in the Transcriptome. Genom. Proteom. Bioinform. 2018;16:85–98. doi: 10.1016/j.gpb.2018.03.001. 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

He C. Grand Challenge Commentary: RNA Epigenetics? Nat. Chem. Biol. 2010;6:863–865. doi: 10.1038/nchembio.482. PubMed DOI

Legartová S., Sehnalová P., Malyšková B., Küntziger T., Collas P., Cmarko D., Raška I., Sorokin D.V., Kozubek S., Bártová E. Localized Movement and Levels of 53BP1 Protein Are Changed by γ-irradiation in PML Deficient Cells. J. Cell. Biochem. 2016;117:2583–2596. doi: 10.1002/jcb.25551. PubMed DOI

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. doi: 10.1093/nar/gkx778. PubMed DOI PMC

Bromberg K.D., Mitchell T.R., Upadhyay A.K., Jakob C.G., Jhala M.A., Comess K.M., Lasko L.M., Li C., Tuzon C.T., Dai Y., et al. The Suv4-20 Inhibitor a-196 Verifies a Role for Epigenetics in Genomic Integrity. Nat. Chem. Biol. 2017;13:317–324. doi: 10.1038/nchembio.2282. 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

Sorokin D.V., Stixova L., Sehnalova P., Legartova S., Suchankova J., Simara P., Kozubek S., Matula P., Skalnikova M., Raska I., et al. Localized Movement and Morphology of Ubf1-Positive Nucleolar Regions Are Changed by Gamma-Irradiation in G2 Phase of the Cell Cycle. Nucleus. 2015;6:301–313. doi: 10.1080/19491034.2015.1075111. PubMed DOI PMC

Krueger F., Kreck B., Franke A., Andrews S.R. DNA Methylome Analysis Using Short Bisulfite Sequencing Data. Nat. Methods. 2012;9:145–151. doi: 10.1038/nmeth.1828. PubMed DOI

Xi Y., Li W. Bsmap: Whole Genome Bisulfite Sequence Mapping Program. BMC Bioinform. 2009;10:232. doi: 10.1186/1471-2105-10-232. PubMed DOI PMC

Lister R., O’malley R.C., Tonti-Filippini J., Gregory B.D., Berry C.C., Millar A.H., Ecker J.R. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis. Cell. 2008;133:523–536. doi: 10.1016/j.cell.2008.03.029. PubMed DOI PMC

Svobodová Kovaříková A., Legartová S., Krejčí J., Bártová E. H3k9me3 and H4k20me3 Represent the Epigenetic Landscape for 53bp1 Binding to DNA Lesions. Aging. 2018;10:2585–2605. doi: 10.18632/aging.101572. PubMed DOI PMC

Harničarová Horáková A., Galiová G., Legartová S., Kozubek S., Matula P., Bártová E. Chromocentre Integrity and Epigenetic Marks. J. Struct. Biol. 2010;169:124–133. doi: 10.1016/j.jsb.2009.09.007. PubMed DOI

Fodor B.D., Kubicek S., Yonezawa M., O’sullivan R.J., Sengupta R., Perez-Burgos L., Opravil S., Mechtler K., Schotta G., Jenuwein T. Jmjd2b Antagonizes H3k9 Trimethylation at Pericentric Heterochromatin in Mammalian Cells. Genes Dev. 2006;20:1557–1562. doi: 10.1101/gad.388206. PubMed DOI PMC

Engel C., Sainsbury S., Cheung A.C., Kostrewa D., Cramer P. Rna Polymerase I Structure and Transcription Regulation. Nature. 2013;502:650–655. doi: 10.1038/nature12712. PubMed DOI

Xu Y., Bernecky C., Lee C.-T., Maier K.C., Schwalb B., Tegunov D., Plitzko J.M., Urlaub H., Cramer P. Architecture of the Rna Polymerase Ii-Paf1c-Tfiis Transcription Elongation Complex. Nat. Commun. 2017;8:15741. doi: 10.1038/ncomms15741. PubMed DOI PMC

Baral S.S., Dimario P.J. The Nopp140 Gene in Drosophila Melanogaster Displays Length Polymorphisms in Its Large Repetitive Second Exon. Mol. Genet. Genom. 2019;294:1073–1083. doi: 10.1007/s00438-019-01568-6. PubMed DOI

Yuan F., Li G., Tong T. Nucleolar and Coiled-Body Phosphoprotein 1 (Nolc1) Regulates the Nucleolar Retention of Trf2. Cell Death Discov. 2017;3:17043. doi: 10.1038/cddiscovery.2017.43. PubMed DOI PMC

Stixova L., Sehnalova P., Legartova S., Suchankova J., Hruskova T., Kozubek S., Sorokin D.V., Matula P., Raska I., Kovarik A., et al. Hp1beta-Dependent Recruitment of Ubf1 to Irradiated Chromatin Occurs Simultaneously with Cpds. Epigenetics Chromatin. 2014;7:39. doi: 10.1186/1756-8935-7-39. PubMed DOI PMC

Xiong X.-P., Vogler G., Kurthkoti K., Samsonova A., Zhou R. Smd1 Modulates the Mirna Pathway Independently of Its Pre-Mrna Splicing Function. PLoS Genet. 2015;11:e1005475. doi: 10.1371/journal.pgen.1005475. PubMed DOI PMC

Suchankova J., Legartova S., Ruckova E., Vojtesek B., Kozubek S., Bartova E. Mutations in the Tp53 Gene Affected Recruitment of 53bp1 Protein to DNA Lesions, but Level of 53bp1 Was Stable after Gamma-Irradiation That Depleted Mdc1 Protein in Specific Tp53 Mutants. Histochem. Cell Biol. 2017;148:239–255. doi: 10.1007/s00418-017-1567-3. PubMed DOI

Lehnertz B., Ueda Y., Derijck A.A., Braunschweig U., Perez-Burgos L., Kubicek S., Chen T., Li E., Jenuwein T., Peters A.H. Suv39h-Mediated Histone H3 Lysine 9 Methylation Directs DNA Methylation to Major Satellite Repeats at Pericentric Heterochromatin. Curr. Biol. 2003;13:1192–1200. doi: 10.1016/S0960-9822(03)00432-9. PubMed DOI

Qin W., Leonhardt H., Pichler G. Regulation of DNA Methyltransferase 1 by Interactions and Modifications. Nucleus. 2011;2:392–402. doi: 10.4161/nucl.2.5.17928. PubMed DOI

Essers J., Theil A.F., Baldeyron C., Van Cappellen W.A., Houtsmuller A.B., Kanaar R., Vermeulen W. Nuclear Dynamics of Pcna in DNA Replication and Repair. Mol. Cell Biol. 2005;25:9350–9359. doi: 10.1128/MCB.25.21.9350-9359.2005. PubMed DOI PMC

Bartova E., Legartova S., Krejci J., Reznickova P., Kovarikova A.S., Suchankova J., Fedr R., Smirnov E., Hornacek M., Raska I. Depletion of a-Type Lamins and Lap2alpha Reduces 53bp1 Accumulation at Uv-Induced DNA Lesions and Lap2alpha Protein Is Responsible for Compactness of Irradiated Chromatin. J. Cell Biochem. 2018;119:8146–8162. doi: 10.1002/jcb.26770. PubMed DOI

Esteve P.O., Chin H.G., Smallwood A., Feehery G.R., Gangisetty O., Karpf A.R., Carey M.F., Pradhan S. Direct Interaction between Dnmt1 and G9a Coordinates DNA and Histone Methylation During Replication. Genes Dev. 2006;20:3089–3103. doi: 10.1101/gad.1463706. PubMed DOI PMC

Zeng W., Ball A.R., Jr., Yokomori K. Hp1: Heterochromatin Binding Proteins Working the Genome. Epigenetics. 2010;5:287–292. doi: 10.4161/epi.5.4.11683. PubMed DOI PMC

Zhang C., Jia G. Reversible Rna Modification N(1)-Methyladenosine (M(1)a) in Mrna and Trna. Genom. Proteom. Bioinform. 2018;16:155–161. doi: 10.1016/j.gpb.2018.03.003. PubMed DOI PMC

Meier U.T. RNA Modification in Cajal Bodies. RNA Biol. 2017;14:693–700. doi: 10.1080/15476286.2016.1249091. PubMed DOI PMC

Bartova E., Foltankova V., Legartova S., Sehnalova P., Sorokin D.V., Suchankova J., Kozubek S. Coilin Is Rapidly Recruited to Uva-Induced DNA Lesions and Gamma-Radiation Affects Localized Movement of Cajal Bodies. Nucleus. 2014;5:460–468. doi: 10.4161/nucl.29229. PubMed DOI PMC

Will C.L., Luhrmann R. Spliceosome Structure and Function. Cold Spring Harb. Perspect. Biol. 2011:3. doi: 10.1101/cshperspect.a003707. PubMed DOI PMC

N4-acetylcytidine and other RNA modifications in epitranscriptome: insight into DNA repair and cancer development

Correction: Svobodova et al. 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

RNA-related DNA damage and repair: The role of N7-methylguanosine in the cell nucleus exposed to UV light

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

Early recruitment of PARP-dependent m8A RNA methylation at DNA lesions is subsequently accompanied by active DNA demethylation

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

The SC-35 Splicing Factor Interacts with RNA Pol II and A-Type Lamin Depletion Weakens This Interaction

The Distinct Function and Localization of METTL3/METTL14 and METTL16 Enzymes in Cardiomyocytes