{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T12:09:41Z","timestamp":1771243781349,"version":"3.50.1"},"reference-count":100,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T00:00:00Z","timestamp":1771027200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Over the past two decades, it has become clear that gene expression in eukaryotic cells is regulated by diverse RNA molecules. In this process, new RNAs have been discovered, and the roles of their modified molecules have been progressively elucidated. In this review, we first describe how RNA and its modifications function in virus-infected cells. We use adenovirus and several other viruses as models during the early stages of infection, which we believe determines the fate of infected cells. Next, we reviewed the process of identifying the early mRNA transcription initiation sites in adenovirus-infected cells. The results showed that the transcription initiation sites for the E1 and E4 mRNAs\u2014known as adenovirus oncogenes\u2014are highly complex. The same level of complexity in transcription initiation sites has been suggested for oncogenes in several other DNA tumor viruses, including SV40, polyomavirus, and papillomavirus. It is now understood that the transcription of the early adenovirus mRNA involves alternative splicing, rather than constitutive splicing, as we previously demonstrated. Furthermore, recent research indicates that the abnormal alternative splicing of intracellular mRNA may induce cellular carcinogenesis. Finally, we discuss whether alternative splicing plays a role in the carcinogenic effects of DNA tumor viruses, such as adenovirus. Additionally, we discuss that alternative splicing plays a crucial role in adenovirus replication.<\/jats:p>","DOI":"10.3390\/v18020243","type":"journal-article","created":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T11:11:28Z","timestamp":1771240288000},"page":"243","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Inevitable Relationship Between Viruses and RNA Modifications Revealed Through Adenovirus Research"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-3687-0947","authenticated-orcid":false,"given":"Shuichi","family":"Hashimoto","sequence":"first","affiliation":[{"name":"Department of Gene Regulation, Faculty of Pharmaceutical Science, Tokyo University of Science, Niijyuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5759-4829","authenticated-orcid":false,"given":"Fumiaki","family":"Uchiumi","sequence":"additional","affiliation":[{"name":"Department of Gene Regulation, Faculty of Pharmaceutical Science, Tokyo University of Science, Niijyuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hideaki","family":"Furuya","sequence":"additional","affiliation":[{"name":"Department of Gene Regulation, Faculty of Pharmaceutical Science, Tokyo University of Science, Niijyuku 6-3-1, Katsushika-ku, Tokyo 125-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9527-9988","authenticated-orcid":false,"given":"Radhakrishnan","family":"Padmanabhan","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1038\/253374a0","article-title":"A blocked structure at the 5\u2032-terminus of mRNA from cytoplasmic polyhedrosis virus","volume":"253","author":"Furuichi","year":"1975","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1073\/pnas.72.1.362","article-title":"Reovirus messenger RNA contains a methylated blocked 5\u2032-terminal structure m-7G(5\u2032)ppp(5\u2032)G-MPCp-","volume":"72","author":"Furuichi","year":"1975","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/0092-8674(75)90092-6","article-title":"Methylated and blocked 5\u2032 termini in vesicular stomatitis virus in vivo mRNAs","volume":"5","author":"Moyer","year":"1975","journal-title":"Cell"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1128\/jvi.19.3.998-1005.1976","article-title":"Methylated pattern of genomic RNA from Moloney murine leukemia virus","volume":"19","author":"Bondurant","year":"1976","journal-title":"J. Virol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/257618a0","article-title":"Blocked methylated 5\u2032-terminal sequences in avian sarcoma virus RNA","volume":"257","author":"Furuichi","year":"1975","journal-title":"Nature"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"3347","DOI":"10.1073\/pnas.72.9.3347","article-title":"Identification of the 5\u2032 end of Rous sarcoma virus RNA","volume":"72","author":"Keith","year":"1975","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1073\/pnas.72.1.318","article-title":"Methylated nucleotides block 5\u2032-terminus of vaccinia virus messenger RNA","volume":"72","author":"Wei","year":"1975","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/0014-5793(75)80940-9","article-title":"Methylated SV40 mRNAs","volume":"54","author":"Aloni","year":"1975","journal-title":"FEBS Lett."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/S0006-291X(75)80295-6","article-title":"Methylation of cytoplasmic adenovirus RNA synthesized early and late in productive infection","volume":"66","author":"Fernandez","year":"1975","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1128\/jvi.17.2.385-392.1976","article-title":"Sequence of methylated nucleotides at the 5\u2032-terminus of adenovirus specific RNA","volume":"17","author":"Moss","year":"1976","journal-title":"J. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/0006-291X(76)91194-3","article-title":"Methylation of late adenovirus 2 nuclear and messenger RNA","volume":"68","author":"Wold","year":"1976","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/0042-6822(69)90040-3","article-title":"Biochemical studies on adenovirus multiplication XV. Transcription of adenovirus type 2 genome during productive infection","volume":"39","author":"Thomas","year":"1969","journal-title":"Virology"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/0042-6822(71)90122-X","article-title":"Biochemical studies on adenovirus multiplication. 18. Resolution of early virus-specific RNA species in Ad 2 infected and transformed cells","volume":"45","author":"Parsons","year":"1971","journal-title":"Virology"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3171","DOI":"10.1073\/pnas.74.8.3171","article-title":"Spliced segments at the 5\u2032terminus adenovirus 2 late mRNA","volume":"74","author":"Berget","year":"1977","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0092-8674(77)90180-5","article-title":"An amazing sequence arrangement at the 5\u2032 ends of adenovirus 2 messenger RNA","volume":"12","author":"Chow","year":"1977","journal-title":"Cell"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/s41392-021-00486-7","article-title":"Alternative splicing and cancer: A systemic review","volume":"6","author":"Zhang","year":"2021","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_17","first-page":"1997","article-title":"Polyomavirinae: The Viruses and Their Replication","volume":"Volume 2","author":"Fields","year":"1996","journal-title":"Fields Virology"},{"key":"ref_18","first-page":"2045","article-title":"Papillomavirinae: The Viruses and Their Replication","volume":"Volume 2","author":"Fields","year":"1996","journal-title":"Fields Virology"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e0046224","DOI":"10.1128\/mbio.00462-24","article-title":"What are the essential determinants of human papillomavirus carcinogenesis?","volume":"5","author":"Munger","year":"2024","journal-title":"mBio"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1021\/acs.accounts.3c00529","article-title":"General principles and limitations for detection of RNA modifications by sequencing","volume":"57","author":"Motorin","year":"2024","journal-title":"Acc. Chem. Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Sa\u011flam, B., and Akg\u00fcl, B. (2024). An overview of current detection methods for RNA methylation. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25063098"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1016\/j.molcel.2019.04.025","article-title":"Where, When, and How; Context-dependent functions of RNA methylation writers, readers, and erasers","volume":"74","author":"Shi","year":"2019","journal-title":"Mol. Cell"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1186\/s12985-019-1236-3","article-title":"Association of N6-methyadenosine with viruses and related diseases","volume":"16","author":"Wu","year":"2019","journal-title":"Virol. J."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41568-020-0253-2","article-title":"Role of RNA modifications in cancer","volume":"20","author":"Barbieri","year":"2020","journal-title":"Nat. Rev. Cancer"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s12935-022-02452-x","article-title":"Dynamic regulation and functions of mRNA m6A modification","volume":"22","author":"Wang","year":"2022","journal-title":"Cancer Cell Int."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1042\/BST20230574","article-title":"RNA m6A modification, signals for degradation or stability?","volume":"52","author":"Wei","year":"2024","journal-title":"Biochem. Soc. Trans."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2951","DOI":"10.1073\/pnas.71.8.2951","article-title":"Isolation of DNA strand-specific early messenger RNA species in cell infected by human adenovirus 2 infected cells","volume":"71","author":"Green","year":"1974","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/S0022-2836(76)80020-4","article-title":"Preparative isolation and mapping of adenovirus 2 early messenger RNA species","volume":"107","author":"Green","year":"1976","journal-title":"J. Mol. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1128\/jvi.20.2.425-435.1976","article-title":"Multiple methylated cap sequences in adenovirus type 2 early mRNA","volume":"20","author":"Hashimoto","year":"1976","journal-title":"J. Virol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"10540","DOI":"10.1128\/JVI.00885-07","article-title":"Adenovirus virus-associated RNAII- derived small RNAs are efficiently incorporated into the RNA-induced silencing complex and associate with polyribosomes","volume":"81","author":"Xu","year":"2007","journal-title":"J. Virol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.cell.2014.03.008","article-title":"The noncoding RNA revolution-trashing old rules to new ones","volume":"157","author":"Cech","year":"2014","journal-title":"Cell"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1016\/0042-6822(79)90460-4","article-title":"Methylated 5\u2032-terminal caps of adenovirus type 2 early mRNA: Evidence for at least six 5\u2032-termini","volume":"94","author":"Hashimoto","year":"1979","journal-title":"Virology"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1261\/rna.079970.124","article-title":"2\u2032-O-methylation (Nm) in RNA: Progress, challenges, and future directions","volume":"30","author":"Zhou","year":"2024","journal-title":"RNA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1073\/pnas.2333854100","article-title":"Identification of many microRNAs that copurify with polyribosomes in mammalian neurons","volume":"101","author":"Kim","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"7511","DOI":"10.1093\/nar\/gkw551","article-title":"mRNA capping: Biological functions and applications","volume":"44","author":"Ramanathan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1038\/s41467-023-38244-8","article-title":"Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures","volume":"14","author":"Inagaki","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/s41586-022-05668-z","article-title":"mRNA ageing shapes the Cap2 methylome in mammalian mRNA","volume":"614","author":"Despic","year":"2023","journal-title":"Nature"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.immuni.2005.06.008","article-title":"Suppression of RNA recognition by Toll-like receptors: The impact of nucleoside modification and the evolutionary origin of RNA","volume":"23","author":"Kariko","year":"2005","journal-title":"Immunity"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1093\/nar\/3.3.749","article-title":"The methylation of adenovirus-specific nuclear and cytoplasmic RNA","volume":"3","author":"Sommer","year":"1976","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"6016","DOI":"10.1038\/s41467-020-19787-6","article-title":"Direct RNA sequencing reveals m(6)A modifications on adenovirus RNA are necessary for efficient splicing","volume":"11","author":"Price","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"e00696\u201318","DOI":"10.1128\/JVI.00696-18","article-title":"The RNA Epitrascriptome of DNA Viruses","volume":"92","author":"Tan","year":"2018","journal-title":"J. Virol."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Tsai, K., Courtney, D.G., and Cullen, B.R. (2018). Addition of m6A to SV40 structural gene expression and replication. PLoS Patholog., 14.","DOI":"10.1371\/journal.ppat.1006919"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"e2116662119","DOI":"10.1073\/pnas.2116662119","article-title":"The m6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay","volume":"119","author":"Cicerchia","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"e01939-20","DOI":"10.1128\/JVI.01939-20","article-title":"Nonsegmental negative-sense RNA viruses utilize N6-methyladenosine (m6A) as a common strategy to evade host innate immunity","volume":"95","author":"Lu","year":"2021","journal-title":"J. Virol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1038\/s41420-022-01113-2","article-title":"The role of N6-methyladenosine-modified non-coding RNAs in the pathological process of human cancer","volume":"8","author":"Luo","year":"2022","journal-title":"Cell Death Discov."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1159\/000531348","article-title":"Herpes Simplex Virus 1 MicroRNAs: An Update","volume":"66","author":"Duan","year":"2023","journal-title":"Intervirology"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/nature03576","article-title":"SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells","volume":"435","author":"Sullivan","year":"2005","journal-title":"Nature"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1126\/science.1113329","article-title":"Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA","volume":"309","author":"Jopling","year":"2005","journal-title":"Science"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1126\/science.1136319","article-title":"Suppression of microRNA-silencing pathway by HIV-1 during virus replication","volume":"315","author":"Triboulet","year":"2007","journal-title":"Science"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1126\/science.1108784","article-title":"A cellular microRNA mediates antiviral defense in human cells","volume":"308","author":"Lecellier","year":"2005","journal-title":"Science"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.immuni.2007.05.014","article-title":"Hypersusceptibility to vesicular stomatitis virus infection in Dicer1-deficient mice is due to impaired miR24 and miR93 expression","volume":"27","author":"Otsuka","year":"2007","journal-title":"Immunity"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/S0022-2836(66)80153-5","article-title":"RNA of low molecular weight in KB cells infected with adenovirus type 2","volume":"17","author":"Reich","year":"1966","journal-title":"J. Mol. Biol."},{"key":"ref_53","first-page":"2111","article-title":"Adenoviridae: The Viruses and Their Replication","volume":"Volume 2","author":"Fields","year":"1996","journal-title":"Fields Virology"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1016\/j.febslet.2006.01.085","article-title":"Sequence-specific interference by small RNAs derived from adenovirus VAI RNA","volume":"580","author":"Sano","year":"2006","journal-title":"FEBS Lett."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1128\/JVI.80.3.1376-1384.2006","article-title":"Adenovirus associated RNA is processed to functional interfering RNAs involved in virus production","volume":"80","author":"Aparicio","year":"2006","journal-title":"J. Virol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Punga, T., Darweesh, M., and Akusj\u00e4rvi, G. (2020). Synthesis, Structure, and Function of Human Adenovirus Small Non-Coding RNAs. Viruses, 12.","DOI":"10.3390\/v12101182"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1700","DOI":"10.1261\/rna.061291.117","article-title":"An Ago2-associated capped transcriptional start site small RNA suppresses adenovirus DNA replication","volume":"23","author":"Kamel","year":"2017","journal-title":"RNA"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Crisostomo, L., Soriano, A.M., Mendez, M., Graves, D., and Pelka, P. (2019). Temporal dynamics of adenovirus 5 gene expression in normal human cells. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0211192"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1128\/jvi.65.5.2429-2435.1991","article-title":"Fastidious human adenovirus type 40 can propagate efficiently and produce plaques on a human cell line, A549, derived from lung carcinoma","volume":"65","author":"Hashimoto","year":"1991","journal-title":"J. Virol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/0042-6822(91)90478-T","article-title":"Enteric adenovirus type 40: E1B transcription map and identification of novel E1A-E1B cotranscripts in lytically infected cells","volume":"181","author":"Steinthorsdottir","year":"1991","journal-title":"Virology"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1007\/BF01310800","article-title":"Unusual splice sites in the E1A-E1B cotranscripts synthesized in adenovirus type 40-infected A549 cells","volume":"139","author":"Ishida","year":"1994","journal-title":"Arch. Virol."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Clark, D.P., and Pazdernik, N.J. (2013). Polymerase Chain Reaction: In Molecular Biology, Elsevier. [2nd ed.].","DOI":"10.1016\/B978-0-12-378594-7.00030-5"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41592-018-0014-2","article-title":"Comprehensive comparative analysis of 5\u2032-end RNA-sequencing methods","volume":"15","author":"Adiconis","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/0092-8674(78)90252-0","article-title":"Structure of the adenovirus 2 early mRNAs","volume":"14","author":"Berk","year":"1978","journal-title":"Cell"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/0022-2836(79)90036-6","article-title":"Complex splicing patterns of RNAs from the early regions of adenovirus-2","volume":"134","author":"Chow","year":"1979","journal-title":"J. Mol. Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"7383","DOI":"10.1073\/pnas.78.12.7383","article-title":"Specific in vitro initiation of transcription on the adenovirus type 2 early and late EII transcription units","volume":"78","author":"Mathis","year":"1981","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/0378-1119(88)90391-5","article-title":"Activation of the adenovirus-2 E2a late promoter during inhibition of protein synthesis by cycloheximide","volume":"69","author":"Yasuda","year":"1988","journal-title":"Gene"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1021\/bi00543a007","article-title":"Characterization of distinct 5\u2032- terminal cap structures of adenovirus type 2 early messenger ribonucleic acid and KB cell messenger ribonucleic acid","volume":"19","author":"Hashimoto","year":"1980","journal-title":"Biochemistry"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"6780","DOI":"10.1016\/S0021-9258(18)43640-X","article-title":"Adenovirus 2 early messenger RNA-genome mapping of 5\u2032-terminal RNase T1 oligonucleotides and heterogeneity of 5\u2032-termini","volume":"255","author":"Hashimoto","year":"1980","journal-title":"J. Biol. Chem."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1111\/j.1432-1033.1969.tb00786.x","article-title":"Chromatography of 32P-labelled oligonucleotides on thin layers of DEAE-cellulose","volume":"11","author":"Brownlee","year":"1969","journal-title":"Eur. J. Biochem."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/0076-6879(89)80098-9","article-title":"RNA fingerprinting","volume":"Volume 180","author":"Branch","year":"1989","journal-title":"Methods in Enzymology"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1093\/nar\/9.7.1675","article-title":"Nucleotide sequences and mapping of novel heterogenous 5\u2032-termini of adenovirus 2 early region 4 mRNA","volume":"9","author":"Hashimoto","year":"1981","journal-title":"Nucleic Acids Res."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"9067","DOI":"10.1093\/nar\/12.23.9067","article-title":"Unusual heterogeneity of the 5\u2032-termini of human adenovirus type 2 early region E2 mRNA","volume":"12","author":"Hashimoto","year":"1984","journal-title":"Nucleic Acids Res."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1021\/bi00526a019","article-title":"Nucleotide sequences of 5\u2032 termini of adenovirus 2 early transforming region E1a and E1b messenger ribonucleic acids","volume":"20","author":"Hashimoto","year":"1981","journal-title":"Biochemistry"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"7016","DOI":"10.1016\/S0021-9258(17)39831-9","article-title":"Cell-free translation of adenovirus 2 E1a- and E1b-specific mRNAs and evidence that E1a-related polypeptides are produced from E1a-E1b overlapping mRNA","volume":"259","author":"Hashimoto","year":"1984","journal-title":"J. Biol. Chem."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1128\/jvi.20.1.255-263.1976","article-title":"mRNA from the transforming segment of the adenovirus 2 genome in productively infected and transformed cells","volume":"20","author":"Chinnadurai","year":"1976","journal-title":"J. Virol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1128\/jvi.36.2.337-352.1980","article-title":"Unique species of mRNA from adenovirus type 7 early region 1 in cells transformed by adenovirus type 7 DNA fragment","volume":"36","author":"Yoshida","year":"1980","journal-title":"J. Virol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1128\/jvi.36.3.639-651.1980","article-title":"Mapping of adenovirus 12 mRNA\u2019s transcribed from the transforming region","volume":"36","author":"Sawada","year":"1980","journal-title":"J. Virol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/0042-6822(83)90143-5","article-title":"mRNA species and proteins of adenovirus type 12 transforming regions: Identification of proteins translated from multiple coding stretches in 2.2 kb region 1B mRNA in vitro and in vivo","volume":"127","author":"Saito","year":"1983","journal-title":"Virology"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"8321","DOI":"10.1128\/jvi.71.11.8321-8329.1997","article-title":"Readthrough activation of early adenovirus E1b gene transcription","volume":"71","author":"Maxfield","year":"1997","journal-title":"J. Virol."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Price, A.M., Steinbock, R.T., Lauman, R., Charman, M., Hayer, K.E., Kumar, N., Halko, E., Lum, K.K., Wei, M., and Wilson, A.C. (2022). Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts. PLoS Pathog., 18.","DOI":"10.1371\/journal.ppat.1010797"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1093\/intimm\/3.4.343","article-title":"The E1b oncogene of adenovirus confers cellular resistance to cytotoxicity of tumor necrosis factor and monoclonal anti-Fas antibody","volume":"3","author":"Hashimoto","year":"1991","journal-title":"Int. Immunol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.virol.2014.04.006","article-title":"A new look at adenovirus splicing","volume":"456\u2013457","author":"Zhao","year":"2014","journal-title":"Virology"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s42003-020-0849-9","article-title":"Deep splicing plasticity of the human adenovirus type 5 transcriptome drives virus evolution","volume":"3","author":"Turnell","year":"2020","journal-title":"Commun. Biol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"e01869-20","DOI":"10.1128\/JVI.01869-20","article-title":"The human adenovirus 2 transcriptome: An amazing complexity of alternatively spliced mRNAs","volume":"95","author":"Segerman","year":"2021","journal-title":"J. Virol."},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Doerfler, D. (1986). Oncogenic transformation by human adenoviruses and their DNA. Adenovirus DNA, the Viral Genome and Its Expression, Springer.","DOI":"10.1007\/978-1-4613-2293-1"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/30277","article-title":"Regulation of adenovirus alternative RNA splicing by dephosphorylation of SR proteins","volume":"393","author":"Kanopka","year":"1998","journal-title":"Nature"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"2893","DOI":"10.3390\/ijms16022893","article-title":"Regulation of human adenovirus alternative RNA splicing by the adenoviral L4-33K and L4-22K proteins","volume":"16","author":"Biasiotto","year":"2015","journal-title":"Int. J. Mol. Sci."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1128\/MCB.20.7.2317-2325.2000","article-title":"A novel type of splicing enhancer regulating adenovirus pre-mRNA splicing","volume":"20","author":"Yue","year":"2000","journal-title":"Mol. Cell. Biol."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"105503","DOI":"10.1016\/j.antiviral.2022.105503","article-title":"RNA virus infections and their effect on host alternative splicing","volume":"210","author":"Sehrawat","year":"2023","journal-title":"Antivir. Res."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Srivastava, R., Daulatabad, S.V., Srivastava, M., and Janga, S.C. (2020). Role of SARS-CoV-2 in altering the RNA-binding protein and mRNA-directed post-transcriptional regulatory networks in human. Int. J. Mol. Sci., 21.","DOI":"10.1101\/2020.07.06.190348"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1128\/jvi.41.1.334-339.1982","article-title":"Identification of adenovirus 2 early region 4 polypeptides by in vitro translation and tryptic peptide map analysis","volume":"41","author":"Matsuo","year":"1982","journal-title":"J. Virol."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/0378-1119(80)90169-9","article-title":"The nucleotide sequence of the right-hand terminal SmaI-K fragment of adenovirus type 2 DNA","volume":"9","author":"Shinagawa","year":"1980","journal-title":"Gene"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"13475","DOI":"10.1016\/S0021-9258(18)33473-2","article-title":"Nucleotide sequences from the adenovirus-2 genome","volume":"257","author":"Gingeras","year":"1982","journal-title":"J. Biol. Chem."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"6772","DOI":"10.1016\/S0021-9258(18)43639-3","article-title":"Identification and peptide mapping of human adenovirus type 2-induced early polypeptides isolated by two-dimensional gel electrophoresis and immunoprecipitation","volume":"255","author":"Brackmann","year":"1980","journal-title":"J. Biol. Chem."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"3089","DOI":"10.1128\/JVI.75.7.3089-3094.2001","article-title":"\u201cHit-and-run\u201d transformation by adenovirus oncogenes","volume":"75","author":"Nevels","year":"2001","journal-title":"J. Virol."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"1975","DOI":"10.1099\/0022-1317-70-8-1975","article-title":"Role of adenovirus type 2 early rejoin 1B 19K protein stability in expression on the cyt and deg phenotypes","volume":"70","author":"Kumai","year":"1989","journal-title":"J. Gen. Virol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"3499","DOI":"10.1128\/jvi.63.8.3499-3506.1989","article-title":"Multiple transcription factor binding sites mediate adenovirus E1A transcription","volume":"63","author":"Pei","year":"1989","journal-title":"J. Virol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"5844","DOI":"10.1073\/pnas.83.16.5844","article-title":"Adenovirus early region 1A protein increases the number of template molecules transcribed in cell-free extracts","volume":"83","author":"Leong","year":"1986","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/0022-2836(81)90298-9","article-title":"Promoters and heterogeneous 5\u2032-termini of the messenger RNAs of adenovirus serotype 2","volume":"149","author":"Baker","year":"1981","journal-title":"J. Mol. Biol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/2\/243\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T11:21:56Z","timestamp":1771240916000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/18\/2\/243"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,14]]},"references-count":100,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["v18020243"],"URL":"https:\/\/doi.org\/10.3390\/v18020243","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,14]]}}}