{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T02:38:36Z","timestamp":1760236716189,"version":"build-2065373602"},"reference-count":47,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2021,12,23]],"date-time":"2021-12-23T00:00:00Z","timestamp":1640217600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010127","name":"J\u00fcrgen Manchot Foundation","doi-asserted-by":"publisher","award":["\/"],"award-info":[{"award-number":["\/"]}],"id":[{"id":"10.13039\/100010127","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The underlying molecular mechanism and their general effect on the replication capacity of HIV 1 drug-resistance-associated mutations is often poorly understood. To elucidate the effect of two such mutations located in a region with a high density of spicing regulatory elements on the HIV-1-splicing outcome, bioinformatic predictions were combined with transfection and infection experiments. Results show that the previously described R263K drug-resistance-associated integrase mutation has additionally a severe effect on the ESE2b splicing regulatory element (SRE) in exon 2b, which causes loss of SD2b recognition. This was confirmed by an R263R silent mutation with a similar predicted effect on the exon 2b SRE. In contrast, a V260I mutation and its silent counterpart with a lower effect on ESS2b did not exhibit any differences in the splicing pattern. Since HIV-1 highly relies on a balanced splicing reaction, changes in the splicing outcome can contribute to changes in viral replication and might add to the effect of escape mutations toward antiviral drugs. Thus, a classification of mutations purely addressing proteins is insufficient.<\/jats:p>","DOI":"10.3390\/ijms23010156","type":"journal-article","created":{"date-parts":[[2021,12,23]],"date-time":"2021-12-23T21:40:21Z","timestamp":1640295621000},"page":"156","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2\/2b"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0728-0012","authenticated-orcid":false,"given":"Lisa","family":"M\u00fcller","sequence":"first","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wiebke","family":"Moskorz","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna-Lena","family":"Brillen","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frank","family":"Hillebrand","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philipp Niklas","family":"Ostermann","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niklas","family":"Kiel","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lara","family":"Walotka","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johannes","family":"Ptok","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Timm","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadine","family":"L\u00fcbke","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1636-4365","authenticated-orcid":false,"given":"Heiner","family":"Schaal","sequence":"additional","affiliation":[{"name":"Institute of Virology, Medical Faculty, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,12,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.coviro.2016.09.012","article-title":"Antiviral therapy of persistent viral infection using genome editing","volume":"20","author":"Buchholz","year":"2016","journal-title":"Curr. Opin. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1038\/nrmicro3352","article-title":"Eradicating HIV-1 infection: Seeking to clear a persistent pathogen","volume":"12","author":"Archin","year":"2014","journal-title":"Nat. Rev. Genet."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/aps.2015.22","article-title":"Progress and challenges in the use of latent HIV-1 reactivating agents","volume":"36","author":"Shang","year":"2015","journal-title":"Acta Pharmacol. Sin."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2117","DOI":"10.1097\/QAD.0000000000001164","article-title":"Increased antiretroviral therapy prescription and HIV viral suppression among persons receiving clinical care for HIV infection","volume":"30","author":"Bradley","year":"2016","journal-title":"AIDS"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e760","DOI":"10.1016\/S2352-3018(19)30234-6","article-title":"Adolescent Hiv Treatment in South Africa\u2019s National Hiv Programme: A Retrospective Cohort Study","volume":"6","author":"Maskew","year":"2019","journal-title":"Lancet HIV"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Montaner, J.S., Lima, V.D., Harrigan, P.R., Louren\u00e7o, L., Yip, B., Nosyk, B., Wood, E., Kerr, T., Shannon, K., and Moore, D. (2014). Expansion of HAART Coverage Is Associated with Sustained Decreases in HIV\/AIDS Morbidity, Mortality and HIV Transmission: The \u201cHIV Treatment as Prevention\u201d Experience in a Canadian Setting. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0087872"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1093\/jac\/dky382","article-title":"Impact of HIV-1 primary drug resistance on the efficacy of a first-line antiretroviral regimen in the blood of newly diagnosed individuals in Bamako, Mali","volume":"74","author":"Keita","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"167","DOI":"10.2174\/187152611795589663","article-title":"HIV Treatment Adherence, Drug Resistance, Virologic Failure: Evolving Concepts","volume":"11","author":"Nachega","year":"2011","journal-title":"Infect. Disord. Drug Targets"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.virol.2018.01.011","article-title":"Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet","volume":"516","author":"Sertznig","year":"2018","journal-title":"Virology"},{"key":"ref_10","first-page":"70","article-title":"The HIV-1 passage from cytoplasm to nucleus: The process involving a complex exchange between the components of HIV-1 and cellular machinery to access nucleus and successful integration","volume":"3","author":"Jayappa","year":"2012","journal-title":"Int. J. Biochem. Mol. Boil."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1631\/jzus.B1400059","article-title":"Mechanism and factors that control HIV-1 transcription and latency activation","volume":"15","author":"Liu","year":"2014","journal-title":"J. Zhejiang Univ. Sci. B"},{"key":"ref_12","first-page":"a006916","article-title":"Transcriptional and Posttranscriptional Regulation of HIV-1 Gene Expression","volume":"2","author":"Karn","year":"2011","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"6365","DOI":"10.1128\/jvi.67.11.6365-6378.1993","article-title":"Alternative Splicing of Human Immunodeficiency Virus Type 1 Mrna Modulates Viral Protein Expression, Replication, and Infectivity","volume":"67","author":"Purcell","year":"1993","journal-title":"J. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Takata, M.A., Soll, S.J., Emery, A., Blanco-Melo, D., Swanstrom, R., and Bieniasz, P.D. (2018). Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication. PLoS Pathog., 14.","DOI":"10.1371\/journal.ppat.1006824"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"10345","DOI":"10.1093\/nar\/gks753","article-title":"Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing","volume":"40","author":"Ocwieja","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s12977-020-00533-1","article-title":"Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection","volume":"17","author":"Quang","year":"2020","journal-title":"Retrovirology"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e02515-16","DOI":"10.1128\/JVI.02515-16","article-title":"Characterizing HIV-1 Splicing by Using Next-Generation Sequencing","volume":"91","author":"Emery","year":"2017","journal-title":"J. Virol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6963","DOI":"10.1093\/nar\/gkg901","article-title":"A novel approach to describe a U1 snRNA binding site","volume":"31","author":"Freund","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1089\/1066527041410418","article-title":"Maximum Entropy Modeling of Short Sequence Motifs with Applications to Rna Splicing Signals","volume":"11","author":"Yeo","year":"2004","journal-title":"J. Comput. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"43","DOI":"10.2174\/157016206775197655","article-title":"Role of Viral Splicing Elements and Cellular Rna Binding Proteins in Regulation of Hiv-1 Alternative Rna Splicing","volume":"4","author":"Stoltzfus","year":"2006","journal-title":"Curr. HIV Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/1742-4690-3-89","article-title":"The strength of the HIV-1 3\u2032 splice sites affects Rev function","volume":"3","author":"Kammler","year":"2006","journal-title":"Retrovirology"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1093\/nar\/gkm1147","article-title":"Insights into the selective activation of alternatively used splice acceptors by the human immunodeficiency virus type-1 bidirectional splicing enhancer","volume":"36","author":"Asang","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"e00342-00321","DOI":"10.1128\/JVI.00342-21","article-title":"Let it go: HIV-1 cis-acting repressive sequences","volume":"95","author":"Ostermann","year":"2021","journal-title":"J. Virol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Wong, R.W., Balachandran, A., Ostrowski, M.A., and Cochrane, A. (2013). Digoxin Suppresses HIV-1 Replication by Altering Viral RNA Processing. PLoS Pathog., 9.","DOI":"10.1371\/journal.ppat.1003241"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Arias, A., L\u00f3pez, P., S\u00e1nchez, R., Yamamura, Y., and Rivera-Amill, V. (2018). Sanger and Next Generation Sequencing Approaches to Evaluate HIV-1 Virus in Blood Compartments. Int. J. Environ. Res. Public Health, 15.","DOI":"10.3390\/ijerph15081697"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Brillen, A.L., Walotka, L., Hillebrand, F., M\u00fcller, L., Widera, M., Theiss, S., and Schaal, H. (2017). Analysis of Competing Hiv-1 Splice Donor Sites Uncovers a Tight Cluster of Splicing Regulatory Elements within Exon 2\/2b. J. Virol., 91.","DOI":"10.1128\/JVI.00389-17"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2707","DOI":"10.1128\/JVI.02755-12","article-title":"An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of vif mRNA","volume":"87","author":"Widera","year":"2013","journal-title":"J. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"10681","DOI":"10.1093\/nar\/gku736","article-title":"Genomic HEXploring allows landscaping of novel potential splicing regulatory elements","volume":"42","author":"Erkelenz","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1261\/rna.037044.112","article-title":"Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms","volume":"19","author":"Erkelenz","year":"2013","journal-title":"RNA"},{"key":"ref_30","first-page":"17","article-title":"Characterization and structural analysis of HIV-1 integrase conservation","volume":"11","author":"Malet","year":"2009","journal-title":"Aids Rev."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"887","DOI":"10.1056\/NEJMc1806554","article-title":"Failure of Dolutegravir First-Line ART with Selection of Virus Carrying R263K and G118R","volume":"381","author":"Jensen","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"e00157-17","DOI":"10.1128\/mBio.00157-17","article-title":"The R263K Dolutegravir Resistance-Associated Substitution Progressively Decreases HIV-1 Integration","volume":"8","author":"Leng","year":"2017","journal-title":"mBio"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1093\/ofid\/ofy329","article-title":"Development of the R263K Mutation to Dolutegravir in an HIV-1 Subtype D Virus Harboring 3 Class-Drug Resistance","volume":"6","author":"Ahmed","year":"2019","journal-title":"Open Forum Infect. Dis."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Koma, T., Doi, N., Takemoto, M., Watanabe, K., Yamamoto, H., Nakashima, S., Adachi, A., and Nomaguchi, M. (2021). The Expression Level of HIV-1 Vif Is Optimized by Nucleotide Changes in the Genomic SA1D2prox Region during the Viral Adaptation Process. Viruses, 13.","DOI":"10.3390\/v13102079"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"6067","DOI":"10.1128\/JVI.02231-08","article-title":"Regulation of vif mRNA Splicing by Human Immunodeficiency Virus Type 1 Requires 5\u2032 Splice Site D2 and an Exonic Splicing Enhancer To Counteract Cellular Restriction Factor APOBEC3G","volume":"83","author":"Mandal","year":"2009","journal-title":"J. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3712","DOI":"10.1128\/jvi.69.6.3712-3720.1995","article-title":"Growth of Macrophage-Tropic and Primary Human Immunodeficiency Virus Type 1 (Hiv-1) Isolates in a Unique Cd4+ T-Cell Clone (Pm1): Failure to Downregulate Cd4 and to Interfere with Cell-Line-Tropic Hiv-1","volume":"69","author":"Lusso","year":"1995","journal-title":"J. Virol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/S1097-2765(03)00353-8","article-title":"HIV-1 Vif Blocks the Antiviral Activity of APOBEC3G by Impairing Both Its Translation and Intracellular Stability","volume":"12","author":"Stopak","year":"2003","journal-title":"Mol. Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"3921","DOI":"10.1128\/JVI.01558-07","article-title":"Negative and Positive mRNA Splicing Elements Act Competitively to Regulate Human Immunodeficiency Virus Type 1 Vif Gene Expression","volume":"82","author":"Exline","year":"2008","journal-title":"J. Virol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"4563","DOI":"10.1128\/JVI.02939-15","article-title":"Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels","volume":"90","author":"Nomaguchi","year":"2016","journal-title":"J. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Smith, S.J., Zhao, X.Z., Passos, D.O., Lyumkis, D., Burke, T.R., and Hughes, S.H. (2021). Integrase Strand Transfer Inhibitors Are Effective Anti-Hiv Drugs. Viruses, 13.","DOI":"10.3390\/v13020205"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3135","DOI":"10.1093\/jac\/dkz256","article-title":"A systematic review of the genetic mechanisms of dolutegravir resistance","volume":"74","author":"Rhee","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_42","first-page":"63","article-title":"Can the HIV-1 splicing machinery be targeted for drug discovery?","volume":"9","author":"Dlamini","year":"2017","journal-title":"HIV AIDS"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Hillebrand, F., Ostermann, P.N., M\u00fcller, L., Degrandi, D., Erkelenz, S., Widera, M., Pfeffer, K., and Schaal, H. (2019). Gymnotic Delivery of LNA Mixmers Targeting Viral SREs Induces HIV-1 mRNA Degradation. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20051088"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/nbt.3467","article-title":"Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity","volume":"34","author":"Karpinski","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1056\/NEJMc1308413","article-title":"How a Single Patient Influenced HIV\u201415-Year Follow-up","volume":"370","author":"Jessen","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"692","DOI":"10.1056\/NEJMoa0802905","article-title":"Long-Term Control of Hiv by Ccr5 Delta32\/Delta32 Stem-Cell Transplantation","volume":"360","author":"Nowak","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e340","DOI":"10.1016\/S2352-3018(20)30069-2","article-title":"Evidence for Hiv-1 Cure after Ccr5delta32\/Delta32 Allogeneic Haemopoietic Stem-Cell Transplantation 30 Months Post Analytical Treatment Interruption: A Case Report","volume":"7","author":"Gupta","year":"2020","journal-title":"Lancet HIV"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/1\/156\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:52:28Z","timestamp":1760169148000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/23\/1\/156"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,23]]},"references-count":47,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1]]}},"alternative-id":["ijms23010156"],"URL":"https:\/\/doi.org\/10.3390\/ijms23010156","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2021,12,23]]}}}