{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T04:06:48Z","timestamp":1789013208791,"version":"build-2803163510"},"posted":{"date-parts":[[2026,9,7]]},"group-title":"Biochemistry","reference-count":51,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["R01 NS131660"],"award-info":[{"award-number":["R01 NS131660"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["T32 GM142607"],"award-info":[{"award-number":["T32 GM142607"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["AL240155"],"award-info":[{"award-number":["AL240155"]}],"id":[{"id":"https:\/\/ror.org\/03g2zjp07","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Programmed -1 ribosomal frameshifting (-1 PRF) is a conserved translational recoding mechanism that expands proteomic diversity and regulates gene expression through RNA structural elements, most notably stimulatory pseudoknots. This mechanism is common in viruses, where it is used to control stoichiometry of viral protein products generated by the host cell to direct viral replication. Despite its biological importance, strategies to selectively modulate frameshifting remain limited. The mammalian retrotransposon-derived gene\n                  <jats:italic>PEG10<\/jats:italic>\n                  also relies on -1 PRF to produce a fusion protein, gag-pol, which is necessary for reproduction but has also been implicated in neurological diseases. Here, we establish an antisense oligonucleotide (ASO) targeting an RNA structural element as an effective approach to tune\n                  <jats:italic>PEG10<\/jats:italic>\n                  frameshifting. Using structure prediction, systematic antisense tiling across the\n                  <jats:italic>PEG10<\/jats:italic>\n                  pseudoknot, and multiple model systems, we identify a discrete functional hotspot within the lower RNA stem that governs frameshift efficiency. ASOs targeting this region selectively suppress gag-pol production with minimal impact on gag, thereby shifting the ratio of protein products in a dose-dependent manner. Mechanistic dissection using RNase H-active and -inactive ASO designs, pre-annealed duplexes, and fluorescence-based subcellular localization supports a predominantly nuclear mode of action in which ASOs engage nascent\n                  <jats:italic>PEG10<\/jats:italic>\n                  transcripts and bias pseudoknot folding away from the frameshift-competent conformation. Functional effects are conserved between human cell lines and murine models, including neurons, highlighting the generality of this strategy. Together, our results define RNA structural dynamics as a druggable layer of translational regulation and establish antisense modulation of pseudoknot folding as a way to control endogenous frameshifting. This work provides a conceptual and practical framework for targeting recoding-dependent gene products such as PEG10 in disease and suggests broader applicability of structure-directed ASOs to viral and cellular frameshifting elements.\n                <\/jats:p>","DOI":"10.64898\/2026.09.03.748613","type":"posted-content","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T21:05:41Z","timestamp":1788815141000},"source":"Crossref","is-referenced-by-count":0,"title":["Structure-guided antisense oligonucleotides selectively modulate frameshifting of a human gene"],"prefix":"10.64898","author":[{"given":"Ondrej","family":"Kostov","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"},{"name":"Department of Chemistry of Natural Compounds, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myriam Moreno","family":"Swanton","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katie R.","family":"Waldon","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Autumn M.","family":"Matthews","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marija","family":"Ciba","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathias B.","family":"Danielsen","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Balazs","family":"Schafer","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saheli","family":"Ganguly","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher C.","family":"Ebmeier","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marvin H.","family":"Caruthers","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4144-7605","authenticated-orcid":false,"given":"Alexandra M.","family":"Whiteley","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder, Boulder CO 80309 USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026090920150781000_2026.09.03.748613v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-024-07487-W"},{"key":"2026090920150781000_2026.09.03.748613v1.2","doi-asserted-by":"crossref","unstructured":"Atkins JF , Loughran G , Bhatt PR , Firth AE , Baranov PV . 2016. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res gkw 530.","DOI":"10.1093\/nar\/gkw530"},{"key":"2026090920150781000_2026.09.03.748613v1.3","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S1474-4422(24)00479-4","article-title":"Amyotrophic lateral sclerosis caused by SOD1 variants: from genetic discovery to disease prevention","volume":"24","year":"2025","journal-title":"The Lancet Neurology"},{"key":"2026090920150781000_2026.09.03.748613v1.4","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-med-041217-010829"},{"key":"2026090920150781000_2026.09.03.748613v1.5","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.79452"},{"key":"2026090920150781000_2026.09.03.748613v1.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2004.11.022"},{"key":"2026090920150781000_2026.09.03.748613v1.7","doi-asserted-by":"publisher","DOI":"10.1159\/000084963"},{"key":"2026090920150781000_2026.09.03.748613v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1704"},{"key":"2026090920150781000_2026.09.03.748613v1.9","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1547-5"},{"key":"2026090920150781000_2026.09.03.748613v1.10","doi-asserted-by":"crossref","first-page":"e0139036","DOI":"10.1371\/journal.pone.0139036","article-title":"HIV-1 and Human PEG10 Frameshift Elements Are Functionally Distinct and Distinguished by Novel Small Molecule Modulators ed. E. Jan","volume":"10","year":"2015","journal-title":"PLoS ONE"},{"key":"2026090920150781000_2026.09.03.748613v1.11","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M705676200"},{"key":"2026090920150781000_2026.09.03.748613v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/nn.4508"},{"key":"2026090920150781000_2026.09.03.748613v1.13","doi-asserted-by":"publisher","DOI":"10.1021\/ja201561z"},{"key":"2026090920150781000_2026.09.03.748613v1.14","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.042499-0"},{"key":"2026090920150781000_2026.09.03.748613v1.15","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.coviro.2017.07.021","article-title":"Co-option of endogenous viral sequences for host cell function","volume":"25","year":"2017","journal-title":"Current Opinion in Virology"},{"key":"2026090920150781000_2026.09.03.748613v1.16","doi-asserted-by":"crossref","first-page":"2424","DOI":"10.3390\/ijms21072424","article-title":"Functional Study of the Retrotransposon-Derived Human PEG10 Protease","volume":"21","year":"2020","journal-title":"IJMS"},{"key":"2026090920150781000_2026.09.03.748613v1.17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl531"},{"key":"2026090920150781000_2026.09.03.748613v1.18","doi-asserted-by":"crossref","first-page":"24471","DOI":"10.1039\/D2RA04375K","article-title":"Promotion of cytoplasmic localization of oligonucleotides by connecting cross-linked duplexes","volume":"12","year":"2022","journal-title":"RSC Adv"},{"key":"2026090920150781000_2026.09.03.748613v1.19","doi-asserted-by":"publisher","DOI":"10.1261\/rna.7810204"},{"key":"2026090920150781000_2026.09.03.748613v1.20","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20145625"},{"key":"2026090920150781000_2026.09.03.748613v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/35057062"},{"key":"2026090920150781000_2026.09.03.748613v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2016.05.020"},{"key":"2026090920150781000_2026.09.03.748613v1.23","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2017.07.011"},{"key":"2026090920150781000_2026.09.03.748613v1.24","doi-asserted-by":"publisher","DOI":"10.1006\/viro.1993.1174"},{"key":"2026090920150781000_2026.09.03.748613v1.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2020.12.010"},{"key":"2026090920150781000_2026.09.03.748613v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-024-01468-3"},{"key":"2026090920150781000_2026.09.03.748613v1.27","doi-asserted-by":"crossref","first-page":"16240","DOI":"10.1021\/jacs.0c04335","article-title":"Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras","volume":"142","year":"2020","journal-title":"J Am Chem Soc"},{"key":"2026090920150781000_2026.09.03.748613v1.28","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s43856-023-00419-1","article-title":"Possibilities and limitations of antisense oligonucleotide therapies for the treatment of monogenic disorders","volume":"4","author":"N = 1 Collaborative","year":"2024","journal-title":"Commun Med"},{"key":"2026090920150781000_2026.09.03.748613v1.29","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-023-00609-6"},{"key":"2026090920150781000_2026.09.03.748613v1.30","doi-asserted-by":"crossref","first-page":"e2207956119","DOI":"10.1073\/pnas.2207956119","article-title":"Thiomorpholino oligonucleotides as a robust class of next generation platforms for alternate mRNA splicing","volume":"119","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026090920150781000_2026.09.03.748613v1.31","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1038\/s41392-024-02112-8","article-title":"Landscape of small nucleic acid therapeutics: moving from the bench to the clinic as next-generation medicines","volume":"10","year":"2025","journal-title":"Sig Transduct Target Ther"},{"key":"2026090920150781000_2026.09.03.748613v1.32","doi-asserted-by":"crossref","unstructured":"Lux H , Flammann H , Hafner M , Lux A . 2010. Genetic and Molecular Analyses of PEG10 Reveal New Aspects of Genomic Organization, Transcription and Translation ed. H. Matsunami. PLoS ONE 5: e8686.","DOI":"10.1371\/journal.pone.0008686"},{"key":"2026090920150781000_2026.09.03.748613v1.33","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki299"},{"key":"2026090920150781000_2026.09.03.748613v1.34","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2204705"},{"key":"2026090920150781000_2026.09.03.748613v1.35","doi-asserted-by":"publisher","DOI":"10.3390\/v13071230"},{"key":"2026090920150781000_2026.09.03.748613v1.36","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms15582"},{"key":"2026090920150781000_2026.09.03.748613v1.37","doi-asserted-by":"publisher","DOI":"10.1006\/geno.2001.6494"},{"key":"2026090920150781000_2026.09.03.748613v1.38","doi-asserted-by":"publisher","DOI":"10.1038\/ng1699"},{"key":"2026090920150781000_2026.09.03.748613v1.39","doi-asserted-by":"crossref","first-page":"100360","DOI":"10.1016\/j.xcrm.2021.100360","article-title":"Secreted retrovirus-like GAG-domain-containing protein PEG10 is regulated by UBE3A and is involved in Angelman syndrome pathophysiology","volume":"2","year":"2021","journal-title":"Cell Reports Medicine"},{"key":"2026090920150781000_2026.09.03.748613v1.40","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.65.9.5111-5117.1991"},{"key":"2026090920150781000_2026.09.03.748613v1.41","doi-asserted-by":"crossref","unstructured":"Passini MA , Bu J , Richards AM , Kinnecom C , Sardi SP , Stanek LM , Hua Y , Rigo F , Matson J , Hung G , et al. 2011. Antisense Oligonucleotides Delivered to the Mouse CNS Ameliorate Symptoms of Severe Spinal Muscular Atrophy. Sci Transl Med 3. https:\/\/www.science.org\/doi\/10.1126\/scitranslmed.3001777 (Accessed August 15, 2026).","DOI":"10.1126\/scitranslmed.3001777"},{"key":"2026090920150781000_2026.09.03.748613v1.42","doi-asserted-by":"crossref","unstructured":"Roberts JE , Huynh PT , Carale LO , Whiteley AM . 2025. UBQLN2 is necessary for UBE3A-mediated proteasomal degradation of the domesticated retroelement PEG10. J Cell Sci jcs.264105.","DOI":"10.1242\/jcs.264105"},{"key":"2026090920150781000_2026.09.03.748613v1.43","doi-asserted-by":"crossref","unstructured":"Shiura H , Fujii M , Ooga M , Wakayama S , Ito D , Kohda T , Kaneko-Ishino T , Ishino F . 2025. PEG10-ORF1 programs trophoblast progenitor development for placental labyrinth formation. http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.10.08.681076 (Accessed May 5, 2026).","DOI":"10.1101\/2025.10.08.681076"},{"key":"2026090920150781000_2026.09.03.748613v1.44","doi-asserted-by":"crossref","unstructured":"Shiura H , Ono R , Tachibana S , Kohda T , Kaneko-Ishino T , Ishino F . 2021. PEG10 viral aspartic protease domain is essential for the maintenance of fetal capillary structure in the mouse placenta. Development 148: dev199564.","DOI":"10.1242\/dev.199564"},{"key":"2026090920150781000_2026.09.03.748613v1.45","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.26.4.1333-1346.2006"},{"key":"2026090920150781000_2026.09.03.748613v1.46","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2023051118"},{"key":"2026090920150781000_2026.09.03.748613v1.47","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/20.15.3945"},{"key":"2026090920150781000_2026.09.03.748613v1.48","doi-asserted-by":"publisher","DOI":"10.1002\/bies.20452"},{"key":"2026090920150781000_2026.09.03.748613v1.49","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA120.015960"},{"key":"2026090920150781000_2026.09.03.748613v1.50","doi-asserted-by":"publisher","DOI":"10.1021\/acs.analchem.9b00024"},{"key":"2026090920150781000_2026.09.03.748613v1.51","doi-asserted-by":"publisher","DOI":"10.1038\/s41594-021-00653-y"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.03.748613","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T03:15:18Z","timestamp":1789010118000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.03.748613"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,7]]},"references-count":51,"URL":"https:\/\/doi.org\/10.64898\/2026.09.03.748613","relation":{},"subject":[],"published":{"date-parts":[[2026,9,7]]},"subtype":"preprint"}}