{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:21:10Z","timestamp":1785403270100,"version":"3.56.0"},"posted":{"date-parts":[[2026,6,18]]},"group-title":"Molecular Biology","reference-count":83,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["F32 GM147934"],"award-info":[{"award-number":["F32 GM147934"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/006w34k90","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  In 1986, a class of small, noncoding RNAs was discovered in association with an enormous, enigmatic ribonucleoprotein complex \u2013 the \u201cvault\u201d particle \u2013 and thus dubbed vault RNAs (vtRNAs). However, it\u2019s since been recognized that the vast majority (\u226595%) of these noncoding vtRNA molecules are not associated with the mysterious vaults, raising questions about their potential independent function(s). Moreover, humans express four vtRNAs from two different loci, and debate has arisen about whether the vtRNA paralogs share any functional connection, and whether they should remain classified together. Herein, we report the expression patterns of the four\n                  <jats:italic>VTRNA<\/jats:italic>\n                  paralogs in a variety of human cell lines, including various single- and multi-gene\n                  <jats:italic>VTRNA<\/jats:italic>\n                  -knockout cell lines. Knockout of one or more of the three\n                  <jats:italic>VTRNA1<\/jats:italic>\n                  genes leads to increased expression of vtRNA2-1, suggesting that their biological functions are related. Additionally, we interrogated the effects of vtRNA knockout on HEK293T cell growth, viability, and viral infection, and were unable to replicate previously reported associations. Collectively, our findings point to a potential functional connection between even the most distantly related human vtRNA paralogs, while reaffirming that their biological roles and mechanisms still require critical study.\n                <\/jats:p>","DOI":"10.64898\/2026.06.17.732918","type":"posted-content","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T18:35:10Z","timestamp":1781807710000},"source":"Crossref","is-referenced-by-count":0,"title":["Human vault RNAs exhibit diverse expression patterns and inter-locus compensation"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8136-1574","authenticated-orcid":false,"given":"Wayne O.","family":"Hemphill","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder"},{"name":"Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arthur J.","family":"Zaug","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder"},{"name":"Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cody J. S.","family":"Hecht","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas R.","family":"Cech","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Colorado Boulder"},{"name":"Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026072009351253000_2026.06.17.732918v2.1","first-page":"772","article-title":"Vault RNAs (vtRNAs): Rediscovered non-coding RNAs with diverse physiological and pathological activities","volume":"11","year":"2023","journal-title":"Genes Dis"},{"key":"2026072009351253000_2026.06.17.732918v2.2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232113100"},{"key":"2026072009351253000_2026.06.17.732918v2.3","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.202302054"},{"key":"2026072009351253000_2026.06.17.732918v2.4","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms8030"},{"key":"2026072009351253000_2026.06.17.732918v2.5","doi-asserted-by":"publisher","DOI":"10.3390\/biom8040123"},{"key":"2026072009351253000_2026.06.17.732918v2.6","doi-asserted-by":"publisher","DOI":"10.3390\/biom10040614"},{"key":"2026072009351253000_2026.06.17.732918v2.7","doi-asserted-by":"publisher","DOI":"10.1038\/sj.hdy.6800669"},{"key":"2026072009351253000_2026.06.17.732918v2.8","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.13889"},{"key":"2026072009351253000_2026.06.17.732918v2.9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw722"},{"key":"2026072009351253000_2026.06.17.732918v2.10","doi-asserted-by":"publisher","DOI":"10.1261\/rna.079129.122"},{"key":"2026072009351253000_2026.06.17.732918v2.11","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evt113"},{"key":"2026072009351253000_2026.06.17.732918v2.12","doi-asserted-by":"crossref","first-page":"5470","DOI":"10.1021\/ac301546p","article-title":"Detection of a Thousand Copies of miRNA without Enrichment or Modification","volume":"84","year":"2012","journal-title":"Anal Chem"},{"key":"2026072009351253000_2026.06.17.732918v2.13","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)32356-1"},{"key":"2026072009351253000_2026.06.17.732918v2.14","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1002\/cm.10147","article-title":"Vaults bind directly to microtubules via their caps and not their barrels","volume":"56","year":"2003","journal-title":"Cell Motil"},{"key":"2026072009351253000_2026.06.17.732918v2.15","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1016\/j.molcel.2025.02.029","article-title":"Lost in translation: SLFN11 induces p53-independent apoptosis","volume":"85","year":"2025","journal-title":"Mol Cell"},{"key":"2026072009351253000_2026.06.17.732918v2.16","doi-asserted-by":"publisher","DOI":"10.1007\/s12192-015-0583-2"},{"key":"2026072009351253000_2026.06.17.732918v2.17","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3390\/ncrna6010007","article-title":"vtRNA2-1\/nc886 Produces a Small RNA That Contributes to Its Tumor Suppression Action through the microRNA Pathway in Prostate Cancer","volume":"6","year":"2020","journal-title":"Non-Coding RNA"},{"key":"2026072009351253000_2026.06.17.732918v2.18","doi-asserted-by":"publisher","DOI":"10.1186\/s12885-018-4049-7"},{"key":"2026072009351253000_2026.06.17.732918v2.19","doi-asserted-by":"crossref","first-page":"707","DOI":"10.3390\/cancers13040707","article-title":"The Vault Nanoparticle: A Gigantic Ribonucleoprotein Assembly Involved in Diverse Physiological and Pathological Phenomena and an Ideal Nanovector for Drug Delivery and Therapy","volume":"13","year":"2021","journal-title":"Cancers"},{"key":"2026072009351253000_2026.06.17.732918v2.20","doi-asserted-by":"crossref","first-page":"2787","DOI":"10.3390\/cancers14112787","article-title":"Small but Powerful: The Human Vault RNAs as Multifaceted Modulators of Pro-Survival Characteristics and Tumorigenesis","volume":"14","year":"2022","journal-title":"Cancers"},{"key":"2026072009351253000_2026.06.17.732918v2.21","doi-asserted-by":"crossref","first-page":"zcaf028","DOI":"10.1093\/narcan\/zcaf028","article-title":"Regulation of angiogenesis and cancer cell proliferation by human vault RNA1-2","volume":"7","year":"2025","journal-title":"NAR Cancer"},{"key":"2026072009351253000_2026.06.17.732918v2.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-023-01317-3"},{"key":"2026072009351253000_2026.06.17.732918v2.23","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00636-10"},{"key":"2026072009351253000_2026.06.17.732918v2.24","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genet.35.102401.090349"},{"key":"2026072009351253000_2026.06.17.732918v2.25","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-031-58843-3_20"},{"key":"2026072009351253000_2026.06.17.732918v2.26","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1007\/s00018-020-03675-9","article-title":"Vault RNAs: hidden gems in RNA and protein regulation","volume":"78","year":"2021","journal-title":"Cell Mol Life Sci"},{"key":"2026072009351253000_2026.06.17.732918v2.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.01.030"},{"key":"2026072009351253000_2026.06.17.732918v2.28","doi-asserted-by":"crossref","first-page":"gkaf789","DOI":"10.1093\/nar\/gkaf789","article-title":"SLFN11-mediated tRNA regulation induces cell death by disrupting proteostasis in response to DNA-damaging agents","volume":"53","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026072009351253000_2026.06.17.732918v2.29","doi-asserted-by":"crossref","first-page":"801","DOI":"10.3390\/cells9040801","article-title":"A Regulatory Noncoding RNA, nc886, Suppresses Esophageal Cancer by Inhibiting the AKT Pathway and Cell Cycle Progression","volume":"9","year":"2020","journal-title":"Cells"},{"key":"2026072009351253000_2026.06.17.732918v2.30","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2772"},{"key":"2026072009351253000_2026.06.17.732918v2.31","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.110.4.895"},{"key":"2026072009351253000_2026.06.17.732918v2.32","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.103.3.699"},{"key":"2026072009351253000_2026.06.17.732918v2.33","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M206980200"},{"key":"2026072009351253000_2026.06.17.732918v2.34","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.15.8971"},{"key":"2026072009351253000_2026.06.17.732918v2.35","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)53038-6"},{"key":"2026072009351253000_2026.06.17.732918v2.36","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.05512-11"},{"key":"2026072009351253000_2026.06.17.732918v2.37","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2701111"},{"key":"2026072009351253000_2026.06.17.732918v2.38","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.2047"},{"key":"2026072009351253000_2026.06.17.732918v2.39","doi-asserted-by":"crossref","first-page":"26","DOI":"10.5808\/GI.2015.13.2.26","article-title":"A Novel Type of Non-coding RNA, nc886, Implicated in Tumor Sensing and Suppression","volume":"13","year":"2015","journal-title":"Genomics Inform"},{"key":"2026072009351253000_2026.06.17.732918v2.40","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1146\/annurev-virology-110615-042301","article-title":"Structure, Function, and Evolution of Coronavirus Spike Proteins","volume":"3","year":"2016","journal-title":"Annu Rev Virol"},{"key":"2026072009351253000_2026.06.17.732918v2.41","first-page":"9233","article-title":"E2F1-directed activation of nc886 mediates drug resistance in cervical cancer cells via regulation of major vault protein","volume":"10","year":"2017","journal-title":"Int J Clin Exp Pathol"},{"key":"2026072009351253000_2026.06.17.732918v2.42","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1074403"},{"key":"2026072009351253000_2026.06.17.732918v2.43","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms5767"},{"key":"2026072009351253000_2026.06.17.732918v2.44","doi-asserted-by":"publisher","DOI":"10.1002\/hep.25642"},{"key":"2026072009351253000_2026.06.17.732918v2.45","doi-asserted-by":"publisher","DOI":"10.1016\/j.freeradbiomed.2010.09.021"},{"key":"2026072009351253000_2026.06.17.732918v2.46","doi-asserted-by":"crossref","first-page":"167441","DOI":"10.1016\/j.bbadis.2024.167441","article-title":"Major vault protein directly enhances adaptive immunity induced by Influenza A virus or indirectly through innate immunity","volume":"1870","year":"2024","journal-title":"Biochim Biophys Acta BBA - Mol Basis Dis"},{"key":"2026072009351253000_2026.06.17.732918v2.47","doi-asserted-by":"publisher","DOI":"10.3390\/ijms26041562"},{"key":"2026072009351253000_2026.06.17.732918v2.48","doi-asserted-by":"publisher","DOI":"10.1101\/gr.161034.113"},{"key":"2026072009351253000_2026.06.17.732918v2.49","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-33123-0"},{"key":"2026072009351253000_2026.06.17.732918v2.50","doi-asserted-by":"publisher","DOI":"10.1016\/0076-6879(89)80091-6"},{"key":"2026072009351253000_2026.06.17.732918v2.51","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/0378-4274(85)90007-4","article-title":"Induction of cell damage by menadione and benzo(a)-pyrene-3,6-quinone in cultures of adult rat hepatocytes and human fibroblasts","volume":"28","year":"1985","journal-title":"Toxicol Lett"},{"key":"2026072009351253000_2026.06.17.732918v2.52","unstructured":"Mosig A , Stadler PF . 2011. Evolution of Vault RNAs. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/9780470015902.a0022883 (Accessed March 23, 2026)."},{"key":"2026072009351253000_2026.06.17.732918v2.53","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2567.2003.01708.x"},{"key":"2026072009351253000_2026.06.17.732918v2.54","first-page":"7298","article-title":"Disruption of the Murine Major Vault Protein (MVP\/LRP) Gene Does Not Induce Hypersensitivity to Cytostatics1","volume":"62","year":"2002","journal-title":"Cancer Res"},{"key":"2026072009351253000_2026.06.17.732918v2.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2009.03.031"},{"key":"2026072009351253000_2026.06.17.732918v2.56","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2025.01.008"},{"key":"2026072009351253000_2026.06.17.732918v2.57","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2015.00002"},{"key":"2026072009351253000_2026.06.17.732918v2.58","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.00087-08"},{"key":"2026072009351253000_2026.06.17.732918v2.59","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1501481"},{"key":"2026072009351253000_2026.06.17.732918v2.60","doi-asserted-by":"publisher","DOI":"10.1261\/rna.080161.124"},{"key":"2026072009351253000_2026.06.17.732918v2.61","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E10-02-0105"},{"key":"2026072009351253000_2026.06.17.732918v2.62","unstructured":"Raitoharju E , Raji\u0107 S , Marttila S . Non-coding 886 (nc886\/vtRNA2-1), the epigenetic odd duck \u2013 implications for future studies. Epigenetics 19: 2332819."},{"key":"2026072009351253000_2026.06.17.732918v2.63","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1186\/s13148-025-01871-7","article-title":"Regulation of nc886 (vtRNA2-1) RNAs is associated with cardiometabolic risk factors and diseases","volume":"17","year":"2025","journal-title":"Clin Epigenetics"},{"key":"2026072009351253000_2026.06.17.732918v2.64","doi-asserted-by":"publisher","DOI":"10.4161\/epi.28323"},{"key":"2026072009351253000_2026.06.17.732918v2.65","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0718-2_3"},{"key":"2026072009351253000_2026.06.17.732918v2.66","doi-asserted-by":"crossref","unstructured":"Santos TM , Galv\u00e3o E , Gomes H , Del-Bem L-E. 2023. Characterization and Phylogenetic Insights into the First Viral Major Vault Proteins (MVPs), Identified in Bacteriophages from the Human Gut. 2023.11.10.566534. https:\/\/www.biorxiv.org\/content\/10.1101\/2023.11.10.566534v1 (Accessed March 23, 2026).","DOI":"10.1101\/2023.11.10.566534"},{"key":"2026072009351253000_2026.06.17.732918v2.67","doi-asserted-by":"crossref","unstructured":"Sokolskyi T. 2019. Bacterial Major Vault Protein homologs shed new light on origins of the enigmatic organelle. 872010. https:\/\/www.biorxiv.org\/content\/10.1101\/872010v3 (Accessed March 23, 2026).","DOI":"10.1101\/872010"},{"key":"2026072009351253000_2026.06.17.732918v2.68","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp112"},{"key":"2026072009351253000_2026.06.17.732918v2.69","doi-asserted-by":"publisher","DOI":"10.1016\/j.ncrna.2019.02.001"},{"key":"2026072009351253000_2026.06.17.732918v2.70","doi-asserted-by":"crossref","first-page":"115823","DOI":"10.1016\/j.celrep.2025.115823","article-title":"Vault RNAs aid RNA virus infection by facilitating cytoplasmic localization of hnRNP C and ELAVL1","volume":"44","year":"2025","journal-title":"Cell Rep"},{"key":"2026072009351253000_2026.06.17.732918v2.71","doi-asserted-by":"publisher","DOI":"10.1242\/jeb.001800"},{"key":"2026072009351253000_2026.06.17.732918v2.72","doi-asserted-by":"crossref","first-page":"416","DOI":"10.2183\/pjab.88.416","article-title":"Structural studies of large nucleoprotein particles, vaults","volume":"88","year":"2012","journal-title":"Proc Jpn Acad Ser B Phys Biol Sci"},{"key":"2026072009351253000_2026.06.17.732918v2.73","doi-asserted-by":"crossref","first-page":"4072","DOI":"10.3390\/ijms25074072","article-title":"Human Vault RNAs: Exploring Their Potential Role in Cellular Metabolism","volume":"25","year":"2024","journal-title":"Int J Mol Sci"},{"key":"2026072009351253000_2026.06.17.732918v2.74","doi-asserted-by":"crossref","first-page":"1177932219868454","DOI":"10.1177\/1177932219868454","article-title":"Enjoy the Silence: Nearly Half of Human tRNA Genes Are Silent","volume":"13","year":"2019","journal-title":"Bioinforma Biol Insights"},{"key":"2026072009351253000_2026.06.17.732918v2.75","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1002\/wrna.1141","article-title":"The significant other: splicing by the minor spliceosome","volume":"4","year":"2013","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2026072009351253000_2026.06.17.732918v2.76","doi-asserted-by":"publisher","DOI":"10.1016\/j.yexcr.2005.10.016"},{"key":"2026072009351253000_2026.06.17.732918v2.77","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M106055200"},{"key":"2026072009351253000_2026.06.17.732918v2.78","doi-asserted-by":"crossref","first-page":"29752","DOI":"10.1016\/S0021-9258(18)43945-2","article-title":"The rat vault RNA gene contains a unique RNA polymerase III promoter composed of both external and internal elements that function synergistically","volume":"269","year":"1994","journal-title":"J Biol Chem"},{"key":"2026072009351253000_2026.06.17.732918v2.79","doi-asserted-by":"publisher","DOI":"10.1002\/iub.2200"},{"key":"2026072009351253000_2026.06.17.732918v2.80","doi-asserted-by":"publisher","DOI":"10.1261\/rna.079892.123"},{"key":"2026072009351253000_2026.06.17.732918v2.81","doi-asserted-by":"publisher","DOI":"10.1261\/rna.078971.121"},{"key":"2026072009351253000_2026.06.17.732918v2.82","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku560"},{"key":"2026072009351253000_2026.06.17.732918v2.83","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1016\/j.ijsu.2020.05.016","article-title":"Dijerential hypermethylation of the VTRNA2-1 promoter in hepatocellular carcinoma as a prognostic factor: Tumor marker prognostic study","volume":"79","year":"2020","journal-title":"Int J Surg"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.06.17.732918","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T16:35:24Z","timestamp":1784565324000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.06.17.732918"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,18]]},"references-count":83,"URL":"https:\/\/doi.org\/10.64898\/2026.06.17.732918","relation":{},"subject":[],"published":{"date-parts":[[2026,6,18]]},"subtype":"preprint"}}