{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T14:42:39Z","timestamp":1771339359632,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T00:00:00Z","timestamp":1715644800000},"content-version":"vor","delay-in-days":5004,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The direct negative impact of the transcriptional activity of one component on the second one in cis is referred to as transcriptional interference (TI). U6 is a type III RNA polymerase III promoter commonly used for driving small hairpin RNA (shRNA) expression in vector-based RNAi. In the design and construction of viral vectors, multiple transcription units may be arranged in close proximity in a space-limited vector. Determining if U6 promoter activity can be affected by TI is critical for the expression of target shRNA in gene therapy or loss-of-function studies. In this research, we designed and implemented a modified retroviral system where shRNA and exogenous gene expressions were driven by two independent transcriptional units. We arranged U6 promoter driving shRNA expression and UbiC promoter in two promoter arrangements. In primary macrophages, we found U6 promoter activity was inhibited by UbiC promoter when in the divergent arrangement but not in tandem. In contrast, PKG promoter had no such negative impact. Instead of enhancing U6 promoter activity, CMV enhancer had significant negative impact on U6 promoter activity in the presence of UbiC promoter. Our results indicate that U6 promoter activity can be affected by TI in a proximal promoter-specific and arrangement-dependent manner.<\/jats:p>","DOI":"10.1016\/s1672-0229(10)60019-8","type":"journal-article","created":{"date-parts":[[2010,10,22]],"date-time":"2010-10-22T11:07:03Z","timestamp":1287745623000},"page":"170-179","source":"Crossref","is-referenced-by-count":24,"title":["Regulation of U6 Promoter Activity by Transcriptional Interference in Viral Vector-Based RNAi"],"prefix":"10.1093","volume":"8","author":[{"given":"Linghu","family":"Nie","sequence":"first","affiliation":[{"name":"Key Laboratory of Genome Sciences and Information, Cancer Biology and Genetics Group, Beijing Institute of Genomics, Chinese Acadamy of Sciences , Beijing, 100029 , China"}]},{"given":"Meghna Das","family":"Thakur","sequence":"additional","affiliation":[{"name":"Departments of Medicine and Cell Biology, Washington University , St. Louis, MO, 63110 , USA"}]},{"given":"Yumei","family":"Wang","sequence":"additional","affiliation":[{"name":"Departments of Medicine and Cell Biology, Washington University , St. Louis, MO, 63110 , USA"}]},{"given":"Qin","family":"Su","sequence":"additional","affiliation":[{"name":"Immunocore Limited , Abingdon, Oxon, OX14 4RX , UK"}]},{"given":"Yongliang","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Genome Sciences and Information, Cancer Biology and Genetics Group, Beijing Institute of Genomics, Chinese Acadamy of Sciences , Beijing, 100029 , China"}]},{"given":"Yunfeng","family":"Feng","sequence":"additional","affiliation":[{"name":"Departments of Medicine and Cell Biology, Washington University , St. Louis, MO, 63110 , USA"}]}],"member":"286","published-online":{"date-parts":[[2010,10,21]]},"reference":[{"key":"2024051409225777800_bib1","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1038\/35888","article-title":"Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans","volume":"391","author":"Fire","year":"1998","journal-title":"Nature"},{"key":"2024051409225777800_bib2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/S0092-8674(00)80620-0","article-title":"RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals","volume":"101","author":"Zamore","year":"2000","journal-title":"Cell"},{"key":"2024051409225777800_bib3","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/35078107","article-title":"Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells","volume":"411","author":"Elbashir","year":"2001","journal-title":"Nature"},{"key":"2024051409225777800_bib4","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1126\/science.1064921","article-title":"Identification of novel genes coding for small expressed RNAs","volume":"294","author":"Lagos-Quintana","year":"2001","journal-title":"Science"},{"key":"2024051409225777800_bib5","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1016\/S0960-9822(02)00809-6","article-title":"Identification of tissue-specific microRNAs from mouse","volume":"12","author":"Lagos-Quintana","year":"2002","journal-title":"Curr. Biol."},{"key":"2024051409225777800_bib6","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1261\/rna.2146903","article-title":"New microRNAs from mouse and human","volume":"9","author":"Lagos-Quintana","year":"2003","journal-title":"RNA"},{"key":"2024051409225777800_bib7","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1126\/science.1065062","article-title":"An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans","volume":"294","author":"Lau","year":"2001","journal-title":"Science"},{"key":"2024051409225777800_bib8","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1126\/science.1065329","article-title":"An extensive class of small RNAs in Caenorhabditis elegans","volume":"294","author":"Lee","year":"2001","journal-title":"Science"},{"key":"2024051409225777800_bib9","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1126\/science.1080372","article-title":"Vertebrate microRNA genes","volume":"299","author":"Lim","year":"2003","journal-title":"Science"},{"key":"2024051409225777800_bib10","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1101\/gad.981002","article-title":"Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells","volume":"16","author":"Paddison","year":"2002","journal-title":"Genes Dev."},{"key":"2024051409225777800_bib11","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/S1535-6108(02)00122-8","article-title":"Stable suppression of tumorigenicity by virus-mediated RNA interference","volume":"2","author":"Brummelkamp","year":"2002","journal-title":"Cancer Cell"},{"key":"2024051409225777800_bib12","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/nbt0502-505","article-title":"Effective expression of small interfering RNA in human cells","volume":"20","author":"Paul","year":"2002","journal-title":"Nat. Biotechnol."},{"key":"2024051409225777800_bib13","doi-asserted-by":"crossref","first-page":"5515","DOI":"10.1073\/pnas.082117599","article-title":"A DNA vector-based RNAi technology to suppress gene expression in mammalian cells","volume":"99","author":"Sui","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051409225777800_bib14","doi-asserted-by":"crossref","first-page":"6047","DOI":"10.1073\/pnas.092143499","article-title":"RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells","volume":"99","author":"Yu","year":"2002","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051409225777800_bib15","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1472-6750-6-7","article-title":"Criteria for effective design, construction, and gene knockdown by shRNA vectors","volume":"6","author":"Taxman","year":"2006","journal-title":"BMC Biotechnol."},{"key":"2024051409225777800_bib16","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1002\/jgm.860","article-title":"Stable RNA interference: comparison of U6 and H1 promoters in endothelial cells and in mouse brain","volume":"8","author":"Makinen","year":"2006","journal-title":"J. Gene Med."},{"key":"2024051409225777800_bib17","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/j.bbrc.2004.08.128","article-title":"Poly(U) and polyadenylation termination signals are interchangeable for terminating the expression of shRNA from a pol II promoter","volume":"323","author":"Song","year":"2004","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2024051409225777800_bib18","doi-asserted-by":"crossref","first-page":"e62","DOI":"10.1093\/nar\/gni061","article-title":"An RNA polymerase II construct synthesizes short-hairpin RNA with a quantitative indicator and mediates highly efficient RNAi","volume":"33","author":"Zhou","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2024051409225777800_bib19","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1007\/s11033-005-3965-1","article-title":"shRNA transcribed by RNA Pol II promoter induce RNA interference in mammalian cell","volume":"33","author":"Yuan","year":"2006","journal-title":"Mol. Biol. Rep."},{"key":"2024051409225777800_bib20","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nbt1052","article-title":"Synthetic shRNAs as potent RNAi triggers","volume":"23","author":"Siolas","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2024051409225777800_bib21","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1002\/jgm.556","article-title":"Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells","volume":"6","author":"Miyagishi","year":"2004","journal-title":"J. Gene Med."},{"key":"2024051409225777800_bib22","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/nmeth923","article-title":"Lessons from Nature: microRNA-based shRNA libraries","volume":"3","author":"Chang","year":"2006","journal-title":"Nat. Methods"},{"key":"2024051409225777800_bib23","doi-asserted-by":"crossref","first-page":"e100","DOI":"10.1093\/nar\/gng098","article-title":"An enhanced U6 promoter for synthesis of short hairpin RNA","volume":"31","author":"Xia","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2024051409225777800_bib24","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1089\/hum.2005.16.1404","article-title":"Hybrid cytomegalovirus enhancer-h1 promoter-based plasmid and baculovirus vectors mediate effective RNA interference","volume":"16","author":"Ong","year":"2005","journal-title":"Hum. Gene. Ther."},{"key":"2024051409225777800_bib25","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1016\/j.jmb.2006.10.009","article-title":"Promoter crosstalk effects on gene expression","volume":"365","author":"Hampf","year":"2007","journal-title":"J. Mol. Biol."},{"key":"2024051409225777800_bib26","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.tig.2005.04.009","article-title":"Transcriptional interference-a crash course","volume":"21","author":"Shearwin","year":"2005","journal-title":"Trends Genet."},{"key":"2024051409225777800_bib27","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1126\/science.1067081","article-title":"Germline transmission and tissue-specific expression of transgenes delivered by lentiviral vectors","volume":"295","author":"Lois","year":"2002","journal-title":"Science"},{"key":"2024051409225777800_bib28","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1128\/MCB.22.2.469-479.2002","article-title":"Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position","volume":"22","author":"Eszterhas","year":"2002","journal-title":"Mol. Cell Biol."},{"key":"2024051409225777800_bib29","doi-asserted-by":"crossref","first-page":"2973","DOI":"10.1038\/sj.onc.1208472","article-title":"Conditional inhibition of cancer cell proliferation by tetracycline-responsive, H1 promoter-driven silencing of PLK1","volume":"24","author":"Matthess","year":"2005","journal-title":"Oncogene"},{"key":"2024051409225777800_bib30","doi-asserted-by":"crossref","first-page":"2259","DOI":"10.1093\/nar\/23.12.2259","article-title":"Improved accumulation and activity of ribozymes expressed from a tRNA-based RNA polymerase III promoter","volume":"23","author":"Thompson","year":"1995","journal-title":"Nucleic Acids Res."},{"key":"2024051409225777800_bib31","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/0378-1119(96)00075-3","article-title":"Retroviral vectors designed for targeted expression of RNA polymerase III-driven transcripts: a comparative study","volume":"171","author":"Ilves","year":"1996","journal-title":"Gene"},{"key":"2024051409225777800_bib32","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1093\/nar\/gkg704","article-title":"Promoter choice affects the potency of HIV-1 specific RNA interference","volume":"31","author":"Boden","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2024051409225777800_bib33","doi-asserted-by":"crossref","first-page":"e65","DOI":"10.1093\/nar\/gkm152","article-title":"A hybrid CMV-H1 construct improves efficiency of PEI-delivered shRNA in the mouse brain","volume":"35","author":"Hassani","year":"2007","journal-title":"Nucleic Acids Res."}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022910600198?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022910600198?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/8\/3\/170\/57595902\/gpb_8_3_170.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/8\/3\/170\/57595902\/gpb_8_3_170.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,14]],"date-time":"2024-05-14T09:35:55Z","timestamp":1715679355000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/8\/3\/170\/7221859"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,9,1]]},"references-count":33,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2010,9,1]]}},"URL":"https:\/\/doi.org\/10.1016\/s1672-0229(10)60019-8","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"value":"1672-0229","type":"print"},{"value":"2210-3244","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2010,9]]},"published":{"date-parts":[[2010,9,1]]}}}