{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T22:15:46Z","timestamp":1790633746472,"version":"4.1.0"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2016,2,4]],"date-time":"2016-02-04T00:00:00Z","timestamp":1454544000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004744","type":"journal-article","created":{"date-parts":[[2016,2,4]],"date-time":"2016-02-04T19:34:56Z","timestamp":1454614496000},"page":"e1004744","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":85,"title":["MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression"],"prefix":"10.1371","volume":"12","author":[{"given":"Steven W.","family":"Paugh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Coss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ju","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucas T.","family":"Laudermilk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christy R.","family":"Grace","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio M.","family":"Ferreira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M. Brett","family":"Waddell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Granger","family":"Ridout","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deanna","family":"Naeve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Leuze","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip F.","family":"LoCascio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John C.","family":"Panetta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark R.","family":"Wilkinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ching-Hon","family":"Pui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clayton W.","family":"Naeve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward C.","family":"Uberbacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik J.","family":"Bonten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William E.","family":"Evans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,2,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/nchembio860","article-title":"Activating gene expression in mammalian cells with promoter-targeted duplex RNAs","volume":"3","author":"BA Janowski","year":"2007","journal-title":"Nat Chem Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"17337","DOI":"10.1073\/pnas.0607015103","article-title":"Small dsRNAs induce transcriptional activation in human cells","volume":"103","author":"LC Li","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1038\/448855a","article-title":"RNA interference: hitting the on switch","volume":"448","author":"E Check","year":"2007","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1073\/pnas.0707594105","article-title":"MicroRNA-373 induces expression of genes with complementary promoter sequences","volume":"105","author":"RF Place","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"I Dunham","year":"2012","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1097\/PAI.0b013e3181e1ef6a","article-title":"Triplex-forming MicroRNAs form stable complexes with HIV-1 provirus and inhibit its replication","volume":"18","author":"M Kanak","year":"2010","journal-title":"Appl Immunohistochem Mol Morphol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"2264","DOI":"10.1101\/gad.590910","article-title":"Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes","volume":"24","author":"KM Schmitz","year":"2010","journal-title":"Genes Dev"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"354","DOI":"10.1093\/nar\/gkh188","article-title":"Triplex-forming oligonucleotide target sequences in the human genome","volume":"32","author":"JR Go\u00f1i","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"D110","DOI":"10.1093\/nar\/gku970","article-title":"The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome","volume":"43","author":"P Jenjaroenpun","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"S9","DOI":"10.1186\/1471-2164-10-S3-S9","article-title":"TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome","volume":"10","author":"P Jenjaroenpun","year":"2009","journal-title":"BMC Genomics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"5321","DOI":"10.1093\/nar\/22.24.5321","article-title":"Exclusion of RNA strands from a purine motif triple helix","volume":"22","author":"CL Semerad","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1126\/science.165.3891.349","article-title":"Gene regulation for higher cells: a theory","volume":"165","author":"RJ Britten","year":"1969","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"606","DOI":"10.4161\/rna.7.5.13215","article-title":"Mature microRNAs identified in highly purified nuclei from HCT116 colon cancer cells","volume":"7","author":"CW Park","year":"2010","journal-title":"RNA Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"10270","DOI":"10.1074\/jbc.C113.541417","article-title":"Importin 8 regulates the transport of mature microRNAs into the cell nucleus","volume":"289","author":"Y Wei","year":"2014","journal-title":"J Biol Chem"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"19202","DOI":"10.1073\/pnas.1217338109","article-title":"Formation of triple-helical structures by the 3&apos;-end sequences of MALAT1 and MENbeta noncoding RNAs","volume":"109","author":"JA Brown","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1111\/j.1742-4658.2011.08095.x","article-title":"Transient DNA \/ RNA-protein interactions","volume":"278","author":"FJ Blanco","year":"2011","journal-title":"FEBS J"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2663","DOI":"10.1093\/nar\/gkl354","article-title":"Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region","volume":"34","author":"A Bacolla","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1006\/jmbi.2000.4502","article-title":"Searching genomes for sequences with the potential to form intrastrand triple helices","volume":"302","author":"PR Hoyne","year":"2000","journal-title":"J Mol Biol"},{"key":"ref19","doi-asserted-by":"crossref","DOI":"10.1126\/science.1279808","article-title":"Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition","volume":"258","author":"RW Roberts","year":"1992","journal-title":"Science"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1038\/nprot.2007.249","article-title":"Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions","volume":"2","author":"LM Hellman","year":"2007","journal-title":"Nat Protoc"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1006\/bbrc.1994.2578","article-title":"Efficient unwinding of triplex DNA by a DNA helicase","volume":"204","author":"IP Maine","year":"1994","journal-title":"Biochem Biophys Res Commun"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"5174","DOI":"10.1074\/jbc.M114.634923","article-title":"A distinct triplex DNA unwinding activity of ChlR1 helicase","volume":"290","author":"M Guo","year":"2015","journal-title":"J Biol Chem"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.1128\/MCB.24.6.2286-2295.2004","article-title":"Replication stalling at Friedreich&apos;s ataxia (GAA)n repeats in vivo","volume":"24","author":"MM Krasilnikova","year":"2004","journal-title":"Mol Cell Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"R1","DOI":"10.1186\/gb-2003-5-1-r1","article-title":"MicroRNA targets in Drosophila","volume":"5","author":"AJ Enright","year":"2003","journal-title":"Genome Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: a next-generation genome browser","volume":"19","author":"ME Skinner","year":"2009","journal-title":"Genome Res"},{"issue":"Pt 2","key":"ref26","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1042\/bj3160461","article-title":"Triplex DNA in the nucleus: direct binding of triplex-specific antibodies and their effect on transcription, replication and cell growth","volume":"316","author":"YM Agazie","year":"1996","journal-title":"Biochem J"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/s00412-002-0198-0","article-title":"Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine\/polypyrimidine DNA probes and antitriplex antibodies","volume":"111","author":"M Ohno","year":"2002","journal-title":"Chromosoma"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"16810","DOI":"10.1021\/bi991811m","article-title":"Structure of a triple helical DNA with a triplex-duplex junction","volume":"38","author":"S Rhee","year":"1999","journal-title":"Biochemistry"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"427","DOI":"10.4161\/rna.8.3.14999","article-title":"Potential in vivo roles of nucleic acid triple-helices","volume":"8","author":"FA Buske","year":"2011","journal-title":"RNA Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1093\/bioinformatics\/18.12.1585","article-title":"Robust estimators for expression analysis","volume":"18","author":"E Hubbell","year":"2002","journal-title":"Bioinformatics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/bioinformatics\/btg405","article-title":"affy\u2014analysis of Affymetrix GeneChip data at the probe level","volume":"20","author":"L Gautier","year":"2004","journal-title":"Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/ng1151","article-title":"Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells","volume":"34","author":"MH Cheok","year":"2003","journal-title":"Nat Genet"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/S1535-6108(02)00032-6","article-title":"Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling","volume":"1","author":"EJ Yeoh","year":"2002","journal-title":"Cancer Cell"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1056\/NEJMoa033513","article-title":"Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment","volume":"351","author":"A Holleman","year":"2004","journal-title":"N Engl J Med"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/0009-2614(96)00349-1","article-title":"Ab initio study of solvated molecules: A new implementation of the polarizable continuum model","volume":"255","author":"M Cossi","year":"1996","journal-title":"Chemical Physics Letters"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1002\/(SICI)1099-1352(199909\/10)12:5<279::AID-JMR473>3.0.CO;2-3","article-title":"Improving biosensor analysis","volume":"12","author":"DG Myszka","year":"1999","journal-title":"J Mol Recognit"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"R90","DOI":"10.1186\/gb-2010-11-8-r90","article-title":"Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites","volume":"11","author":"D Betel","year":"2010","journal-title":"Genome Biol"},{"key":"ref39","doi-asserted-by":"crossref","unstructured":"Anderson DP (2004) BOINC: A System for Public-Resource Computing and Storage. Proceedings of the 5th IEEE\/ACM International Workshop on Grid Computing: IEEE Computer Society. pp. 4\u201310.","DOI":"10.1109\/GRID.2004.14"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1126\/science.4001930","article-title":"The mosaic genome of warm-blooded vertebrates","volume":"228","author":"G Bernardi","year":"1985","journal-title":"Science"},{"key":"ref41","unstructured":"Keller RLJ (2005) Optimizing the process of nuclear magnetic resonance spectrum analysis and computer aided resonance assignment: Diss., Naturwissenschaften, Eidgen\u00f6ssische Technische Hochschule ETH Z\u00fcrich, Nr. 15947, 2005."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004744","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T08:30:59Z","timestamp":1540283459000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004744"}},"subtitle":[],"editor":[{"given":"Ilya","family":"Ioshikhes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,2,4]]},"references-count":41,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2016,2,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004744","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,2,4]]}}}