{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T02:32:22Z","timestamp":1773455542930,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In mammalian cells, many genes are silenced by genome methylation. DNA methyltransferases and polycomb repressive complexes, which both lack sequence-specific DNA-binding motifs, are recruited by long non-coding RNA (lncRNA) to specific genomic sites to methylate DNA and chromatin. Increasing evidence indicates that many lncRNAs contain DNA-binding motifs that can bind to DNA by forming RNA:DNA triplexes. The identification of lncRNA DNA-binding motifs and binding sites is essential for deciphering lncRNA functions and correct and erroneous genome methylation; however, such identification is challenging because lncRNAs may contain thousands of nucleotides. No computational analysis of typical lncRNAs has been reported. Here, we report a computational method and program ( LongTarget ) to predict lncRNA DNA-binding motifs and binding sites. We used this program to analyse multiple antisense lncRNAs, including those that control well-known imprinting clusters, and obtained results agreeing with experimental observations and epigenetic marks. These results suggest that it is feasible to predict many lncRNA DNA-binding motifs and binding sites genome-wide.<\/jats:p>\n               <jats:p>Availability and implementation: Website of LongTarget : lncrna.smu.edu.cn , or contact: hao.zhu@ymail.com .<\/jats:p>\n               <jats:p>Contact: \u00a0zhuhao@smu.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu643","type":"journal-article","created":{"date-parts":[[2014,9,28]],"date-time":"2014-09-28T00:25:27Z","timestamp":1411863927000},"page":"178-186","source":"Crossref","is-referenced-by-count":118,"title":["LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis"],"prefix":"10.1093","volume":"31","author":[{"given":"Sha","family":"He","sequence":"first","affiliation":[{"name":"1 Bioinformatics Section, School of Basic Medical Sciences and 2 Network Center, Southern Medical University, Guangzhou 510515, China"}]},{"given":"Hai","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Section, School of Basic Medical Sciences and 2 Network Center, Southern Medical University, Guangzhou 510515, China"}]},{"given":"Haihua","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Section, School of Basic Medical Sciences and 2 Network Center, Southern Medical University, Guangzhou 510515, China"}]},{"given":"Hao","family":"Zhu","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Section, School of Basic Medical Sciences and 2 Network Center, Southern Medical University, Guangzhou 510515, China"}]}],"member":"286","published-online":{"date-parts":[[2014,9,26]]},"reference":[{"key":"2023020116141765900_btu643-B1","doi-asserted-by":"crossref","first-page":"1407","DOI":"10.1093\/nar\/gkr810","article-title":"Comprehensive survey and geometric classification of base triples in RNA structures","volume":"40","author":"Abu Almakarem","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023020116141765900_btu643-B2","doi-asserted-by":"crossref","first-page":"a018382","DOI":"10.1101\/cshperspect.a018382","article-title":"Genomic imprinting in mammals","volume":"6","author":"Barlow","year":"2014","journal-title":"Cold Spring Harbor Perspect. 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