title: LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Website of LongTarget: lncrna.smu.edu.cn, or contact: hao.zhu@ymail.com.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China.
authors.forename: Sha
authors.initials: S
authors.lastname: He
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China.
authors.forename: Haihua
authors.initials: H
authors.lastname: Liu
authors.affiliation: Bioinformatics Section, School of Basic Medical Sciences and Network Center, Southern Medical University, Guangzhou 510515, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhu
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005786:Gene Expression Regulation; D015894:Genome, Human; D018392:Genomic Imprinting; D006801:Humans; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; D062085:RNA, Long Noncoding