LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis

• DOI: 10.1093/bioinformatics/btu643
• Publication Date: 2014-09-28T00:25:27Z
• Authors: Sha He; Hai Zhang; Haihua Liu; Hao Zhu
• Keywords: 0301 basic medicine; Binding Sites; Genome, Human; Computational Biology; Sequence Analysis, DNA; DNA Methylation; DNA-Binding Proteins; Genomic Imprinting; 03 medical and health sciences; Gene Expression Regulation; Humans; RNA, Long Noncoding; Promoter Regions, Genetic; Base Pairing; Software

Abstract 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. Availability and implementation: Website of LongTarget : lncrna.smu.edu.cn , or contact: [e-mail] . Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.