General Information
| Description | A tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis |
| Homepage | http://www.lncrna.smu.edu.cn |
Publications
LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis
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: hao.zhu@ymail.com .
Contact:
zhuhao@smu.edu.cn
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
PreDNA
Published January 2013
Accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information
lncRNAtor
Published May 2014
A comprehensive resource for functional investigation of long non-coding RNAs
RIblast
Published April 2017
An ultrafast RNA–RNA interaction prediction system based on a seed-and-extension approach
LncVar
Published September 2016
A database of genetic variation associated with long non-coding genes
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
