LncRNA:DNA Binding Prediction Using LongTarget and Its Revised Version.

Many noncoding RNAs, especially long noncoding RNAs (lncRNAs), can bind to DNA sequences in specific regulatory regions in genomes, thereby regulating gene expression by recruiting epigenomic modification enzymes to their DNA-binding sites (DBSs). Experimental identification of DBSs genome-wide for the abundant lncRNAs in genomes of humans, mice, and other model animals is infeasible, making accurate and fast computational prediction of lncRNA:DNA-binding indispensable. Multiple methods and programs have been developed. This chapter describes LongTarget and its variant, Fasim-LongTarget, including how to use them step by step to predict DNA-binding domains (DBDs) and DBSs in multiple situations. Both the online and offline versions are described. In addition, we describe how to use the LongMan database, which stores orthologous sequences of human and mouse lncRNAs in other mammals, to explore species-specific lncRNAs and lncRNA:DNA binding. We also demonstrate how to evaluate predicted DBDs and DBSs using publicly available data in the UCSC Genome Browser.