Genome-Wide Computational Analysis and Validation of Potential Long Noncoding RNA-Mediated DNA-DNA-RNA Triplexes in the Human Genome

Long noncoding RNAs are well studied for their regulatory actions through interaction with DNA regulating biological roles of DNA, RNA, or protein. However, direct binding of lncRNA with DNA is rarely demonstrated in experiments. The present protocol explains genome wide computational strategies to choose lncRNAs that can bind directly to the chromatin by forming highly stable DNA-DNA-RNA triplexes. The chapter also focuses on biophysical methods that can be used to validate the computationally derived lncRNA-gene targets in vitro.