Efficient and selective knockdown of small non-coding RNAs

Abstract

Small non-coding RNAs (ncRNAs), less than 200 nucleotides in length, play important roles in various biological processes, such as pre-mRNA splicing, pre-rRNA processing and modification, and gene expression regulation. However, characterization of small ncRNAs remains difficult mainly due to methodological obstacles in selective reduction of these RNAs. Here we describe an approach to deplete small ncRNAs, in principle any types of RNAs, using second generation antisense oligonucleotide-directed RNase H cleavage pathway in human cells. This protocol includes oligonucleotide design, transfection, RNA preparation, and target RNA detection.