Detecting sRNAs by Northern blotting

Small RNAs (sRNAs) play fundamental roles in modifying the transcriptomes and proteomes of organisms. sRNAs can be classified according to their origin and way of action into classes such as microRNAs, trans-acting siRNAs, heterochromatin siRNAs, Piwi-interacting RNAs, and natural antisense siRNAs, although microRNAs are the most conserved and studied class. The expression pattern of a sRNA can be indicative of its biological function. Northern blotting is one of the most widely used methods to identify, validate, and study the expression profile of sRNAs because it is a quantitative, relatively inexpensive technique that is readily available for most laboratories. This chapter describes a protocol for sRNA Northern blot analysis, which includes RNA extraction, polyacrylamide gel electrophoresis, hybridisation, or the detection of sRNA using oligonucleotide probes.