Detecting Noncoding RNA Expression: From Arrays to Next-Generation Sequencing

Detection and quantification of noncoding(nc) RNA species can present specific challenges as compared to mRNA. Among them, ncRNA sequences are generally less well annotated, can include extraordinarily small species such as miRNA or piRNA, can have repetitive sequences or have high GC content, or even have antisense expression. Despite this, many different traditional technologies have been adapted to measure ncRNAs and include those based on a priori knowledge of sequence such as probe detection (qRT-PCR) and hybridization (arrays), and those where such knowledge is not required (next-generation sequencing). A summary of these experimental techniques is reviewed in this chapter, including the available chemistries, throughput, starting material, and species interrogated. Subsequent focus is on the computational analysis for next-generation sequencing since this technology can not only detect and measure ncRNAs but more excitingly also lead to the discovery of new or isomeric forms.