Visualizing Noncoding RNA – A Guide to Investigating Noncoding RNA Species

from Genetic Engineering News by Xiao-Jun Ma, Ph.D.

rna-seq

Figure 1. RNA ISH in prostate tumor tissue. This whole-tissue section was probed for the noncoding PCA3 transcript using RNAscope ISH technology

The significance of noncoding RNA is becoming increasingly recognized as new classes involved in genetic regulatory control and diverse cellular activities are being uncovered on a regular basis. Discovering the world of noncoding RNAs has already unlocked many secrets about how life’s incredible phenotypic diversity arises from a relatively small and fixed set of protein-coding genes.

Moreover, transcriptomic profiling has also proven that, like protein, RNA is a rich source of biomarkers. Having long been used for diagnostic testing and the identification of potential therapeutic targets, biomarkers are growing exponentially in their importance within the era of personalized medicine. In fact, several noncoding RNA candidates have shown promising diagnostic and prognostic utility (Figure 1).

To fully capitalize on the properties of noncoding RNA, it is crucial that effective analytical technologies are employed, and this presents a challenge. For protein coding genes, immunohistochemistry is used routinely to map gene expression to specific cells in situ, yet noncoding RNA species lack protein counterparts. For these molecules, gene expression can only be visualized by RNA in situ hybridization (ISH).

This tutorial describes a modern approach to investigating noncoding RNA for advancing studies in a range of areas from cancer research to neuroscience.

From Discovery to Understanding

In order to interrogate the transcriptome for noncoding RNA species, a fully comprehensive transcriptomic discovery program will involve utilizing technologies such as the microarray or RNA-Seq. Once a set of transcripts exhibiting differential expression has been identified, the investigation must then focus in on validating their functional significance and biological or clinical relevance. When it comes to studying those transcripts of interest in greater depth, RNA ISH provides information regarding the expression of noncoding RNA species within the morphological context, which is vital for understanding underlying biological mechanisms. (read more…)

Source – Genetic Engineering News

 

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