Experimental Rnomics: A Global Approach to Identifying Small Nuclear RNAs and Their Targets in Different Model Organisms

Non-messenger RNAs (nmRNAs) play a wide and essential role in cellular functions. Computational identification of novel nmRNAs in genomes of model organisms is severely restricted owing to their lack of an open reading frame. Hence, we describe experimental approaches for their identification by generating c
DNA
libraries derived from nmRNAs for which we coined the term
experimental RNomics
. Two different procedures are introduced for
cDNA
library construction. First, we describe the construction of a general purpose cDNA library from sized RNA fractions. Second, we introduce a more specialized RNomics strategy employing this approach to generate a cDNA library from a specific abundant class of nmRNAs. This is illustrated using as a paradigm the two families of small nucleolar RNAs that guide modification of nucleotides in rRNAs or spliceosomal RNAs small nuclear RNAs (snRNAs) by short antisense elements complementary to the modification site. Following the identification of novel members from the class of small nuclear RNAs by experimental RNomics, we demonstrate how their target sequences in rRNAs or snRNAs can be identified.