Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression

Model 1 is based on the difference between conservation between ncRNA-containing introns and the total intron population when comparing Caenorhabditis elegans to Caenorhabditis briggsae. Basically, the introns shorter than 130 bp are taken to represent non-ncRNA introns, and the fraction of ncRNA-containing introns in the total intron population is inferred by linear regression analysis. Correcting for the fraction of intergenic ncRNA loci yields the estimated number of ncRNAs. Model 2 is based on the occurrence of upstream motif 1 (UM1) in the C. elegans genome, corrected for one highly repetitive sequence, and adjusted for nonmotif loci. Model 3 is a statistical calculation based on the correlation between the frequency of identical clones in the ncRNA library, and the concentration (expression level) of the corresponding ncRNA as estimated from Northern blots. (All three models are explained in detail in the Supplemental material.)