Critical association of ncRNA with introns

Abstract

It has been widely acknowledged that non-coding RNAs are master-regulators of genomic functions. However, the significance of the presence of ncRNA within introns has not received proper attention. ncRNA within introns are commonly produced through the post-splicing process and are specific signals of gene transcription events, impacting many other genes and modulating their expression. This study, along with the following discussion, details the association of thousands of ncRNAs--snoRNA, miRNA, siRNA, piRNA and long ncRNA--within human introns. We propose that such an association between human introns and ncRNAs has a pronounced synergistic effect with important implications for fine-tuning gene expression patterns across the entire genome.

Figure 1.

Distribution of piRNA along mRNA and introns. (A) piRNA location along each mRNA was determined by dividing mRNA into five equal segments. The total number of piRNAs within each quintile was determined. (B) The location of piRNA along introns was determined by dividing each intron into quintiles and calculated as in (A). Vertical bars show the standard error of the means.

Figure 2.

Evolutionarily conserved regions within the third intron of the Heparanase 2 (HPSE2) gene. The intron–exon structure of HPSE2 is shown at the top, with vertical lines depicting exons. In the bottom diagram, the cylinders depict 13 highly conserved regions with the coordinates specified below.