Abstract

In this presentation, I will describe results from our analyses of the intergenic and intronic regions of several genomes. Working with the human genome, we identified large numbers of statistically significant, distinct, variable-length motifs in its intergenic and intronic regions with intact copies that total in the millions. A subset of more than one hundred thousand of these conserved motifs, which we termed ‘pyknons’ have several hundred thousand instances in the untranslated and coding regions of more than 90% of all known human genes, in addition to their numerous human intergenic and intronic copies. Additional analysis showed that pyknons are enriched in a statistically significant manner in genes involved in specific processes, e.g. cell communication, transcription, regulation of transcription, signaling, transport, etc. Cross-genome comparisons revealed that many human pyknons have instances in the 3’UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. We also obtained analogous results from our analyses of a number of other genomes. In fact, we found that pyknon collections exist in vertebrates and invertebrates, and that they exhibit similar properties. A notable observation is that pyknon collections from different genomes have generally little overlap suggesting that these motifs are organism-specific. I will also discuss recent experimental evidence from several genomes that provides support to the hypothesis that pyknons indeed correspond to active molecules with regulatory role and that they are linked with RNAi. The sheer number of pyknons in a given organism suggests the existence of a very broad, endogenous layer of organization and cellular process regulation that remains largely uncharacterized.