ncRNAs ARE KEY REGULATORS IN TUMORIGENESIS – WHAT’S REGULATED IN ‘GENE REGULATION’?

Michael Rossbach

Biotech Développement Conseils, 182 Avenue Charles de Gaulle, 92200 Neuilly-sur-Seine, Paris, France

Abstract

As a basis for differential gene regulation, the selective recognition of regulatory DNA sequences is widely accepted. Most transcription factor binding sites, however, are short, degenerate and have a strong affinity for homologous proteins, even ones with antagonistic effects. A complex network of overlapping, bi-directional transcripts and a plethora of non-protein coding transcripts arising from the same locus characterize the mammalian transcriptome. Genome-wide transcription factor binding site (TFBS) studies show that key regulators such as nanog, sox2, oct4 or klf4 co-occupy many binding sites. Thus, the prediction of gene activities based on such data is rather poor. Both experimental and computational evidence suggest that many of the newly discovered transcripts and “processing products”, such as the non-coding small (ncRNA) interfering (siRNA) or microRNAs (miRNA), are functional. Likely, we underestimate the complexity of the regulatory circuitry by assuming a hierarchical structure of well-separated layers in transcriptional regulation. At least a large fraction of the non-coding transcripts themselves are functional, begging the question what is regulated in ‘gene regulation’.

Non-coding transcripts are far from being just transcriptional noise. Many of them show a differential expression in differentiation and disease, particularly in tumor progression; there is also sequence conservation and many of the highly conserved elements give rise to ncRNAs of heretofore unknown function. Transcriptional interference plays an important role when transcripts compete for transcription; for instance, anti-sense RNA can alter the expression of the sense mRNAs. Typical ncRNAs appear to be spliced, polyadenylated, exported just like regular mRNA and processed from longer precursors.

We will present our studies on the ncRNAome in tumorigenesis and present a model for micro-RNA replacement therapy in miR-7 deficient cancer cells, as well as our model, stem cells deficient for dicer (dcr-/-) and targeted with either dcr-1 or dcr-2 from Drosophila, giving insight into the pathways that underlie the si- and miRNA networks.