An open question in cancer research is how distinct programs of cellular behaviour are orchestrated, leading to complex properties such as invasion and escape from the immune system, abolishing contact inhibition, tolerating numerous genomic failures without initiating cell death, as well as providing defence against various combinations of chemotherapy. Contemporary models suggest non-coding RNAs (ncRNAs) to be main players in this process. ncRNAs have emerged as key transcriptional- and post-transcriptional regulators of protein-coding gene expression at many different levels. Members of iSEQ have worked intensively on ncRNAs, their general biogenesis pathways and functions as well as their specific roles in cancer. These expertises are now combined in iSEQ projects to generate further synergy.
While the importance of long intergenic nc (linc) RNAs and micro (mi) RNAs in differentiation and pathogenic processes by now is well established, the biological relevance of other less well-studied ncRNAs is elusive. These include RNAs emanating from upstream- and intra-genic regions of the human genome. Most of these transcripts are low-abundant; and not yet characterized in cancers e.g. the so-called transcription start site-associated (TSSa) RNAs and PROMoter uPstream Transcripts (PROMPTs). Another merging group of ncRNA is Natural Antisense Transcripts (NATs) that in several instances have been shown to regulate expression of protein coding genes. iSEQ groups have recently demonstrated that a NAT can circularize and be regulated via miRNA-dependent degradation.
Since circular RNAs are not detected by standard RNA cloning protocols the generality of such non-canonical structures remains an open question. iSEQ is therefore establishing a protocol for purifying circular RNA and making these amenable to deep sequencing in a number of projects.