Overlapped genes: mutual regulation of coding and noncoding genes biogenesis

Abstract

Gene expression process has been linked to numerous cis and trans elements. Nowadays, more precise and powerful bioinformatics coupled to the DNA/RNA sequencing methods revolution improves gene regulation understanding dramatically. Evidences of increasingly strong interaction between overlapped genes, according to genomic coordinates, has been published relating biogenesis, function, expression and conservation. The combination of such mechanisms are complex and need to be analysed in a broad and integrated manner, which demands bioinformatics analysis. Intron importance has also been reviewed, mostly concerning its role and classification as a simple bypass product. Up to date it is known that the majority of small nucleolar RNAs (snoRNAs) ~90% and miRNAs (miRNAs) ~60% are intragenic. lncRNAs are still subject of characterization studies and has not reached stable numbers for intragenic/intergenic proportions, although many important functions has been attributed to them and count with significant intragenic elements according to recent studies. In this project, we propose an analysis of long noncoding RNAs (lncRNAs) collocated with coding genes (mainly in introns). In a more detailed manner we propose to: i) systematically characterize the intragenic long noncoding RNAs; ii) to study a few evolutive features; iii) to study the expression and possible coexpression of these long noncoding RNAs and their host genes; iv) and to explore the occurrence of alternative splicing in gene regions containing these lncRNAs. The expression and alternative splicing analysis will also be done in a context of health versus tumoral tissues. Overall, we hope to give a considerable contribution for the wide features of this important group of noncoding RNAs at the end of this project. (AU)