Romero, PedroK., S.Perumal, Narayanan B.Dunker, Keith2011-10-192011-10-192011-10-19https://hdl.handle.net/1805/2681http://dx.doi.org/10.7912/C2/905Indiana University-Purdue University Indianapolis (IUPUI)There are many mechanisms for the creation of new genes. In this study, the newborn genes i.e. de novo genes are the genes that are created from scratch. These are created by two mechanisms, polymerization (de novo genes produced from non-coding regions) and overprinting (de novo genes produced from overlapping frames). Rancurel et al has found that de novo genes in overlapping coding regions tend to be more disordered than their ancestral counterparts. It was suggested that it is natural for the newborn genes to be disordered, as it must be very difficult for newborn genes to obtain order at such an early stage, so that the structure is only developed after the evolutionary development. The two hypotheses tested in this study state (1) that genes generated de novo will have a tendency to be disordered, and (2) this tendency is due to a natural inclination of these genes to be disordered at birth. The origin and evolution of some de novo coding regions have been studied in detail. We analyzed genes reported in literature that have been produced de novo; either by overprinting or by polymerization, and their tendency for disorder was evaluated using the VSL2 disorder predictor. The de novo coding regions produced by both ways indeed shows a tendency towards disorder, which supports hypothesis 1. For hypothesis 2 to be tested on a larger dataset the exonic and intronic materials of two human chromosomes were studied and the tendency for disorder was assessed for any new peptide sequence arising from the translation of non-coding sequences arising from introns and exons (overlapping frames). It was shown that the tendency of disorder for protein products of newborn genes arising from introns were not inclined towards being ordered or disordered, but they can become disordered by evolution. The new exonic material created from the existing exons tends to be more disordered when translated, and this tendency does not seem to be dependent upon the disorder content of the original exons. This difference could be a consequence of the fact that the overlapping frames of coding sequences have indirectly been subjected to evolutionary pressure along with the original exon, whereas intronic sequences do not seem to have this constraint, but the exact nature of this discrepancy needs further study to be explained. The tendency of disorder in the existing new exons seems to be higher than the artificial exons (generated in this study). We conclude that the intrinsic disorder in the protein products of de novo genes is selected by the evolution rather than an initial condition. Thus, the newborn genes were not born disordered.en-USnewborn geneGenetic engineeringGenetic codeNucleotide sequenceThesis