Conserved signals of non coding RNA across 73 genes associated with Autistic Spectrum Disorders

by Rais, Theodor Bernard

The Autistic Spectrum Disorders (ASD), are known for their heterogenic clinical presentation. Linkage studies have pointed toward very diverse areas of the genome and of the brain related to ASD. We hypothesized that small non-coding RNA (ncRNA), like miRNA, siRNA or orphan snoRNAs, could be involved in the pathogenesis of ASD. The complex regulatory roles of miRNA’s have been implicated in diseases like Tourette’s syndrome and Fragile X syndrome. Since ncRNAs have been found abundantly in introns, we set out to find evolutionarily conserved areas in the introns of ASD associated genes, which may play a causal role in some clinical phenotypic forms of ASD. A group of 73 genes associated with ASD were selected. A control group of 75 genes, which were predominantly expressed in non-brain tissues was selected. We procured in this fashion an ASD set, which contained 540 introns and a non-brain set, which consisted of 522 introns. Using the protein sequences of these two sets of genes, their orthologs in dog, mouse and rat were obtained. We then developed a PERL program to investigate the degree of conservation among the different species’ orthologous intronic sequences aligned by ClustalW. A threshold of 50% was set to qualify a segment of sequence as conserved, and a minimum of 50 nucleotides was used as the window size. Several filters excluded the possibility of the conserved sequence being a part of alternatively spliced exons. For each intron in the two sets of genes we quantified the total number and length of conserved segments, and used them to compare the two groups. The results showed that the average number of conserved segments per intron in autism specific genes was 3.9, while it was 1.4 in the genes minimally expressed in the brain. A non-parametric statistical test (Mann-Whitney) showed a significant difference in degree of conservation between the two groups. Application of RNA Vienna package for prediction of RNA secondary structures demonstrated that many conserved segment sequences have stable RNA structures and show cross-species evolutionary conservation. Our findings could help to shed light on possible etiologies of development and genetic susceptibility of ASD.