Abstract

Targeting Regulatory Antisense RNAs for Locus-Specific Gene Upregulation

Roya Pedram Fatemi, Staff Scientist, Faghihi Lab, University of Miami

Collective efforts of the large-scale transcriptomics projects, such as ENCODE and FANTOM indicate that human genome is pervasively transcribed in a cell-type and developmental-specific manner and that the majority of transcription is non-protein coding. Many noncoding RNAs have been shown to play important functional roles in regulating the expression of protein coding genes. Furthermore, it has been shown that some noncoding RNAs help confer specificity to ubiquitously expressed epigenetic enzymes by serving as guides to position them to genomic loci. Our published data shows that silencing or blocking of regulatory natural antisense transcripts (NATs) by single-stranded oligonucleotides or siRNAs can transiently and reversibly upregulate locus-specific gene expression. We showed that Brain-derived neurotrophic factor (BDNF) is repressed by a noncoding antisense RNA transcript, BDNF-AS. Inhibition of this transcript upregulates BDNF mRNA, and protein, alters chromatin marks at the BDNF locus, and induces neuronal outgrowth and differentiation. More recently, we have developed a novel pharmacological assay to characterize the interaction between antisense RNAs and their epigenetic targets using Amplified Luminescent Proximity Homogeneous Assay. Utilizing this technology, we characterized interaction between BDNF-AS transcript and the effector enzyme. We believe this technology can serve to achieve locus-specific up-regulation of BDNF gene, which holds great therapeutic promises.