Computational prediction and experimental verification of gene regulatory elements in neuronal development

• Main Author: Doh, Sung Tae
• Format: Dissertation
• Language: English
• Subjects: biology, molecular; engineering, biomedical; health sciences, human development
• ISBN: 1124419403; 9781124419404

Completion of the human genome sequence along with other species allows for greater understanding of the biochemical mechanisms and processes that govern healthy as well as diseased states. Non-coding regions have been shown to play a critical role as gene regulatory elements. Enhancers that regulate transcription processes have been found in intergenic regions. Many regulatory elements found in non-coding regions are highly conserved across different species. While current sequence based computational methods are continuously improving in accuracy and scope, determining the time and tissue specific function of gene regulatory elements remain largely elusive.
The goal of this dissertation is to identify novel gene regulatory elements involved in neuronal development using a combined approach which utilizes both computational prediction and experimental verification. We describe a method for utilizing genomes, annotations, computational tools, expression data, and molecular genetics methods to predict gene regulatory elements and confirm the function of these elements. In particular, the non-coding regions of homologous and functionally related genes are analyzed to identify highly conserved regions predicted to have gene regulatory function. To facilitate in the acquisition of desired sequences, a web tool was created to retrieve non-coding sequences based on annotations. Using multiple pair-wise alignments of non-coding sequence, over 502 conserved regions have been identified, at least 3 of which are well characterized, known enhancer elements. Previous studies utilized transgenic animals to experimental confirm the function of conserved regions. These animals are time consuming and expensive to generate. In contrast this study uses in ovo and in vivo electroporation of a plasmid DNA reporter construct for the confirmation of function. By transfecting the plasmid DNA reporter constructs into an animal model, enhancer function can be confirmed by the expression pattern of the reporter gene. Ten novel enhancers have been experimentally verified of which 2 have been characterized for the purpose of this study. Identification of novel gene regulatory elements allows for a better understanding of the mechanisms of gene regulation which may lead to the eventual control of gene expression. This has important implications and applications ranging from directing stem cell differentiation to designing new sequence based therapeutics.