Bioinformatic Studies of Gene Regulation Involving Sox9 and Hoxb3 with Reference to Craniofacial Development and Other Processes

This dissertation, "Bioinformatic Studies of Gene Regulation Involving SOX9 and HOXB3 With Reference to Craniofacial Development and Other Processes" by Chi-yan, Angel, Mak, 麥志昕, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled "Bioinformatic Studies of Gene Regulation Involving SOX9 and HOXB3 with Reference to Craniofacial Development and Other Processes" Submitted by Mak Chi Yan Angel for the degree of Master of Philosophy at The University of Hong Kong in August 2005 SOX9 and HOXB3 are two transcription factors which have important roles in development. HOXB3 belongs to the HOX family of genes which are important to specify the anterior-posterior body axis. SOX9 is important in various developmental processes including chondrogenesis, sex determination and craniofacial development. Discovering what genes are regulated by SOX9 and HOXB3 will help to understand the molecular events and pathways involved in these developmental processes. The aims of this project are to: (1) identify genes regulated by SOX9 (its target genes), (2) identify HOXB3 target genes and genes likely to be important in craniofacial development, and (3) develop a bioinformatic pipeline to make these identification processes more efficient. To achieve the above aims, analyses have been conducted on the data from two main experimental approaches - chromatin immunoprecipitation of SOX9 and microarray studies on transgenic mice ectopically expressing either Hoxb3 or Sox9. Chromatin immunoprecipitation (ChIP) assays of SOX9 identified potential regulatory regions that SOX9 bound. A bioinformatic pipeline was developed to automate the identification of target genes and the analyses on these DNA sequence data. Genes nearest to the genomic locations of the ChIP-derived DNA sequences have been identified as potential SOX9 target genes. They were then prioritized to be further analyzed for the presence of SOX9 binding sites and sequence conservation across genomes. Microarray data from two transgenic mice (YH26 and SL2) were analyzed to identify potential SOX9 and HOXB3 target genes. YH26 mice have ectopic expression of SOX9 in the gut. Genes that are differentially expressed between YH26 and control mice were identified as potential SOX9 target genes. SL2 mice showed craniofacial abnormalities and they ectopically express HOXB3 in rhombomere 4 and branchial arch 2, both of which are important structures in craniofacial development. Genes whose expression differs between SL2 and WT branchial arch 2 are potentially regulated by HOXB3. As many structures of the face and neck are derived from the branchial arches, genes which are expressed specifically in the branchial arches may be important for craniofacial development. Genes that are expressed at a higher level in the branchial arches compared to whole embryo have been identified. These genes are likely to have special roles in the functions of the branchial arches, and thus also in craniofacial development. In this project, a bioinformatic pipeline has been developed to facilitate the identification of target genes and regulatory regions by DNA sequence analyses. Potential SOX9 and HOXB3 target genes and genes that may be important in craniofacial development have also been identified. This advances our understanding of the molecular basis of craniofacial development and other processes that SOX9 and HOXB3 are involved in. DOI: 10.5353/th_b3746540 Subjects: Homeobox genes Transcription factors Face - Growth Skull - Growth