Genomic Exploration of Transcriptional Regulation and Evolution in Vertebrates

All cellular processes depend on the coordinate expression of genes and their interactions. Regulatory sequences encoded in the genome stipulate the necessary instructions interpreted by sequence-specific transcription factors (TFs) to control the spatial-temporal output of gene expression. Detection of cis-regulatory signals is challenging, owing to the lack of distinguishing features such as open reading frames and an overwhelming excess of spurious to functional TF binding site matching sequences embedded within the vast non-coding regions of vertebrate genomes. From an evolutionary standpoint, functional alterations in cis-regulatory architecture are thought to be important in diversifying morphology and physiology in the evolution of vertebrates, which share a similar body plan and complement of genes. Correspondingly, recent studies have highlighted the plasticity of cis-regulatory architecture organization over evolutionary time, finding associations with examples of both diverged and conserved patterns of gene expression. These observations underscore the gap in our collective knowledge with respect to the rules by which TFs recognize and bind their targets in vivo, as well as how this process evolves in vertebrates, and serve as a motivating basis for this thesis work. To begin, I probed the extent of conservation and divergence of sequence and expression profiles across tissues of diverse vertebrate species, identifying thousands of candidate genes with conserved expression by microarray analysis. However, corresponding conservation of non-exonic and potentially regulatory sequence was lacking, suggestive of binding site turnover over evolutionary time. Next, I analyzed the sequence specificity of a wide array of mouse and yeast TFs, finding great diversity and complexity in their binding preferences, with many factors recognizing multiple distinct motifs. Furthermore, comparative analysis of orthologous TFs suggest well conserved binding specificities. I also demonstrate the likely biological relevance of sequences highly preferred by these TFs by revealing distinctive signatures in their distribution and organization within putative regulatory regions in each genome. Lastly, I have begun to explore the organization of cis-regulatory sequences active in vertebrate tissues by high-throughput sequencing of open chromatin. Together, these data help illuminate the organization and evolution of vertebrate regulatory architectures, providing a useful toolkit for the testing of new models and hypotheses.

Department dc:contributor.department

Molecular and Medical Genetics

Year dc:date.issued

2011

Author dc:creator

• Chan, Esther T. M.

Advisor dc:contributor.advisor

• Hughes, Timothy R.

• comparative genomics
• transcription regulation
• bioinformatics
• vertebrates
• evolution

Statement dc:rights

• Attribution-NonCommercial-NoDerivs 3.0 Unported

Licence dc:rights.uri

• http://creativecommons.org/licenses/by-nc-nd/3.0/

Language dc:language.iso

en_ca

Handle dc:identifier.uri

http://hdl.handle.net/1807/26503

OAI identifier oai:identifier

oai:utoronto.scholaris.ca:1807/26503