A computational pipeline to catalogue and annotate transcription factors in metazoa

Abstract

Transcription factors are DNA-binding proteins that regulate gene expression. They do this by binding to cis-regulatory elements in the genome, from where they can recruit the molecular machinery required for gene expression. As such, they play crucial roles in many developmental and regulatory pathways. In Chapter 2 we create a computational tool to catalogue and annotate transcription factors from any eukaryotic species. This computational tool was named CREPE, or the Cis- Regulatory Element-binding Protein Elucidator. CREPE was validated using curated human transcription factor datasets. Overall, by using CREPE we can retrieve nearly all of the human transcription factors. In Chapter 3, we decided to apply CREPE to Lepidopteran (e.g. butterflies and moths) species. We chose this taxonomic group due to the broad range of interest seen in the scientific community (e.g. ecology and evolution), as well as a catalogue of transcription factors not available. We validate CREPE for use in Insecta by applying it to the fruit fly and comparing the results to curated transcription factor references. Next, we applied CREPE to high-quality Lepidopteran assemblies. Finally, we examined transcription factor conservation across Lepidoptera and highlight their patterns of evolution. In Chapter 4, we focus on the nuclear receptor transcription factor family in Lepidoptera. The nuclear receptor family is very important to insect development (e.g. molting). We annotated the Lepidopteran nuclear receptors, then survey their expression in selected tissue/timepoints of the butterfly <em>Bicyclys anynana</em>. This work provides a framework on how to catalogue and annotate transcription factors, and how to examine their evolution.