Characterising the function and evolution of transcription factor binding sites in Drosophila enhancers - WCUB, ENWW

增强子基本上被定义为促进基因转录的顺式调节元件。由于它们在转录中的关键作用，我们对这些元件进行分析以更好地理解基因调控背后的机制是很重要的。此外，人们认为这些增强子序列的变化是形态进化的主要机制之一;这些变化通常是点突变和插入/缺失，最终导致转录因子结合位点的完全转换。因此，我们不仅必须表征这些增强子元件，以提供有关基因调控的信息，而且还有助于我们理解顺式调控进化。许多增强子研究都集中在它们重现受调控基因表达的能力上，然而这种方法有局限性，现在有了新技术，如开放染色质测序（ATAC-seq）和靶向基因组编辑（CRISPR/Cas9），我们可以联合收割机多种方法来鉴定、鉴定和研究这些增强子元件的进化。该项目旨在利用这些技术来识别并完全鉴定果蝇腿中Hox基因Ubx的新增强子。该项目还将通过CRISPR分析和数学建模研究果蝇gap基因hunchback增强子的进化，旨在更好地了解顺式调控进化背后的机制。BBSRC优先领域生物科学的系统方法本项目将把数据收集活动与计算/数学建模活动结合起来，以更好地了解生物系统（或子系统）。这将涉及生物信息学数据和体内转录研究的整合，以产生一个转录模型来推断祖先增强子序列。数据驱动生物学这个项目将使用生物信息学工具和计算方法来帮助发现新的增强子元件，然后在体内进行功能验证。生物信息学和计算工具也将用于推断增强子进化的信息。

Enhancers are basically defined as cis-regulatory elements that facilitate the transcription of genes. Due to their crucial role in transcription it is important that we characterise these elements to provide a better understanding of the mechanisms behind gene regulation. Additionally, it is thought that changes in these enhancer sequences are one of the main mechanisms underlying morphological evolution; these changes are usually point mutations and insertion/deletions, which can ultimately lead to complete turnover of transcription factor binding sites. Not only is it therefore imperative that we characterize these enhancer elements to provide information about gene regulation but also to aid our understanding of cis-regulatory evolution. Many enhancer studies have focussed on their ability to recapitulate the expression of the gene under regulation, however this approach has limitations and now with new technologies such as open chromatin sequencing (ATAC-seq) and targeted genome editing (CRISPR/Cas9) we can combine multiple methods to identify, characterise and study the evolution of these enhancer elements. This project will aim to exploit these techniques to identify and fully characterise a novel enhancer of the Hox gene Ubx in the legs of the fruit fly, Drosophila melanogaster. This project will also investigate the evolution of an enhancer of the Drosophila gap gene hunchback through CRISPR analysis and mathematical modelling with an aim to better understand the mechanisms behind cis-regulatory evolution. BBSRC Priority AreasSystems approaches to the biosciencesThis project will integrate data collection activities with computational/ mathematical modelling activities to produce a better understanding of biological systems (or sub-systems). This will involve the integration of bioinformatics data and in vivo transcriptional studies to produce a transcriptional model to infer an ancestral enhancer sequence.Data driven biologyThis project will use bioinformatics tools and computational approaches to aid in the discovery of novel enhancer elements, which will then be functionally verified in vivo. Bioinformatic and computational tools will also be used infer information on enhancer evolution.