Genetic, Genomic and Molecular Studies of the Drosophila Genome

Lead Research Organisation: University of Cambridge
Department Name: Genetics

Abstract

The success of projects aimed at determining the sequence of the Genomes of several organisms have given biologists a huge amount of data to explore. Now the key challenge is how to utilise and apply this information to improving human health. The task is daunting; the human genome contains over 3 billion letters of code and, at present, we know the function of only a tiny fraction of this. For many years biologist have used simpler organisms to study biological processes in the belief that they represent heuristically useful model systems for understanding human biology. In the case of the fruit fly, Drosophila melanogaster, this belief has been vindicated time and again over the last few decades, and, with the comparison of the human and fly genomes, looks likely to continue to provide fruitful information. The challenge facing us is understanding where all the genes in a genome are, what their structure is, how they are controlled and most importantly, what their function is. To address these questions biologists must move from experimental strategies that examine one or a few genes at a time to large scale approaches that deal will all the genes or the whole genome simultaneously; this new approach is known as genomics. This paradigm shift in biology requires the development of technologies and methodologies that can extract reliable data from genomics studies, most importantly informatics and computing tools. Our research is aimed at applying focused genomics approaches to understanding basic biological questions; how is a defined region of the genome organised, where are the genes, how are they controlled and what do they do? How are conserved early events in the developing nervous system controlled by a set of regulatory genes? How do a conserved group of regulatory proteins function to control the activation and repression of sets genes? By focusing our research on well-defined biological problems that are conserved between fly and man we hope to provide a deeper understanding of how the genome is decoded and how errors or breakdowns in that decoding lead to illness and disease. Our research is communicated to the public via a number of routes including participation in National Science Week, presentations and talks to schools as well as public events such as the British Association Festival of Science.

Technical Summary

The application proposes using the fruit fly, D. melanogaster, to explore conserved aspects of genome structure and function. We will use state-of-the-art genomics technologies combined with sophisticated genetics techniques in a highly focused way to study how genome sequence is translated into function. Our proposal focuses on the Adh region, a 3Mb portion of the fly genome that we have studied extensively over the past 20 years. We will determine the complete transcriptional output of the region by DNA microarray analysis using cDNA, oligonucleotide and genome tile arrays and map the location of transcription factor binding sites using chromatin immunopurification studies. Novel transcribed regions and predicted genes with no known function will be mutated by a combination of genetic techniques, including targeted knockout and the generation of custom deletions. In addition, we will explore the relationship between genome sequence and chromatin structure by a series of experiments aimed at identifying the molecular basis behind polytene chromosome banding patterns using a combination of molecular genetic and genomics techniques. We will explore the function of a set of conserved transcriptional regulators, the Sox family of transcription factors, at the molecular and whole genome level via targeted chromatin immunopurification, transcriptional profiling with DNA microarrays, proteomics and genetic analysis. We will focus on conserved aspects of Sox function in the developing CNS to understand how Sox proteins control aspects of CNS development and with what factors they interact with to regulate gene expression. Conservation between mammalian and fly Sox proteins will, be examined by a set of in vivo functional rescue assays we have developed. Underpinning these analyses we will employ a range of sophisticated bioinformatics tools. We will use the sequences of other drosophilids as well as that of the mosquito to examine conserved aspects of genome structure, identifying conserved regulatory motifs as well as exploring the relationship between genome organisation and speciation. Over the tenure of the current programme we have invested considerable effort to develop and establish key technologies, including genomics, microarray, proteomics and informatics, and we are well placed to capitalise on the application of these genomics technologies to explore conserved biological processes. As with our previous programmes, we will continue to collaborate, both nationally and internationally, in focused areas that will include the development of genomics technologies and advanced genetics methods.
 
Description BBSRC Project
Amount £650,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2008 
End 04/2011
 
Description BBSRC Project Grant (Sox gene function in Drosophila testis development)
Amount £453,140 (GBP)
Funding ID BB/E015492/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2007 
End 02/2010
 
Description WT Project
Amount £236,147 (GBP)
Organisation Society for Endocrinology 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2010 
End 03/2013
 
Description modENCODE
Amount £150,000 (GBP)
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 03/2007 
End 03/2011
 
Title INDAC array probes 
Description Set of Microarray Probes designed against drosophila transcriptome 
Type Of Material Technology assay or reagent 
Year Produced 2008 
Provided To Others? Yes  
Impact Several publications using FlyChip INDAC arrays 
 
Title New Drosophila stocks 
Description New Drosophila stocks deposited in US Stock Center. 
Type Of Material Database/Collection of Data/Biological Samples 
Year Produced 2006 
Provided To Others? Yes  
Impact Widespread use of DrosDel reagents by international fly community. 
 
Description Fly Insulators 
Organisation University of Cambridge
Department Department of Physiology, Development and Neuroscience
Country United Kingdom 
Sector Academic/University 
PI Contribution ChIP-array and computational expertise
Impact in progress
Start Year 2010
 
Description FlyProt 
Organisation University of Cambridge
Department Gurdon Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Development of protein trap screening strategy Generation of protein trap fly lines MApping lines to fly genome stock maintenance and distribution Development of we interface
Collaborator Contribution Expertise in proteomics/mass spectrometry
Impact Several hundred fly stocks Papers Database
 
Description Notch 
Organisation University of Cambridge
Department Department of Physiology, Development and Neuroscience
Country United Kingdom 
Sector Academic/University 
PI Contribution Microarray analysis of response to Notch signalling Genome wide ChIP-on-chip analysis of su(h) and PolII binding
Collaborator Contribution Expertise in the analysis of signalling pathways
Impact Work in progress
Start Year 2008
 
Description School 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Primary Audience Schools
Results and Impact 30 primary school children learning about drosophila research

none
Year(s) Of Engagement Activity 2006,2007