Functional genomics and analysis of small RNA function
Complete genome sequencing projects are generating enormous amounts of data. Although progress has been rapid, a significant proportion of genes in any given genome are either unannotated or possess a poorly characterised function. Our group aims to predict and describe the functions of genes, proteins and regulatory RNAs as well as their interactions in living organisms. Regulatory RNAs have recently entered the limelight, as the roles of a number of novel classes of non-coding RNAs have been uncovered. Our work involves the development of algorithms, protocols and datasets for functional genomics. We focus on determining the functions of regulatory RNAs including microRNAs, piwiRNAs and long non-coding RNAs. We collaborate extensively with experimental laboratories on commissioning experiments and analysing experimental data. Some laboratory members take advantage of these close collaborations to gain hands-on experience in the wet lab.
Our long-term goal is to combine regulatory RNA target prediction, secondary effects and upstream regulation into complex regulatory networks. We will continue to build an accurate database of piRNA loci in animals and explore the importance and evolution of these molecules. We are extremely interested in the evolution of regulatory RNAs and developing phylogenetic techniques appropriate for short non-coding RNA. We will continue to build strong links with experimental laboratories that work on miRNAs in different systems, as this will allow us to build better datasets with which to train and validate our computational approaches. The use of visualisation techniques to assist with the interpretation and display of complex, multi-dimensional data will continue to be an important parallel aspect of our work.
Kraken: A set of tools for quality control and analysis of high-throughput sequence data.
Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Methods. 2013
Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis.
Di Giacomo M, Comazzetto S, Saini H, De Fazio S, Carrieri C, Morgan M, Vasiliauskaite L, Benes V, Enright AJ, O'Carroll D. Mol Cell. 2013
Guerra-Assunção, J.A. and Enright A.J. (2012) Large-scale analysis of microRNA evolution. BMC Genomics 13 (1), 218.
The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements.
De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D. Nature. 2011
Detecting microRNA binding and siRNA off-target effects from expression data.
van Dongen S, Abreu-Goodger C, Enright AJ. Nat Methods. 2008