Small RNAs have diverse functions in eukaryotic gene regulation. They function through binding the target RNA to suppress translation and/or induce degradation. Since the target recognition is mediated by nucleotide complementarity, it is crucial to produce small RNAs of the right sequences. Here, we present the computational methods to analyse the sequence of small RNAs to examine their capacity to target host messenger RNAs and transposable elements. We also discuss how to study the biogenesis pathways of small RNAs.
Keywords: micro RNA, piwi-interacting RNA, transposable elements, fruit flies
Requirements: Laptop computer, UNIX, bash/R coding
Relevance: The workshop aims to cover the whole workflow of analyzing small RNAs by next generation sequencing. This includes library preparation, processing of raw-sequencing data, and the analysis of processed reads. Gained knowledge should be applied to handle any types of publicly available datasets as well as to generate and analyse your own sequencing libraries.
Group Leader – The Wen Group and ARC Future Fellow, The John Curtin School of Medical Research, Australian National University
Dr Jean Wen received her BEng in Electronic Engineering in Beijing, China, her MSc in Computer Science from Lakehead University, Canada, and her PhD in Computational Biology from The Australian National University (ANU). She was a postdoc at The Bioinformatics Center at Copenhagen University, Denmark under Professor Anders Krogh researching the development of machine learning and statistical modeling methods for miRNA-target regulation, and was a research fellow at Memorial Sloan-Kettering Cancer Center/Sloan-Kettering Institute, New York under Professor Eric Lai researching RNA-mediated post-transcriptional gene regulation, before returning to RSB, ANU to take up the ARC future fellowship. She has been involved in large international consortium collaborations: The modEncode Consortium, The 29 Mammalian Genome Project, and The Ant Genome Project.
Group Leader, The John Curtin School of Medical Research, Australian National University
Dr Rippei Hayashi is a group leader in Australian National University. Dr Hayashi studies the mechanism of transposon silencing using fruit flies Drosophila. During his postdoc trainings, Dr Hayashi uncovered the link between the embryonic body axis formation and the transposon defence pathway in Drosophila and identified the novel mechanism of producing piwi-interacting RNA in Drosophila germline. Dr Hayashi is interested in understanding how the selective silencing of transposons is ensured and the diversity of transposon silencing mechanisms across species.