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MicroRNA genomics: evolution, expression and function


   Faculty of Biology, Medicine and Health


About the Project

MicroRNAs are 22 nt single-stranded RNA molecules that modulate gene function primarily through translational repression. There are thousands of microRNA genes in mammalian genomes, and hundreds in invertebrate genomes. Nearly all novel microRNAs are discovered by deep sequencing approaches. The Griffiths-Jones lab runs the miRBase database, which acts as the public repository for published microRNA sequences and annotation. There are thousands of publicly-available RNAseq datasets that describe the expression of microRNAs in animal cells and tissues, and during developmental time-course experiments. This project will aim to use these data to understand the expression and conservation of animal microRNA genes, and to analyse the quality of microRNA gene annotations in available animal genome sequences. These data will allow us to ask questions such as:

 1. Which sets of microRNAs are highly conserved in different clades?

2. Do clade-specific microRNAs display characteristic expression patterns during development?

3. What are the predicted functions of microRNAs that display particular patterns of conservation and expression?

The project will involve genome-scale data analysis, and computational approaches to understand microRNA conservation, expression and function. There will be an opportunity to design and carry out genetic experiments to validate predictions and findings in model organisms including Drosophila melanogaster. The results of large-scale data analyses will be used to improve the functionality of the miRBase database.

1.     Candidates are expected to hold (or be about to obtain) a minimum upper second class honours degree (or equivalent) in a biological or computational science.  Candidates with experience or specific interest in analysing large-scale biological datasets are encouraged to apply. 

2.     For information on how to apply for this project, please visit the Faculty of Biology, Medicine and Health Doctoral Academy website (https://www.bmh.manchester.ac.uk/study/research/apply/). Informal enquiries may be made directly to the primary supervisor. On the online application form select the PhD title.

3.     For international students, we also offer a unique 4 year PhD programme that gives you the opportunity to undertake an accredited Teaching Certificate whilst carrying out an independent research project across a range of biological, medical and health sciences. For more information please visit www.internationalphd.manchester.ac.uk


Funding Notes

Applications are invited from self-funded students. This project has a Band 1 fee. Details of our different fee bands can be found on our website View Website
Equality, diversity and inclusion is fundamental to the success of The University of Manchester, and is at the heart of all of our activities. The full Equality, diversity and inclusion statement can be found on the website View Website

References

Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, Griffiths-Jones S, Toffano-Nioche C, Gautheret D, Weinberg Z et al. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res (2021) 49: D192-D200.
RNAcentral Consortium. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res (2021) 49: D212-D220.
Minchington TG, Griffiths-Jones S, Papalopulu N. Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. Sci Rep (2020) 10: 12960.
Kozomara A, Birgaoanu M, Griffiths-Jones S. miRBase: from microRNA sequences to function. Nucleic Acids Res (2019) 47: D155-D162.
Ninova M, Ronshaugen M, Griffiths-Jones S. MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum. Genome Res (2016) 26: 85-96.

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