Improving miRNA target prediction in animals

Lead Research Organisation: University of East Anglia
Department Name: Biological Sciences

Abstract

Gene expression is a complex process and can be regulated at several levels. One of the most recently discovered regulatory layers, called RNA silencing, involves microRNAs (miRNAs) a class of small noncoding RNA of around 22 nucleotides in length. MiRNAs interact with messenger RNAs (mRNAs) by binding to complementary regions called target sites. This interaction, which can be predicted by computer algorithms, typically leads to translational repression and/or mRNA degradation in animals, thus repressing gene expression post-transcriptionally. MiRNAs are important regulators playing key roles in development, and misregulation of these tiny molecules can cause many diseases such as neurodegeneration and cancer in humans.

Since the advent of next-generation sequencing thousands of miRNA sequences have been identified in plants, animals and viruses. However determining the targets (and therefore function) of these molecules is still a major challenge in the field as currently purely computational prediction methods are prone to false positive predictions.

This project aims to use a combined computational and experimental approach to better understand and improve miRNA target prediction in animals. The student will develop and apply novel bioinformatics techniques to further our knowledge of miRNA targeting and improve the accuracy of computational target prediction by integrating multiple sequencing data types (e.g. RNA-Seq & small RNA-Seq) from individual tissues under the supervision of Dr. Simon Moxon at The Genome Analysis Centre (TGAC). They will then go on to experimentally validate the predicted targets with Prof. Tamas Dalmay at the University of East Anglia.

Publications

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Bradley T (2017) An Assessment of the Next Generation of Animal miRNA Target Prediction Algorithms. in Methods in molecular biology (Clifton, N.J.)

Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011216/1 01/10/2015 30/09/2023
1653558 Studentship BB/M011216/1 01/10/2015 30/09/2019 Thomas Bradley
 
Description PubHD (Norwich) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact I was the first person to present at a Norwich 'PubHD' event in which early career researchers give a brief summary of their intended PhD research to a lay audience, at a neutral public house venue, in which the general public are welcome to attend for a small fee. The intended purpose of the visit was to increase awareness of the research conducted at the Earlham Institute amongst the general public. Audience members were impressed by the talks given by myself and other participants, as judged by enthusiastic questions and responses after the talks.
Year(s) Of Engagement Activity 2016
URL https://pubhd.wordpress.com/2016/01/28/pubhd-norwich-pints-and-phds/
 
Description Visit by College of West Anglia 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The Earlham Institute had a visit from local sixth form students from the college of West Anglia. As I understand, the student were in the point of their education were they still unsure about how to proceed with their education. I gave a brief talk about my own education, career progression, and my own thoughts about pursuing a career in computational biology. I also participated in an extensive Q&A sessions after the talks by myself and my colleagues, in which we were free to answer the queries of the young students. The purpose of the visit was to expose the students to a modern, forward-looking, scientific institute, and to demonstrate that these institutes are more accessible and inclusive than they otherwise might think. The students responded positively to the talk, and were eager to ask questions about progression into a research career.
Year(s) Of Engagement Activity 2016