My undergraduate degree was in bioinformatics at the University of Birmingham. This is where I learned to write C and java programs; how to write Perl, PHP and shell scripts and use R. Programming was my favourite part of my time at Birmingham and I was keen to continue developing these skills in postgraduate study.

 

I have completed two project towards my MSc: one lab-based and one computational. Both were 12 weeks long and applied systems biology techniques.

Bioimaging of the early stages of chloroplast import

Supervisor: Professor Colin Robinson

In my lab-based project, I identified key features of the translocation signal by replacing specific amino acids in the amino terminal peptide. Using fluorescence confocal microscopy, I was able to detect the accumulation of GFP within or excluded from the chloroplast, depending on whether the terminal peptide was functional or had been modified.

Identifying conserved non-coding regions in Basidiomycetes

Supervisor: Dr. Laura Baxter

For my computational project, I wrote a component of a genome-wide analysis framework in Perl. The script that I wrote analysed sliding windows with a homology score and grouped them into regions of similarity between multiple genomes, while accounting for the evolutionary distance between genomes. The analysis framework was subsequently published in Plant Cell:

L. Baxter, A. Jironkin, R. Hickman, J. Moore, C. Barrington, P. Krusche, N. P. Dyer, V. Buchanan- Wollaston, A. Tiskin, J. Beynon, K. Denby, and S. Ott. Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. The Plant Cell Online, 24(10):3949–3965, 2012

Supervisors: Dr. Jose Gutierrez-Marcos (Life Sciences) and Dr. Sara Kalvala (Computer Science)

A poster describing some of the results from the early stages of my PhD can be viewed here. The poster was presented at symposia to inter-disciplinary audiences and was awarded prizes.

Epigenetic Responses to Environmental Stress in Plants

Environmental signals can directly influence gene expression through epigenetic mechanisms, causing phenotypic changes that can be transmitted to progeny. In plants, this is in part achieved by short interfering RNA (siRNA) which guide covalent modification of DNA, such as cytosine methylation, to specific targets including repetitive sequences and transposable elements. Environmental stress also leads to genome-wide DNA hypomethylation, misregulation of transposable elements and ultimately ‘genomic shock’.

Although most stress-induced epigenetic modifications are not thought to be heritable, there is increasing evidence for the inheritance of novel environmentally-induced epigenetic states or ‘environmental epialleles’. The formation of environmental epialleles represents an important source of variation and a powerful driving force of adaptive evolution but the precise mechanism remains unclear.

The aim of this thesis is to identify environmental epialleles through computational methods. Analysis of Illumina sequencing data from environmentally stressed maize plants sampled during stress and after a recovery period has so far revealed that a significant proportion of the maize genome is misregulated at both the genetic and epigenetic level. These findings indicate that plants continue to respond after exposure to stress and that this response is likely mediated by at least one epigenetic mechanism, including siRNA-directed DNA modifications.

My PhD project was computationally-based and involved analysis of three types of genome-wide Illumina dataset:

• Gene expression using the Digital Gene Expression protocol
• small RNA using RNA-seq
• DNA methylation using bisulphite converted DNA and DNA-seq

Working with lab-based colleagues, my role was to analyse the Illumina data to identify stress-induced changes to gene expresion and the epigenome. I used Perl and MySQL to prepare and store the data for analysis in R using published Bioconductor packages.

My results suggested interaction between the small RNA and DNA methylation datasets, confirming that small RNA could direct this epigenetic modification and identifying that transposable elements were important epigenetic targets. The proximity of stress-induced epigenetic change to stress-induced genes indicated a possible influence on gene regulation by epigenetically targeted regions.

c dot p dot j dot barrington at warwick dot ac dot uk