Forest Tree Epigenomics: Searching the Epigenetic Archive of Forest Trees for Traces of Historic Climate Change.

SUMMARY
DNA preserved in the wood of a tree represents an epigenetic “diary” often spanning centuries; with information on genes and pathways involved in the tree’s responses to environmental changes. Retrieving this information is valuable to the fundamental understanding of tree biology and to climate research, including mediating the effects of climate change on forests (Bräutigam K et al. Ecol Evol 2013). Using our unique collection of trunk bore cores of trees affected by an extreme climate event in 1816, the Year without Summer (Stothers RB. Science 1984; Mann et al. Nature Geosci 2012), the student will explore their epigenetic “diaries” by whole genome DNA methylation profiling and a careful search of the resulting data for traces of the 1816 event.

SPECIFIC AIMS
Individual plants cannot escape changes in their environment but have to adapt to them throughout their lifetime. In forest trees, these adaptations include changes to wood anatomy, most apparent as ring formation due to seasonal variation in growth conditions (Schoch W et al. 2004: www.woodanatomy.ch). Macroscopic features of growth rings have long been recognised as informative of past environmental conditions (Speer JH. Fundamentals of Tree Ring Research. Univ of Arizona Press 2010). Ultimately however, wood anatomy is an emergent property of events at the molecular level in wood-forming cells, including environmentally triggered alterations of their gene expression profile.

Epigenetic chromatin modifications including DNA methylation are central to gene expression regulation (Jaenisch R & Bird A. Nat Genet 2003). DNA methylation is sufficiently biochemically stable for characteristic, locus-specific methylation patterns to be recoverable with high fidelity even from ancient DNA (Llamas et al. PLoS ONE 2012). The wood of forest trees is a viable source of DNA (e.g., Liepelt et al. Annals Botany 2006). Wood being a terminal tissue, the methylation profile of its DNA represents epigenetic history: the epigenetic states of wood-forming cells that were alive and responding to the environment during a particular period in the life of the tree.

The student will generate genomewide DNA methylation profiles at single base resolution for dendrochronologically dated wood samples of living veteran forest trees that cover the period from <1750AD to the present (Meaburn E & Schulz R. Sem Cell Dev Biol 2012). From these and supplementary data they will generate novel, widely applicable genomics resources for key forest tree species (oak; Quercus). Using these resources, they will test the hypothesis that past adaptive responses of the trees in the study to the historic instance of extreme climate change in 1816 are reflected in corresponding DNA methylation changes over time at specific and functionally relevant genomic loci. Such loci inform on the molecular coping mechanisms that forest trees employ in response to climate change and thus, can inform efforts to better reconstruct, predict and mediate the impact of climate change.

CANDIDATE PROFILE
In their application cover letter and CV, candidates are asked to include and highlight their skills, experience and/or knowledge relevant to this project; in particular:
- sample preparation and DNA extraction
- next generation sequencing (NGS) library preparation
- NGS data analysis
- applied statistics (in genomics)
- computing (programming, high performance computing, Linux)
Candidates with relevant skills and experience will be preferred. However, the student will have opportunities for formal and informal training to obtain necessary skills. Throughout their studies, they will be supported by a thesis committee composed of five academics with relevant scientific backgrounds. They will work in the Bioinformatics and Epigenomics group of Dr Reiner Schulz (http://atlas.genetics.kcl.ac.uk/~rschulz), alongside peers, postdocs and PIs in a state-of-the-art and collaborative work environment where the exchange of ideas, knowledge and skills is everyday practice.

START DATE: 4 January 2016 (negotiable)

HOW TO APPLY: Email me a cover letter and CV (including the contact details of at least two referees) that demonstrate why you are interested in and qualified to undertake this PhD project. I thank all applicants for their interest; however, only those selected for interviews will be contacted.