Dave Burt Genetics and Genomics Post Doc Le Yu's Data

This is an entry to archive the data created by the PostDoc, Le Yu, who worked at Roslin between 2012-2014.

Animals inhabiting seasonal environments need to adapt their physiology to survive in anticipation of climate change. To achieve this, sophisticated internal clockworks have evolved which drives annual cycles of behaviour, reproduction, metabolism and growth. Many of these processes take time and need to be activated over many weeks to months. In many animals, such seasonal rhythms are driven by deep-rooted internal clockwork, which drives cycles of physiology and behavior within the body over the course of the year. These “circannual” rhythms are synchronised to the external world by a brain hormone called Melatonin (MEL), produced at night from the pineal gland in the brain, the activity of which is regulated by the light-dark cycle. Accordingly, MEL targets are exposed to seasonal changes in duration of the MEL signal – long in winter and short in summer. It is this MEL signal which acts on hormone secreting circuits (neuroendocrine), which in turn drive annual reproductive and metabolic cycles.

Recent studies show that MEL acts on targets sites in a specific region at the base of the brain in the pituitary gland called the pars tuberalis (PT). This tissue acts as a seasonal conductor – controlling secretion of hormones such as prolactin (a hair growth regulator) in the main pituitary gland, and also remarkably within another part of the brain nearby called the hypothalamus, where it regulates the thyroid hormone concentrations. This latter circuit is believed to control seasonal reproduction and metabolic cycles. A key transcriptional regulator of gene expression is a gene within the PT called EYA3, which we discovered recently. Eya3 is rapidly activated by long-days in the PT and is probably part of the early switch mechanism leading to hypothalamic thyroid hormone changes. We have also discovered that many genes in the PT are regulated by a process called DNA methylation. Methylation is mechanism used in cells to suppress activity of particular genes and is essential to the function of normal cells. Our studies show that both de-methylation – removal of the suppressive imprint – and methylation – imposition of the imprint – are remarkably dynamic. So much so, that each night MEL induces changes affecting the methylated state of over 1000 genes. Such DNA modifications are termed epigenetic – the process of heritable changes in gene expression caused by mechanisms other than changes in the underlying DNA sequence. Other studies show that epigenetic regulation is crucial in diseases like cancer, but also underpins normal physiology including ageing and the differentiation of stem cells.

We propose to map all the methylated sites in the sheep genome (the “methylome”) in response to seasonal signals (the “seasonal-methylome”) simulated by changes in photoperiod using high-resolution bisulphite sequencing. This is important, as our current methylation screen was based on a low-resolution and less sensitive method that cannot identify specific methylated DNA nucleotides. In this new analysis, we will be able to define methylation changes that may affect the function of specific DNA signals, such as binding sites for specific transcriptional regulators. We will compare material collected from animals maintained on short or long photoperiods, using tissue from the PT and also the ventral hypothalamus (where thyroid hormone metabolism is controlled), and examine how gene methylation changes in different photoperiods. The pattern of methylation under different photoperiods will also be correlated with changes in the expression of genes as determined by whole genome RNA Sequencing (the “seasonal-transcriptome”). We will test the hypothesis that pre-exposure to specific photoperiods can affect an animal’s response to current changes in photoperiod. Finally, we will test the hypothesis that the “methylome” drives long-term seasonal rhythms, by studying how it changes in animals exposed to prolonged fixed photoperiods.

These studies will provide the first insight into epigenetic control of gene expression in brain structures that control seasonal reproduction and growth in a mammal. Finally, our studies may reveal general features of the biology of livestock domestication, since components of the PT circuit (thyroid hormone receptor) have already been identified as being under strong selection in comparative studies of chicken domestication. Our proposal may lead to new models for understanding mechanisms controlling reproduction and growth, which may be of commercial significance to the livestock industry in the UK and may reveal more about how animals can adapt to climate change through the interaction of external signals in the environment, such as changes in day length, and DNA modification sin their genomes.