Epigenetic control of seasonal timing

栖息在季节性环境中的动物需要适应它们的生理机能，以适应环境的变化。为了实现这一点，复杂的内部时钟已经进化出来，驱动着每年的行为和生理周期。这些可以在恒定的条件下自由运行（“昼夜”节律），并通过大脑激素褪黑激素（MEL）与环境同步，褪黑激素在夜间由松果体产生，其活动受光暗周期的调节。因此，MEL目标暴露于MEL信号持续时间的季节性变化-冬季长而夏季短。MEL信号作用于激素分泌回路（神经内分泌），进而驱动每年的生殖和代谢周期。MEL作用于脑垂体中称为结节部（PT）的大脑底部特定区域中的靶位点，该区域充当季节性导体-控制激素分泌，如催乳素（一种毛发生长调节剂）在主脑下垂体中，也在下丘脑的另一个紧邻的大脑结构中，在那里它调节甲状腺激素水平，控制季节性繁殖和新陈代谢周期。我们在PT中发现了一个调节长光周期（LP）反应的关键基因，称为EYA 3，它被LP快速激活，并作为驱动下丘脑甲状腺激素变化的开关机制。我们还发现PT中的许多基因受到称为DNA甲基化的过程的调控。甲基化抑制基因的活性，对正常细胞的功能至关重要。我们的研究表明，去甲基化（去除抑制性印记）和甲基化（施加印记）都是非常动态的。如此之多，以至于每天晚上MEL都会诱导影响1000多个基因甲基化状态的变化。这种DNA修饰被称为表观遗传-可遗传的变化，其由基础DNA序列变化以外的机制引起，并且在许多疾病中至关重要，但也支持正常生理学，包括干细胞的老化和分化。我们的目标是映射绵羊基因组中的所有甲基化位点（“甲基化组”），以响应季节性信号（“季节性甲基化组”），模拟光周期的变化，使用高分辨率亚硫酸氢盐测序。这一点很重要，因为我们目前的甲基化筛选是基于一种低分辨率和不太敏感的方法，无法识别特定的甲基化DNA核苷酸。我们现在将能够定义影响特定DNA信号功能的甲基化变化，例如特定转录调节因子的结合位点。我们将使用PT和腹侧下丘脑（控制甲状腺激素代谢的地方）的组织，比较从短或长光周期动物中收集的材料，并研究甲基化组在不同光周期中的变化。不同光周期下的甲基化模式也将与基因表达的变化相关，这是通过全基因组RNA测序（“季节性转录组”）确定的。我们将测试这一假设，即预先暴露于特定的光周期可以影响动物对光周期变化的反应，以及“甲基化”如何驱动长期的季节性节律。这些研究将首次深入了解控制哺乳动物季节性繁殖和生长的大脑结构中基因的表观遗传控制。我们的研究还可能揭示家畜驯化生物学的一般特征，因为PT回路（TSH-R）的组成部分已被确定为在鸡的比较研究中处于强选择下。这可能导致对控制繁殖和生长的机制的新理解，对英国畜牧业具有商业意义，并揭示动物如何通过环境中外部信号的相互作用和DNA修饰来适应气候变化。

Animals inhabiting seasonal environments need to adapt their physiology to survive to anticipate environmental change. To achieve this, sophisticated internal clockworks have evolved which drives annual cycles of behaviour and physiology. These can free-run in constant conditions ("circannual" rhythms) and are synchronised to the environment by a brain hormone Melatonin (MEL), produced at night from the pineal gland, 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. The MEL signal acts on hormone secreting circuits (neuroendocrine), which in turn drive annual reproductive and metabolic cycles. MEL acts on targets sites in a specific region at the base of the brain in the pituitary gland called the pars tuberalis (PT), which acts as a seasonal conductor - controlling hormone secretion such as prolactin (a hair growth regulator) in the main pituitary gland, and also within another immediately adjacent brain structure in the hypothalamus, where it regulates the thyroid hormone levels, controlling seasonal reproduction and metabolic cycles. We discovered a key gene regulating long-photoperiod (LP) responses in the PT called EYA3 which is rapidly activated by LP's and acts as a switch mechanism driving hypothalamic thyroid hormone changes. We have also discovered many genes in the PT are regulated by a process called DNA methylation. Methylation suppresses activity of 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 - heritable changes caused by mechanisms other than changes in the underlying DNA sequence, and are crucial in many diseases, but also underpins normal physiology including ageing and differentiation of stem cells. We aim to map all 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. We will now be able to define methylation changes that 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 the methylome changes in different photoperiods. The pattern of methylation under different photoperiods will also be correlated with changes in the expression of genes, 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 changes in photoperiod, and how the "methylome" drives long-term seasonal rhythms. These studies will provide the first insight into epigenetic control of genes in brain structures that control seasonal reproduction and growth in a mammal. Our studies may also reveal general features of the biology of livestock domestication, since components of the PT circuit (TSH-R) have been identified as being under strong selection in comparative studies of chickens. This may lead to new understanding of mechanisms controlling reproduction and growth, of commercial significance to the livestock industry in the UK, and reveal how animals could adapt to climate change through interaction of external signals in the environment, and DNA modifications.