Epigenetic Changes in the Hypothalamus of Offspring Following Maternal Undernutrition
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Epigenetic changes in the hypothalamus of offspring following maternal undernutrition A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences Ghazala Begum September 2013 Contents Page No. List of Figures 5 List of Tables 8 Abstract 9 Declaration 10 Copyright Statement 10 Abbreviations 11 Nomenclature 13 Acknowledgements 14 Chapter 1 15 Introduction 15 1.1 The implications of maternal programming 16 1.1.1 Maternal undernutrition induces programming 17 1.1.2 Maternal overnutrition induces programming 18 1.1.3 Stress-induced maternal programming 19 1.1.4 Twinning as a programming paradigm 20 1.2 Programming of the hypothalamic energy regulating pathway 21 1.2.1 Hypothalamic energy regulating pathway 21 1.2.2 Role of glucocorticoids in the hypothalamic energy regulating pathway 26 1.2.3 Effects of maternal undernutrition on the offspring’s energy regulating 27 athway pathway 1.3 Programming of the HPA axis 31 1.3.1 Key components of the HPA axis 31 1.3.2 Effects of maternal undernutrition on the offspring’s HPA axis 32 1.4 The potential involvement of epigenetics in programming 34 1.4.1 DNA methylation 35 1.4.2 Histone Modifications 37 1.4.3 The GR gene as a potential target for epigenetic modification 38 1.4.4 Epigenetic alterations of fetal GR following maternal programming 39 1.4.5 POMC as a potential target of epigenetic modification 40 1.4.6 Epigenetic alterations of fetal POMC following maternal nutritional 40 dsjdsddsdinsults 1.5 Overview 42 1.5.1 Maternal undernutrition sheep model 42 1.5.2 Aims 44 1.6 Alternative format 47 Chapter 2 49 Methods 49 2.1 Animal Management 50 2.2 DNA, RNA and protein purification from brain tissues 51 2.3 Whole blood DNA and protein purification 52 2.4 Bioinformatic analysis 53 2.5 DNA methylation analysis 53 2.6 mRNA expression analysis 55 2.6.1 mRNA expression analysis during the fetal study 55 2 2.6.2 mRNA expression analysis during the twin study 55 2.6.3 mRNA expression analysis during the adult study 56 2.7 Chromatin immunoprecipitation 57 2.7.1 Chromatin immunoprecipication for fetal tissues 57 2.7.2 Chromatin immunoprecipitation for adult brain tissues 58 2.8 Western blots 59 2.9 POMC ELISA 60 2.10 DNA methyltransferase activity/inhibition assay 61 2.11 Buffers 61 2.12 Statistical analysis 62 Chapter 3: Publication I 63 Epigenetic changes in the hypothalamic pro-opiomelanocrotin and glucocorticoid ssreceptor genes in the ovine fetus after periconceptional undernutrition Chapter 4: Publication II 64 Epigenetic changes in fetal hypothalamic energy regulating pathways are dlassociated with maternal undernutrition and twinning 4.1 Supplemental data 65 Chapter 5: Publication III 67 Maternal undernutrition programs tissue-specific epigenetic changes in the bglucocorticoid receptor in adult offspring Chapter 6 68 Maternal undernutrition induces tissue specific changes in POMC in adult 68 gioffspring 6.1 Introduction 69 6.1.1 Aims 70 6.2 Materials and methods 71 6.2.1 Animal management 71 6.2.2 Isolation of DNA and RNA and protein from tissue and blood 71 6.2.3 DNA methylation enrichment 71 6.2.4 Chromatin immunoprecipitation of H3K9AC and H3K27me3 71 6.2.5 qRT-PCR analysis 72 6.2.6 Western blot 72 6.2.7 Statistical analysis 72 6.3 Epigenetic changes in hypothalamic POMC 73 6.4 Comparable levels of hypothalamic POMC protein 75 6.5 Epigenetic changes in the POMC promoter amplicon in the pituitary of 76 fddffdpericonceptionally undernourished adult offspring 6.6 POMC mRNA and protein levels in the pituitary of adult offspring 77 6.7 POMC status in the peripheral leukocytes of maternally undernourished adult 78 vcvccoffspring 6.8 Summary 79 Chapter 7 81 Discussion 7.1 The impact of the length and timing of maternal undernutrition on the 83 3 hghghoffspring in sheep 7.2 Epigenetic changes in hypothalamic GR as a consequence of maternal 84 ghghgprogramming persisting from fetal life to adulthood 7.3 Epigenetic changes in hypothalamic POMC as a consequence of maternal 87 ghghhprogramming 7.4 Tissue specific changes in GR and POMC 90 7.5 NPY expression in the hypothalami of maternally underfed offspring 92 7.6 Sex-specific outcomes in the maternally undernourished offspring 93 7.7 Twinning as an intrauterine programming paradigm 94 7.8 Phenotypic outcome in the adult offspring subject to periconceptional 95 cvcvcundernourishment 7.9 Mechanisms of action underlying epigenetic changes in the offspring as a 97 cvcvvconsequence of maternal programming 7.10 Conclusion 98 7.11 Future work 99 7.11.1 Analysis of the role of exon 1 of the GR gene in the hypothalamus 99 7.11.2 POMC hypothalamic specific enhancer region 102 7.11.3 Candidate gene approach verses genome wide analysis 103 7.11.4 Potential models of maternal nutritional programming 104 Chapter 8 107 References Chapter 9 128 Appendix Final word count is 52,545. 4 List of Figures Page No. Page No. in thesis in paper Chapter 1: Figure 1.01. Programming paradigms 17 Figure 1.02. Tissue specific POMC processing 22 Figure 1.03. Hypothalamic appetite regulatory pathway 25 Figure 1.04. The HPA axis 31 Figure 1.05. DNA methylation 37 Figure 1.06. Histone modifications 38 Figure 1.07. The GR exon 1 promoter region 39 Figure 1.08: Maternal programming sheep model 43 Chapter 2: Figure 2.01. RNA integrity gel 52 Figure 2.02. RNA integrity of whole and ventral hypothalamic 52 samples Chapter 3: FIG. 1. POMC and GR gene region screening to identify highly 3656 conserved, CpG-rich regions. FIG. 2. HPA axis activity in fetal sheep from control ewes or 3657 ewes subjected to periconceptional undernutrition (underfed from 60 d before conception to 30 d after conception). FIG. 3. Epigenetic changes associated with the POMC gene in 3658 the fetal hypothalamus. Fetal hypothalamic tissue samples were obtained from normal and underfed maternal sheep (underfed from 60 d before to 30 d after conception). FIG. 4. Expression of the POMC gene in the fetal hypothalamus. 3658 Fetal hypothalamic tissue samples were obtained from control and underfed (from 60 d before conception to 30 d after conception). FIG. 5. Presence of H3K9Ac associated with the GR gene 3659 promoter in the fetal hypothalamus 5 Page No. Page No. in thesis in paper FIG. 6. Methylation of GR gene promoter region in the fetal 3659 hypothalamus. Hypothalamic tissue samples were obtained from control and underfed (from 60 d before conception to 30 d after conception) fetal sheep. FIG. 7. Expression of GR gene in the fetal hypothalamus. Fetal 3660 hypothalamic tissue samples were obtained from control and underfed maternal sheep (from 60 d before conception to 30 d after conception); 2 μg of total RNA were used to quantify expression levels of GR. FIG. 8.The effect of different periods of periconceptional 3661 undernutrition on hypothalamic GR, POMC, and NPY methylation and gene expression. The −60 to +30 group (UN −60 to +30) was underfed from 60 d before conception to 30 d after conception. The −60 to 0 group (UN −60 to 0) were fed the same diet as the −60 to +30 group but were allowed to feed ad libitum from conception. The −2 to +30 group (UN −2 to +30) were fed the same diet for 30 d after conception. Fetal ventral hypothalamic tissue samples, enriched for the ARC, were obtained from all sample groups at d 131 of gestation Chapter 4: Figure 1.Summary of ENCODE data from different human cell 1696 lines. Data analysis from the UCSC genome browser depicts cell line-specific changes in chromatin over the POMC promoter marker region. Figure 2.Histone modifications of the POMC promoter in 1698 response to twinning and periconceptional maternal undernutrition. Figure 3.DNA methylation and expression levels of fetal 1699 hypothalamic neuropeptides Figure 4.Changes in the histone patterns of the GR promoter as a 1700 result of twinning and maternal periconceptional undernutrition. Figure 5.Effects of twinning and periconceptional maternal 1700 undernutrition on fetal hypothalamic GR promoter methylation and GR mRNA expression levels. Figure 6.Fetal HPA axis dynamics following twinning and 1701 maternal periconceptional undernutrition. 4.1 Supplemental data: Fig. S1. Summary of ENCODE data 65 6 Page No. Page No. in thesis in paper Fig. S2. NPY mRNA expression levels determined using qRT- 66 PCR. Groups were compared to the control via the one-way ANOVA with Tukey HSD Post Hoc test. *p<0.05, **p<0.01, ***p<0.005. Chapter 5: Figure 1. Periconceptional undernutrition is associated with 4 altered glucocorticoid receptor (GR) epigenetic status in the ventral hypothalamus of adult offspring. Figure 2. Altered glucocorticoid receptor (GR) expression levels 5 in the ventral hypothalamus of adult offspring following periconceptional undernutrition. Figure 3. Ventral hypothalamic neuropeptide mRNA expression. 6 Figure 4. Altered epigenetic and expression status of 6 hippocampal glucocorticoid receptor (GR) epigenetic and expression status in offspring from undernourished mothers. Figure 5. No change in glucocorticoid receptor (GR) promoter 7 methylation or protein expression in leukocytes. Figure 6. Increased fat:lean mass ratio in adult males whose 8 mothers were periconceptionally undernourished Chapter 6: Figure 6.01. Altered epigenetic status of the POMC gene in the 74 ventral hypothalamus of maternally undernourished adult offspring. Figure 6.02. Similar levels of hypothalamic POMC protein in 75 adult animals following periconceptional undernutrition. Figure 6.03. Gender specific epigenetic changes in the POMC 76 promoter region in the pituitary in maternally undernourished adult offspring. Figure 6.04. Comparable POMC mRNA and protein levels in the 77 pituitary.