In eukaryotic cells, transcription factors and polymerases must access DNA in the context of nucleosomes and chromatin. The accessibility of DNA sequences to such trans-acting factors is an important feature of gene regulatory elements, including promoters. In vertebrates, the majority of gene promoters coincide with CpG islands (CGIs), which remain free from DNA methylation and exhibit elevated CpG densities. This hypomethylated and CpG-rich state at CGI promoters is associated not only with transcriptional activity, but also with high levels of chromatin accessibility. However, the causes and consequences of such chromatin accessibility remain unclear. To address this, I have profiled chromatin accessibility in mouse embryonic stem cells (ESCs). In addition to confirming that CGI accessibility is independent of transcriptional activity, I was able to demonstrate that the loss of DNA methylation in ESCs resulted in increased chromatin accessibility at a subset of CpG-rich repetitive elements, suggesting that non-methylated CpG-rich sequences may, at least partially, facilitate open chromatin states. This was supported by preliminary work targeting bacterial CpG-rich sequences into the mouse genome, where they were sufficient to establish novel regions of chromatin accessibility. To examine potential mechanisms by which hypomethylated DNA could serve to promote chromatin accessibility, I profiled chromatin accessibility in mouse ESCs lacking various chromatin-modifying proteins which are normally enriched at CGIs, with the histone demethylases KDM2A/B linked to maintaining open chromatin at CGIs. As an alternative approach to understanding the causes of chromatin accessibility in mouse ESCs, I examined the mechanism by which the pioneer transcription factor OCT4 is able to access previously inaccessible chromatin, and reveal that it requires the chromatin remodeller BRG1 to remodel chromatin and facilitate transcription factor binding at distal regulatory elements. Ultimately, this work provides an insight into some of the molecular determinants of chromatin accessibility in mouse ESCs, although many of the consequences of such chromatin states remain unclear.

Orientador: Joaquim Mansano Garcia / Coorientador: Flávia Lombardi Lopes / Banca: Gisele Zoccal Mingoti / Banca: Simone Cristina Méo Niciura / Resumo: A produção in vitro de embriões (PIVE) bovinos é uma biotecnologia de grande impacto econômico por maximizar o potencial reprodutivo de animais geneticamente superiores resultando em maior eficiência reprodutiva. Apesar dos avanços da PIVE, a porcentagem de embriões que se desenvolvem ainda são inferiores aos produzidos in vivo. Epigenética é a regulação da expressão gênica sem alteração na sequência do DNA. Mecanismos epigenéticos, como o remodelamento das histonas, controlam expressão gênica e são fundamentais para o correto desenvolvimento embrionário. Dessa forma, modificações específicas nas histonas podem reprimir ou estimular a transcrição gênica. Os mecanismos epigenéticos são vulneráveis aos fatores ambientais, assim, os sistemas de cultivo in vitro podem ter um impacto no perfil de expressão de importantes genes relacionados ao desenvolvimento embrionário pré-implantacional. Dada a importância e a aplicabilidade da PIVE como biotecnologia reprodutiva, o papel vital dos mecanismos epigenéticos durante o desenvolvimento embrionário, e a importante correlação entre as condições de cultivo embrionário e o perfil epigenético, o presente estudo investigou a influência de diferentes condições de cultivo durante o desenvolvimento embrionário por meio da utilização de diferentes concentrações de soro fetal bovino (SFB) (0% ou 2,5%) e diferentes tensões de oxigênio (O2) (5% ou 20%) durante o cultivo embrionário in vitro (CIV) na regulação epigenética, especificamente no remodelamento das histonas H3K9me2 (repressiva) e H3K4me2 (permissiva) de embriões bovinos produzido in vitro. Para este fim, foram delineados quatro tratamentos durante o cultivo embrionário. T1: embriões foram cultivados em meio de cultivo "Synthetic Oviduct Fluid" (SOF) com 0% SFB sob tensão de 5% de O2; T2: embriões foram cultivados em meio SOF com 2,5% SFB sob ... / Abstract: In vitro production (IVP) of bovine embryos is a biotechnology of great economic impact, as it maximizes the reproductive potential of genetically superior animals, resulting in greater reproductive efficiency. Despite advances in technology in IVP, the percentage of embryos that develop to the transfer stage is still inferior to those seen in vivo. Epigenetics is the regulation of gene expression without altering DNA sequence. Epigenetic processes, such as histone remodeling, control gene expression and are essential for proper embryo development. Specific histone modifications can repress or stimulate gene transcription. Epigenetic mechanisms are under intense environmental control, therefore in vitro culturing systems can impact the expression patterns of genes that support pre-implantation embryo development. Given the importance of IVP as a reproductive biotechnology, the role of epigenetic processes during embryo development, as well the important correlation between culture conditions and epigenetic patterns, the present study was designed to investigate the influence of different culture conditions on embryo development, through the use of different concentrations of fetal bovine serum (FBS) (0% and 2,5%) and different oxygen tensions (O2) (5% and 20%) during in vitro culture, in epigenetic regulation, specifically in the histone remodeling H3K9me2 (repressive) and H3K4me2 (permissive) marks, in bovine embryos produced in vitro. Four treatments were designed and utilized during embryo culture: T1: embryos were cultured in Synthetic Oviduct Fluid (SOF) media with 0% FBS, under 5% O2 tension; T2: embryos were cultured in SOF media with 2.5% FBS, under 5% O2 tension; T3: embryos were cultured in SOF media with 0% FBS, under 20% O2 tension and T4: embryos were cultured in SOF media with 2.5% FBS, under 20% O2 tension. Cleavage and expanded blastocyst development rates were evaluated, as ... / Mestre

The JmjC-histone lysine demethylases (JmjC-KDMs) are epigenetic regulators responsible for the demethylation of methylated lysine residues on the N-terminal histone tails. As Fe²⁺ and 2-oxoglutarate dependent oxygenases (2OG oxygenases), the JmjC-KDMs possess an absolute requirement for molecular oxygen and are related to the cellular oxygen sensing HIF hydroxylases, PHD2 and FIH. Several JmjC-KDMs are known HIF target genes, hence are upregulated in hypoxia. Moreover, a number of JmjC-KDMs have been shown to have differential oxygen dependences, while aberrant histone methylation has been observed in both hypoxic cells and disease states such as cancer and cardiovascular disease. The work described in this thesis aimed to investigate the impact of hypoxia on the JmjC-KDM, KDM4A. In vitro kinetic analyses revealed a K_m^app(O₂) for recombinant KDM4A of 173 ± 23 μM, which is higher than reported values for the 2OG oxygenases C-P4H, mPAHX and even FIH, and approaching those evaluated for the key oxygen sensor PHD2 (230-1746 μM). These results indicate that KDM4A activity is highly sensitive to oxygen availability, and has the biochemical potential to act as an oxygen sensor in the context of epigenetic regulation. Subsequent investigation of the cellular oxygen dependence of KDM4A, and found that the activity of ectopically expressed KDM4A in U2OS cells demonstrates a graded response to oxygen. Importantly, this trend correlates with the in vitro results, providing further evidence that hypoxia may impact upon epigenetic regulation by the JmjC-KDMs. The various factors that may contribute to the hypoxic inhibition of KDM4A were investigated both in vitro and in cells. The results of these studies suggested that altered concentrations of TCA cycle intermediates, comprising reduced levels of the 2OG oxygenase co-substrate 2OG and increased concentrations of the reported inhibitor 2HG, are likely to only minimally affect the activity of KDM4A in hypoxia. Interestingly, the 2OG oxygenase inhibitor IOX1 possessed increased inhibitory potency against KDM4A under conditions of low oxygen, implying that the use of mixed-mode inhibitors against KDM4A may be of therapeutic benefit in hypoxic disease states. This may be of particular pertinence to cardiac hypertrophy (CH), in which KDM4A activity is reported to have pathophysiological consequences. In a collaboration with Dr Tim McKinsey (University of Colorado, Denver), the KDM4 inhibitor CCT1 was tested in a phenotypic screen of cardiomyocyte hypertrophy, the results of which further support a role for KDM4A in this disease, and suggest that the use of small-molecule inhibitors of KDM4A may be a viable therapeutic strategy in CH. Finally, the effect of reactive oxygen species, levels of which may be increased in hypoxia, on KDM4A activity was explored. Recombinant KDM4A was found to be acutely sensitive to inhibition by hydrogen peroxide (H₂O₂) when compared to the HIF hydroxylases PHD2 and FIH. These results imply that KDM4A may act as a sensor of oxidative stress at the chromatin level, and further investigation in a more biologically relevant context is proposed. Overall, the work described herein demonstrates that the activity of KDM4A is sensitive to oxygen availability, a phenomenon that is likely to have significant implications for epigenetic regulation in hypoxia and the expression of KDM4A-regulated genes in ischaemic disease states.

Malignant melanoma, which comprises only 2% of skin cancers cases, but is the most lethal form of skin cancer. With the prevalence of melanoma continuing to rise, there is a greater need to elucidate the mechanisms underlying disease initiation and progression. Because mutations in melanoma-associated genes account for only 10% of cases, epigenome-altering environmental factors must have a role in pathogenesis. DNA methylation and demethylation are key epigenetics processes which govern cell differentiation and development. 5-methylcytosine (5mC) is a key epigenetic mark, which undergoes oxidation to 5-hydroxymethylcytosine (5hmC), 5formylcytosine (5fC) and 5carboxycytosine (5caC) during demethylation. In melanoma, it has been established that the loss of 5hmC is a cancer hallmark and is associated with poor prognostic outcome. The roles of 5fC/5caC, however, are not known. Here, I aimed to investigate the role of 5fC/5caC in melanoma and its contribution to disease development. Using methylase-assisted bisulfite sequencing, I have mapped the genome-wide distribution of 5fC/5caC at base pair resolution in two melanoma cell lines, A2058 and Mel Juso. In both cell lines, this modification is enriched at distal regulatory elements. Comparisons of differentially methylated sites and regions between the cell lines revealed that the products of 5fC/5caC enriched genes participate in cell adhesion and cell signaling, both of which are altered during melanoma initiation and progression. Increased levels of 5fC/5caC in these genes may be a contributing factor to this deregulation. Through these studies, we aim to identify distinct regions undergoing alterations in melanoma, which can serve as diagnostic and prognostic biomarkers. / 2018-06-16T00:00:00Z

The epigenetics of the aging brain is a growing field of study that holds great promise for the discovery of mechanisms and potential treatments for neurodegenerative diseases. In this current study, a novel, accelerated aging murine model, the I-PpoI/Cre, or ICE (Inducible Changes in the Epigenome) mouse, is studied to test its potential for demonstrating the theory of the rearrangement of chromatin (RCM) as the main cause of aging, and in particular, the mechanism through which the brain ages. Immunohistochemistry and behavioral assays are utilized to determine whether there are morphological changes, inflammatory response, and changes in learning and memory. Results showed a significant increase in microglia and astrocytes, markers of inflammation, in I-PpoI/Cre mice compared to their Cre controls. Long term memory performance was also significantly decreased in the I-PpoI/Cre mice, demonstrated through contextual fear conditioning (CFC) testing, and Morris Water Maze (MWM) testing. Results from this study are in support of the I-PpoI/Cre mouse as a model of accelerated aging of the brain, with deficits in learning and memory. Further studies are needed to further characterize this murine model of accelerated aging.

Trimethylation of histone H3 lysine 9 (H3K9me3) and DNA methylation mark heterochromatin, contributing to gene silencing and normal cellular functions. My research investigated the control of H3K9me3 and DNA methylation in the filamentous fungus Neurospora crassa. The H3K9 methyltransferase complex, DCDC, consists of DIM-5, DIM-7, DIM-9, DDB1, and CUL4. Each component of DCDC is required for H3K9me3. The DIM-9/DDB1/CUL4 subunits are reminiscent of known cullin E3 ubiquitin ligases. I showed that core features of CUL4-based E3 ubiquitin ligases are not required for H3K9me3 and DNA methylation in Neurospora. H3K9me3 is bound by heterochromatin protein 1 (HP1) to recruit the DIM-2 DNA methyltransferase and the HCHC histone deacetylase complex. HCHC consists of HP1, CDP-2, HDA-1, and CHAP. Both HP1 and CDP-2 harbor conserved chromodomains that bind H3K9me3, and CHAP contains two putative AT-hook domains that bind A:T-rich DNA. To test the contributions of these domains to HCHC function, I deleted the chromodomains of HP1 and CDP-2. Deletion of the HP1 chromodomain resulted in a reduction of DNA methylation, which was not exacerbated by deletion of the CDP-2 chromodomain. A strain with deletions of chap and the HP1 chromodomain showed a DNA methylation phenotype comparable to the loss of the HDA-1 catalytic subunit. These findings support a model in which recognition of H3K9me3 and A:T-rich DNA by HP1 and CHAP, respectively, are required for proper HCHC function. To examine the relationships between H3K9me3, DNA methylation, and histone acetylation, I utilized in vivo protein tethering of core heterochromatin components. The requirement of DIM-7 for native heterochromatin, previously implicated in localizing the H3K9 methyltransferase DIM-5, was not bypassed by DIM-5 tethering, indicating that DIM-7 has additional roles within the DCDC. Artificial localization of the HCHC histone deacetylase, by tethering HP1 or HDA-1, resulted in induction of H3K9me3, DNA methylation, and gene silencing, but silencing did not require H3K9me3 or DNA methylation. HCHC-mediated establishment of H3K9me3 was not required for de novo heterochromatin formation at native heterochromatic loci suggesting a role in heterochromatin spreading. Together, this work implicates HDA-1 activity as a key driver of heterochromatin spreading and silencing. This dissertation includes previously published co-authored material.

Despite the general advice of avoiding medication during pregnancy, the majority of pregnant woman use one or more ‘over the counter’ analgesics. During the last few years there has been growing evidence that analgesic exposure, such as paracetamol, ibuprofen or indomethacin, during pregnancy can have detrimental effects on rodent and human fetal gonads. The majority of previous studies have focused in alterations in testosterone production and male reproductive disorders. However, few studies have analysed the effect of these analgesics on fetal germ cells and possible consequences on fertility. During my thesis, I first focused on the effect of paracetamol and indomethacin exposure during pregnancy on rat fetal gonads. These showed that both paracetamol and indomethacin are able to alter the expression of genes important for fetal gonad and germ cell development. Previous studies on germ cells and analgesics have focused on rat models, but there is a lack of similar studies performed in human models. Therefore, I investigated the consequences of exposure of therapeutically relevant doses of paracetamol and ibuprofen on human gonads, with a special attention to the germ cells. Fetal gonads from the 1st and 2nd trimester were used in two different models: hanging drop cultures for 1st trimester testes and ovaries and a xenograft system for 2nd trimester fetal testes. Fetal gonad culture in the presence of paracetamol or ibuprofen reduced AP2γ+ (gonocyte) GC number in both 1st trimester fetal testes (22-28% reduction) and ovaries (43-49% reduction). 2nd trimester fetal testes were exposed to three different regimes, 1 or 7 days paracetamol and 7 days ibuprofen, which led to reductions of 17% and 30%, respectively in AP2γ+ GC number for paracetamol and a 53% reduction in total germ cell number for ibuprofen.

Neuroblastoma (NB) é a forma mais indiferenciada de tumores neuroblásticos e a principal causa de morte por câncer pediátrico. Alterações epigenéticas interagem em todas as etapas do desenvolvimento do câncer, promovendo a progressão tumoral. A remodelação da cromatina é influenciada pela acetilação de histonas e a metilação de DNA. Acetiltransferases de histona (HATs), desacetilases de histonas (HDAC) e metiltransferase de DNA (DNMTs) são alvos de estratégias terapêuticas em tumores. Os retinoides agem nas vias de diferenciação celular, anti-proliferação e pró-apoptose. Nesse trabalho, é proposto que a combinação desses moduladores epigenéticos e de diferenciação em linhagens de células de NB humano é mais efetiva que os agentes isolados. Os tratamentos induziram mudanças na expressão de marcadores de diferenciação e indiferenciação, como c-Myc, β-3tubulina, NeuN e Bmi1, e alterações morfológicas nas duas linhagens celulares utilizadas, SK-N-BE(2) e SH-SY5Y. Os dados encontrados podem contribuir para uma melhor compreensão dos mecanismos moleculares dos moduladores retinoides e epigenéticos em NB capazes de acrescentar melhorias nas atuais estratégias terapêuticas. / Neuroblastoma (NB) is the most undifferentiated form of neuroblastic tumors and the leading cause of death from pediatric cancer. Epigenetic changes interact at all stages of cancer development, promoting tumor progression. Chromatin remodeling is influenced by histone acetylation and DNA methylation. Histone acetyltransferases (HATs), histone deacetylases (HDAC), and DNA methyltransferase (DNMTs) are targets for therapeutic strategies in cancer. Retinoids act on cell differentiation pathways and display anti-proliferation and pro-apoptotic actions. In the present research we examined the effects of combining epigenetic modulators and a retinoid receptor agonist in human NB cells. The retinoid all trans-retinoic acid (ATRA) combined with inhibitors of either histone deacetylases (HDACs) or DNA methyltransferase was more effective than any drug given alone in impairing the proliferation of SH-SY5Y and SK-N-BE(2) NB cells. In addition, the treatments induced differential changes in the expression of differentiation markers including c-Myc, β-3tubulin, NeuN and Bmi1, and morphological changes in SK-N-BE(2) e SH-SY5Y cell lines. The data contribute to a better understanding of the molecular mechanisms of retinoid modulators and epigenetic in NB able to add improvements in current therapeutic strategies.

Preterm infants are at increased risk of cardiometabolic and neurodevelopmental disorders in later life. The typical postnatal growth pattern of failure to achieve the equivalent of a normal fetal growth rate, followed up by catch-up growth, altered adiposity and altered hypothalamic-pituitary-adrenal axis (HPA) activity may be predisposing factors. Potential mechanisms that may mediate such programmed effects include altered DNA methylation and faster telomere attrition. A prospective cohort of 46 very preterm (25+2 to 31+5 weeks’ gestation, mean 28.6) and 40 full term (38+3 to 42+2 weeks’ gestation, mean 40.2) infants was established to investigate potential mechanisms. Infants were studied at birth, term equivalent age, 3 months and 1 year corrected for prematurity. At all time points, linear growth and body composition (by densitometry) were measured and buccal (epithelial) cells was collected for measurement of DNA methylation (5mC) and relative telomere length. Compared with full term infants, preterm infants were lighter (p < 0.001) and had a smaller head circumference (p < 0.05) at all time-points and were shorter at term equivalent (p < 0.001) and 3 months corrected age (p = 0.002). Preterm infants also had greater percentage body fat at term equivalent age (mean difference = 5.5%, p < 0.001), which normalised by 3 months corrected (mean difference = 0.9%, p = 0.4). Preterm infants had a blunted salivary cortisol response (mean difference 0.4 μg/dL, p = 0.02) to a stressor (physical examination) at 3 months compared to term infants at this age, suggesting altered activity of the HPA axis. 5mC is fundamental in the control of expression of imprinted genes involved in fetal growth. Notably, a number of studies in humans exposed to an adverse environment in early life have demonstrated altered 5mC at the differentially methylated regions (DMRs) controlling the expression of the key fetal growth factor insulin like growth factor 2 (IGF2) and at the linked H19 imprinting control region (H19 ICR). At birth, preterm infants had a significant decrease in 5mC at DMR2 compared with term infants at birth (β = –11.5, p < 0.001) and compared with preterm infants at term equivalent age (mean difference = -7.4, p = 0.01). By term equivalent age, preterm infants had decreased 5mC at both DMR2 (β = –2.8, p = 0.01) and the H19 ICR (β = –2.3, p = 0.048) compared with term infants at birth, although this difference disappeared at 1 year corrected. Although research has suggested that catch up growth may confer an unfavourable metabolic phenotype, poor initial weight gain can associate with worse cognitive outcome. A pathway was established for obtaining advanced magnetic resonance images of the preterm brain. 5mC at H19 ICR and DMR2 in buccal DNA showed no association with measures of white matter microstructure or whole brain volumes. Term infants demonstrated telomere lengthening over the first year of life (mean difference = -0.3, p = 0.02). There was no significant change in telomere length over the first year of life in preterm infants (mean difference = 0.2, p = 0.34). However, as preterm infants at term equivalent age had longer telomeres compared to term infants at birth (β = 0.6, p < 0.001), ultimately there were no differences between the term and the preterm groups at 1 year corrected age (β = 0.3, p = 0.07). The DNA modification 5-hydroxymethylcytosine (5hmC) is a stable modification in its own right and is also thought to be an intermediate step in DNA demethylation. 5hmC is abundant in the placenta but has not been studied in the context of fetal programming. Additionally, previous research using methods such as bisulphite conversion would not have discriminated between 5mC and 5hmC and therefore the role of 5mC may not have been accurately measured. To study the relationship between 5mC, 5hmC and fetal growth, gene expression of candidate imprinted and non-imprinted genes in full term placental samples from the Edinburgh Reproductive Tissue BioBank was analysed. 5mC and 5hmC within the IGF2/H19 and KvDMR (controlling CDKN1C) loci was estimated using chemical capture and immunoprecipitation techniques that discriminate between modifications. Relationships between the expression of IGF2 (r = 0.3, p = 0.02) and CDKN1C (r = -0.3, p = 0.01) and birth weight across the normal range were found and in keeping with the known action of these genes. 5mC at IGF2 DMR0 (β = 0.3, p = 0.02) and KvDMR (β = 0.3, p = 0.02) and 5hmC at H19 gene body (β = 0.2, p = 0.04) associated with birth weight. Thus, DNA modifications at imprinted DMRs may modulate environmental influences on fetal growth across the normal range. DNA methylation at IGF2/H19 can be influenced by early life events. It remains to be seen whether any changes are present later in childhood and whether they associate with risk factors for the metabolic syndrome.

DNA methylation is an epigenetic mark that is deposited throughout the genome of mammals and plays an important role in the maintenance of transcriptionally repressive states across cell divisions. There are two major mechanisms by which DNA methylation has been proposed to act: one involves the recognition of the mark by protein complexes containing histone deacetylases (HDACs) that can remodel the local chromatin. Alternatively, methylation has been suggested to directly affect the interaction between transcription factors and their cognate binding sequence. The aim of this research was to determine the contributions of these two mechanisms in cells. The importance of HDAC activity in mediating DNA methylation-dependent transcriptional repression was assessed by comparing the genes and retrotransposons that are upregulated in response to DNA methylation loss or the disruption of HDAC activity. To this purpose, we performed whole-genome transcriptional analysis in wild type and DNA methylation-deficient mouse embryonic stem cells (DNMT.TKO mESCs) in the presence and absence of the HDAC inhibitor trichostatin A. Our data suggests that there are few genes whose repression is solely dependent on the recruitment of HDACs by DNA methylation in mESCs. Rather it appears that DNA methylation and HDAC-mediated silencing represent two independent layers of repression that converge at certain transcriptional elements. To investigate the contribution of DNA methylation on the genome-wide occupancy of transcription factors, we compared the global chromatin accessibility landscape and the binding profile of candidate transcription factors in the absence or presence of DNA methylation. We found that loss of DNA methylation associates with localised gains in accessibility, some of which can be linked to the novel binding of transcription factors such as GABPA, MAX, NRF1 and YY1. Altogether, our results present new insights into the interplay between DNA methylation and histone deacetylation and their impact on the localisation of transcription factors from different families.