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Linker histone H1 plays a key role in facilitating folding of higher order chromatin structure. Previous studies have shown that deletion of three somatic H1 subtypes together leads to embryonic lethality and that H1c/H1d/H1e triple knockout (TKO) embryonic stem cells (ESCs) display bulk chromatin decompaction. Following this initial work, we investigated the role of H1 and chromatin compaction in stem cell pluripotency and differentiation, as well as the regulation of Hox genes expression. We find that H1 TKO ESCs are more resistant to spontaneous differentiation, impaired in embryoid body differentiation, and largely blocked in neural differentiation. We present evidence that H1 contributes to efficient repression of the expression of pluripotency factors, Oct4 and Nanog, and participates in establishment and maintenance of DNA methylation and histone modification necessary for silencing pluripotency genes during stem cell differentiation and embryogenesis. In addition, we find reduced expression of a distinct set of Hox genes in embryos and ESCs, respectively. Furthermore, by characterizing H1c−/−; H1d−/−; and H1e−/− single-H1 null ESCs established in this study, we showed that individual H1 subtypes regulated specific Hox genes in ESCs. Finally, we demonstrate that the levels of H3K4me3 were significantly diminished at the affected Hox genes in H1 TKO- and single-H1 KO- ESCs, whereas H3K27me3 occupancy is modestly increased at specific Hox genes. Our results suggest that marked reduction of H1 levels and decondensation of bulk chromatin affect the expression of pluripotency genes and Hox genes in embryos and ESCs, which may be in part mediated through establishment and maintenance of epigenetic marks.

O câncer de mama representa problema mundial de saúde pública e a causa mais frequente de morte por câncer entre as mulheres. A identificação de agentes moduladores de marcas epigenéticas, tais como metilação global do DNA e modificações pós-tradução em histonas, compreende alternativa promissora para estabelecimento de estratégias de controle da carcinogênese mamária. Dentre os nutrientes, o elemento traço essencial selênio (Se) pode ser destacado como agente dietético com potencial anti-câncer de mama e que poderia atuar modulando processos epigenéticos. Entretanto seus mecanismos de ação são pouco elucidados. Este estudo objetivou, assim, identificar efeitos do tratamento com selênio no crescimento e marcas epigenéticas de células de adenocarcinoma mamário humano MCF-7. Células MCF-7, positivas para o receptor de estrógeno, foram tratadas com ácido metilselenínico (MSA) ou selenito de sódio (ST) por diferentes tempos e em diferentes concentrações. Foram avaliados: padrão de proliferação (ensaio cristal violeta) e viabilidade celular (método de exclusão azul de tripan); integridade de membrana plasmática (citometria de fluxo); níveis de fragmentação do DNA (citometria de fluxo), distribuição das fases do ciclo celular (citometria de fluxo); apoptose (citometria de fluxo/ marcação dupla com Anexina V - Iodeto de propídio); níveis de lisina 9 acetilada (H3K9ac) e trimetilada (H3K9me3) em histona H3; níveis de lisina 16 acetilada (H4K16ac) em histona H4 (Western blot); padrão de metilação global do DNA (HPLC-DAD); expressão de gene supressor de tumor (RASSF1a; qPCR) e padrão de metilação da região promotora (RASSF1a e RAR&#946;; MS-PCR); expressão da enzima DNA metilstransferase 1 (DNMT1) (Western Blotting). Comparado ao grupo controle de células não tratadas (GC), ambos os tratamentos com MSA ou ST inibiram a proliferação e viabilidade de células MCF-7 de forma dose e tempo dependente. Ambas as formas químicas de Se induziram a parada do ciclo celular, aumentando (p< 0,05) a proporção de células na fase G2/M e reduzindo (p< 0,05) a proporção daquelas nas fases G0/G1 e S. Os tratamentos com MSA favoreceram a morte celular por apoptose, que foi associada com nível de fragmentação de DNA aumentado (p< 0,05), e reduzida ruptura da membrana plasmática associada com a exposição aumentada (p< 0,05) de fostadilserina. Por outro lado, o ST aumentou (p< 0,05) a fragmentação do DNA e (p< 0,05) a positividade ao iodeto de propídio associado à indução de necrose (p< 0,05). Dentre os mecanismos epigenéticos investigados, 1,6&#181;M e 2&#181;M reduziram a acetilação de H3K9ac (72h; p< 0,05) e aumentaram a de H4K16ac (96h; p< 0,05). O tratamento por 96h com 2&#181;M de MSA reduziu (p< 0,05) a metilação de H3K9me3. Ambos MSA e ST não alteraram o padrão de metilação global do DNA, mas reduziram a expressão de DNMT1, após 96h com 2&#181;M de MSA (p< 0,001; 88%) e após 120h com 10&#181;M de ST (p< 0,001; 96%). ST, mas não o MSA, aumentou (p< 0,05; 45%) a expressão do gene RASSF1a. Em ambos os grupos tratados com MSA ou ST, bem como no GC, a região promotora dos genes RASSF1a e RAR estavam predominantemente metiladas. Estes resultados fornecem evidências de que as ações anti-câncer de mama de compostos do selênio dependem de sua forma química. Além disso, a modulação de processos epigenéticos parecem ser relevantes para as ações inibitórias do MSA em células de câncer de mama. / Breast cancer is a global public health problem and the most frequent cause of cancer death among women. The identification of agents able to modulate epigenetic marks, such as global DNA methylation and histone post-translational modifications, comprises promising alternative for establishing control strategies on mammary carcinogenesis. Among the nutrients, the essential trace element selenium (Se) can be highlighted as a dietary agent with potential anti-breast cancer and could act by modulating epigenetic processes. However its mechanisms of action are poorly understood. This study aimed, therefore, to identify the effects of selenium treatment on growth and epigenetic marks of MCF-7 human breast adenocarcinoma cells. MCF-7 cells, positive for estrogen receptor, were treated with methylseleninic acid (MSA) or sodium selenite (ST) for different times and in different concentrations. Evaluated parameters included: cell proliferation (crystal violet assay) and cell viability (trypan blue exclusion assay); plasma membrane integrity (flow cytometry); levels of DNA fragmentation (flow cytometry), apoptosis (flow cytometry - double labeling with Annexin V - propidium iodide); distribution of cell cycle phases (flow cytometry); acetylated (H3K9ac) and trimethylated (H3K9me3) lysine 9 levels on histone H3; acetylated (H4K16ac) lysine 16 level on histone H4 (Western blot); global DNA methylation (HPLC-DAD); tumor suppressor gene expression (RASSF1a; qPCR) and promoter methylation (RASSF1a, RAR&#946;; MS-PCR); DNA methyltransferase 1 (DNMT1) expression (Western blot). Compared to untreated cells (controls), both MSA and ST inhibited (p< 0.05) MCF-7 cell proliferation and viability in a dose- and time-dependent manner. Treatments with MSA favored cell death by apoptosis, that was associated with increased (p< 0.05) DNA fragmentation level, reduced plasma membrane rupture associated with high (p< 0.05) phosphatidylserine exposure. On the other hand, ST increased (p< 0.05) DNA fragmentation, enhanced (p< 0.05) propidium iodide positivity associated to necrosis induction (p< 0,05). Both chemical forms of Se induced nduced cell cycle arrest, increasing (p< 0.05) the proportion of cells in G2/M phase and reducing (p< 0.05) the proportion of those in G0/G1 and S phases. Among the epigenetic mechanisms investigated, 1.6&#181;M and 2&#181;M of MSA reduced acetylation of H3K9ac (72h, p< 0.05) and increased the H4K16ac (96h, p< 0.05). The treatment for 96h with 2&#181;M of MSA reduced (p< 0.05) the H3K9me3 methylation. Neither MSA nor ST altered (p> 0.05) global DNA methylation, while both compounds reduced (p< 0.05) DNMT1 protein expression, after 96h with 2&#181;M of MSA (p< 0.001; 88%) and after 120h with 10&#181;m of ST (p< 0.001; 94%). ST, but not MSA, increased (p< 0.05; 45%) RASSF1a gene expression. In control and Se-treated cells promoter regions of RASSF1a and RAR&#946; were predominantly methylated. These results provide evidence that the anti-breast cancer actions of selenium compounds depend on its chemical form. Additionally, modulation of epigenetic processes seems to represent a relevant feature of MSA inhibitory effects in breast cancer cells.

Biological molecules often undergo large structural changes to perform their function. Computational methods can provide a fine-grained description at the atomistic scale. Without sufficient approximations to accelerate the simulations, however, the time-scale on which functional motions often occur is out of reach for many traditional methods. Natural Move Monte Carlo belongs to a class of methods that were introduced to bridge this gap. I present three novel applications for Natural Move Monte Carlo, two on proteins and one on DNA epigenetics. In the second part of this thesis I introduce a new protocol for the testing of hypotheses regarding the functional motions of biological systems, named customised Natural Move Monte Carlo. Two different case studies are presented aimed at demonstrating the feasibility of customised Natural Move Monte Carlo.

O câncer de mama representa problema mundial de saúde pública e a causa mais frequente de morte por câncer entre as mulheres. A identificação de agentes moduladores de marcas epigenéticas, tais como metilação global do DNA e modificações pós-tradução em histonas, compreende alternativa promissora para estabelecimento de estratégias de controle da carcinogênese mamária. Dentre os nutrientes, o elemento traço essencial selênio (Se) pode ser destacado como agente dietético com potencial anti-câncer de mama e que poderia atuar modulando processos epigenéticos. Entretanto seus mecanismos de ação são pouco elucidados. Este estudo objetivou, assim, identificar efeitos do tratamento com selênio no crescimento e marcas epigenéticas de células de adenocarcinoma mamário humano MCF-7. Células MCF-7, positivas para o receptor de estrógeno, foram tratadas com ácido metilselenínico (MSA) ou selenito de sódio (ST) por diferentes tempos e em diferentes concentrações. Foram avaliados: padrão de proliferação (ensaio cristal violeta) e viabilidade celular (método de exclusão azul de tripan); integridade de membrana plasmática (citometria de fluxo); níveis de fragmentação do DNA (citometria de fluxo), distribuição das fases do ciclo celular (citometria de fluxo); apoptose (citometria de fluxo/ marcação dupla com Anexina V - Iodeto de propídio); níveis de lisina 9 acetilada (H3K9ac) e trimetilada (H3K9me3) em histona H3; níveis de lisina 16 acetilada (H4K16ac) em histona H4 (Western blot); padrão de metilação global do DNA (HPLC-DAD); expressão de gene supressor de tumor (RASSF1a; qPCR) e padrão de metilação da região promotora (RASSF1a e RAR&#946;; MS-PCR); expressão da enzima DNA metilstransferase 1 (DNMT1) (Western Blotting). Comparado ao grupo controle de células não tratadas (GC), ambos os tratamentos com MSA ou ST inibiram a proliferação e viabilidade de células MCF-7 de forma dose e tempo dependente. Ambas as formas químicas de Se induziram a parada do ciclo celular, aumentando (p< 0,05) a proporção de células na fase G2/M e reduzindo (p< 0,05) a proporção daquelas nas fases G0/G1 e S. Os tratamentos com MSA favoreceram a morte celular por apoptose, que foi associada com nível de fragmentação de DNA aumentado (p< 0,05), e reduzida ruptura da membrana plasmática associada com a exposição aumentada (p< 0,05) de fostadilserina. Por outro lado, o ST aumentou (p< 0,05) a fragmentação do DNA e (p< 0,05) a positividade ao iodeto de propídio associado à indução de necrose (p< 0,05). Dentre os mecanismos epigenéticos investigados, 1,6&#181;M e 2&#181;M reduziram a acetilação de H3K9ac (72h; p< 0,05) e aumentaram a de H4K16ac (96h; p< 0,05). O tratamento por 96h com 2&#181;M de MSA reduziu (p< 0,05) a metilação de H3K9me3. Ambos MSA e ST não alteraram o padrão de metilação global do DNA, mas reduziram a expressão de DNMT1, após 96h com 2&#181;M de MSA (p< 0,001; 88%) e após 120h com 10&#181;M de ST (p< 0,001; 96%). ST, mas não o MSA, aumentou (p< 0,05; 45%) a expressão do gene RASSF1a. Em ambos os grupos tratados com MSA ou ST, bem como no GC, a região promotora dos genes RASSF1a e RAR estavam predominantemente metiladas. Estes resultados fornecem evidências de que as ações anti-câncer de mama de compostos do selênio dependem de sua forma química. Além disso, a modulação de processos epigenéticos parecem ser relevantes para as ações inibitórias do MSA em células de câncer de mama. / Breast cancer is a global public health problem and the most frequent cause of cancer death among women. The identification of agents able to modulate epigenetic marks, such as global DNA methylation and histone post-translational modifications, comprises promising alternative for establishing control strategies on mammary carcinogenesis. Among the nutrients, the essential trace element selenium (Se) can be highlighted as a dietary agent with potential anti-breast cancer and could act by modulating epigenetic processes. However its mechanisms of action are poorly understood. This study aimed, therefore, to identify the effects of selenium treatment on growth and epigenetic marks of MCF-7 human breast adenocarcinoma cells. MCF-7 cells, positive for estrogen receptor, were treated with methylseleninic acid (MSA) or sodium selenite (ST) for different times and in different concentrations. Evaluated parameters included: cell proliferation (crystal violet assay) and cell viability (trypan blue exclusion assay); plasma membrane integrity (flow cytometry); levels of DNA fragmentation (flow cytometry), apoptosis (flow cytometry - double labeling with Annexin V - propidium iodide); distribution of cell cycle phases (flow cytometry); acetylated (H3K9ac) and trimethylated (H3K9me3) lysine 9 levels on histone H3; acetylated (H4K16ac) lysine 16 level on histone H4 (Western blot); global DNA methylation (HPLC-DAD); tumor suppressor gene expression (RASSF1a; qPCR) and promoter methylation (RASSF1a, RAR&#946;; MS-PCR); DNA methyltransferase 1 (DNMT1) expression (Western blot). Compared to untreated cells (controls), both MSA and ST inhibited (p< 0.05) MCF-7 cell proliferation and viability in a dose- and time-dependent manner. Treatments with MSA favored cell death by apoptosis, that was associated with increased (p< 0.05) DNA fragmentation level, reduced plasma membrane rupture associated with high (p< 0.05) phosphatidylserine exposure. On the other hand, ST increased (p< 0.05) DNA fragmentation, enhanced (p< 0.05) propidium iodide positivity associated to necrosis induction (p< 0,05). Both chemical forms of Se induced nduced cell cycle arrest, increasing (p< 0.05) the proportion of cells in G2/M phase and reducing (p< 0.05) the proportion of those in G0/G1 and S phases. Among the epigenetic mechanisms investigated, 1.6&#181;M and 2&#181;M of MSA reduced acetylation of H3K9ac (72h, p< 0.05) and increased the H4K16ac (96h, p< 0.05). The treatment for 96h with 2&#181;M of MSA reduced (p< 0.05) the H3K9me3 methylation. Neither MSA nor ST altered (p> 0.05) global DNA methylation, while both compounds reduced (p< 0.05) DNMT1 protein expression, after 96h with 2&#181;M of MSA (p< 0.001; 88%) and after 120h with 10&#181;m of ST (p< 0.001; 94%). ST, but not MSA, increased (p< 0.05; 45%) RASSF1a gene expression. In control and Se-treated cells promoter regions of RASSF1a and RAR&#946; were predominantly methylated. These results provide evidence that the anti-breast cancer actions of selenium compounds depend on its chemical form. Additionally, modulation of epigenetic processes seems to represent a relevant feature of MSA inhibitory effects in breast cancer cells.

H1 linker histone facilitates the formation of higher order chromatin structure and is essential for mammalian development. Mice have 11 H1 variants which are differentially regulated and conserved in human. Previous research indicates that H1 regulates the expression of specific genes in mouse embryonic stem cells (ESCs). However, whether individual variants have distinct functions and how H1 participates in gene regulation remain elusive. An investigation of the precise localization of individual H1 variants in vivo would facilitate the elucidation of mechanisms underlying chromatin compaction regulated gene expression, while it has been extremely difficult due to the lacking of specific antibodies toward H1 variants. In this dissertation, I have generated a knock-in system in ESCs and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d ,and H1e causes pericentric chromocenter clustering and de-repression of major satellites. Collectively, these results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and demonstrate significant changes at pericentric heterochromatin upon depletion of this epigenetic mark.