No description available.

Synaptogenesis is a critical process in the establishment of neuronal connectivity during brain development. The key step is to transduce external stimuli into the internal signaling cascades. Cell adhesion molecules and scaffold proteins facilitate the transduction to achieve optimal connectivity through PDZ domain mediated interaction. FRMPD2, a product of a human-specific multi-copy gene with three PDZ domains, has been shown to localize to the tight junctions in epithelial cells, suggesting a role in inter-cellular interaction. Although the correlation between neurodevelopmental disorders and gene dosage alteration of FRMPD2 has been observed, its role in the nervous system remains unknown. Therefore, I investigated the role of FRMPD2 in neurodevelopment. I found that FRMPD2 localizes at the excitatory synapses and promotes synaptogenesis in rat neurons. Mechanistically, FERM domain is required for synaptic localization of FRMPD2 through the interaction with F-actin in spines. More importantly, I found that FRMPD2 associates with cell adhesion molecule Neuroligin-1 through PDZ domain mediated interaction, resulting in an increase in Neuroligin-1 surface expression and up-regulation of synaptogenesis. Results from in utero electroporation showed that overexpression of FRMPD2 in mouse brains delayed neuronal migration and increased dendritic arborization and spine formation. Remarkably, viral overexpression of FRMPD2 in mouse brains improved memory retention. Abnormalities in synaptogenesis during neurodevelopment can cause neurodevelopmental disorders, such as Autism Spectrum Disorders (ASDs). Genomic studies from cohorts of ASD patients have revealed the prevalence of dysfunctional genes in the ubiquitin-proteasome pathway, especially the E3 ligases, suggesting the E3 ligase as a key component in ASD pathogenesis. Genomic duplication or deletion of PARK2 gene, a E3 ligase gene, has been identified in ASD patients. Therefore, I explored the autistic phenotypes of the Park2 knockout (KO) mice. Indeed, the KO mice demonstrated features of typical ASD behaviors. Further, Park2 KO mice showed a reduction in spine number, dendritic arborization, and levels of neuronal activity. The alterations in synaptic property in Park2 KO mice may serve as the etiological factor for ASD. These findings provide insights into the role of a novel synaptic organizer scaffold protein for synapse formation during brain development, and a novel ASD model. / 2020-11-12T00:00:00Z

Development of the central nervous system requires the precise coordination of intrinsic genetic programs to instruct cell fate, synaptic connectivity and function. The MEF2 family of transcription factors (TFs) plays many essential roles in neural development; however, the mechanisms of gene regulation by MEF2 in neurons remain unclear. This dissertation focuses on the molecular mechanisms by which MEF2 binds to the genome, activates enhancers, and regulates gene expression within the developing nervous system. We find that one MEF2 family member in particular, MEF2D, is an essential regulator of the development and function of retinal photoreceptors, the primary sensory neurons responsible for vision. Despite being expressed broadly across many tissues, in the retina MEF2D binds to retina-specific enhancers and regulates photoreceptor-specific transcripts, including critical retinal disease genes. Functional genome-wide analyses demonstrate that MEF2D achieves tissue-specific binding and action through cooperation with a retina-specific TF, CRX. CRX recruits MEF2D away from canonical MEF2 binding sites by promoting MEF2D binding to retina-specific enhancers that lack a strong consensus MEF2 binding sequence. MEF2D and CRX then synergistically co-activate these enhancers to regulate a cohort of genes critical for normal photoreceptor development. These findings demonstrate that MEF2D, a broadly expressed TF, contributes to retina-specific gene expression in photoreceptor development by binding to and activating tissue-specific enhancers cooperatively with CRX, a tissue-specific co-factor. A major unresolved feature of MEF2D function in the retina is that the number of MEF2D binding sites significantly exceeds the number of genes that are dependent on MEF2D for expression. We investigated causes of this discrepancy in an unbiased manner by characterizing the activity of MEF2D-bound enhancers genome-wide. We find that many MEF2D-bound enhancers are inactive. Furthermore, less than half of active MEF2D-bound enhancers require MEF2D for activity, suggesting that significant redundancies exist for TF function within enhancers. These findings demonstrate that observed TF binding significantly overestimates direct TF regulation of gene expression. Taken together, our results suggest that the broadly expressed TF MEF2D achieves tissue specificity through competitive recruitment to enhancers by tissue-specific TFs and activates a small subset of enhancers to regulate genes.

Pediatric acute lymphoblastic leukemia (ALL) is the most common malignancy in children, which results from the malignant transformation of progenitor cells in the bone marrow into leukemic cells. The precise mechanisms for this transformation are not well defined, however recent studies suggest that aberrant regulation of gene expression or DNA methylation may play an important role. Hence, the aim of this thesis was to use novel methods to investigate genome-wide gene expression and DNA methylation patterns in a large collection of primary ALL cells from pediatric patients. With these studies, we aimed to increase the understanding of factors that regulate gene expression and DNA methylation in ALL. In the first study of the thesis we found that data obtained from genome-wide digital gene expression analysis enabled excellent cytogenetic subtype-specific classification of ALL cells and revealed new features of gene expression within the disease, such as prevalent antisense transcription and alternative polyadenylation. In the second study we used technology developed for large-scale single nucleotide polymorphism (SNP) genotyping for quantitative analysis of allele-specific gene expression (ASE), revealing widespread ASE in ALL cells. Analysis of DNA methylation in promoter regions of the genes displaying ASE using DNA-microarrays revealed frequent regulation of gene expression by DNA methylation. In the third study, using the same DNA methylation array, we identified differences in the DNA methylation patterns in ALL cells at diagnosis compared to healthy mononuclear cells from the bone marrow of the same children at remission. In the fourth study we measured the DNA methylation of >450,000 CpG sites across the genome in a large collection of ALL samples and non-leukemic control cells. We found that ALL cells displayed highly divergent DNA methylation patterns depending on their cytogenetic subtype and widespread regions of differential methylation were enriched for repressive histone marks. DNA methylation levels at distinct regions in the genome were substantially increased at relapse compared to matched cells from diagnosis. Collectively, the results presented in this thesis provide new insights into the patterns of gene expression and epigenetic changes in ALL and further increase our understanding of the development and progression of the disease, which will hopefully lead to better treatment options in the future.

Abstract Clarification of the mechanisms of cardiac-specific gene expression provides not only basic knowledge about how the gene expression is regulated in the heart, but also about the changes in the gene expression during the development of cardiovascular diseases. The purpose of this study was to analyze the mechanisms of cardiac chamber-specific gene expression and cardiac gene activation induced by mechanical load. In the present study, the experiments were carried out by using two cardiac genes, salmon cardiac peptide (sCP) and rat B-type natriuretic peptide (BNP) genes as models. sCP was discovered previously in our laboratory and turned out to be extremely cardiac-specific, representing A-type natriuretic peptide characters in an exaggerated way. In neonatal rat cardiomyocytes, the sCP promoter activity was shown to be strictly restricted to atrial cells and the promoter to be inert to cardiac hypertrophy-inducing factors. In order to find out the mechanisms of earlier proved BNP gene activation by mechanical load, BNP promoter activity was studied in vivo in adult rat hearts. The tandem GATA transcription factor binding site at position -80/-91 was shown to be essential for the BNP gene induction by angiotensin II. To clarify the possiblity to transfer the characters of the BNP gene into the sCP gene, short BNP fragments were inserted to the sCP gene promoter. The otherwise atrial-restricted sCP promoter was shown to be switched on in rat ventricular cardiomyocytes by adding a short BNP proximal promoter element to the sCP promoter, preferably near to the transcription start site. This activity was partly dependent on the -80/-91 GATA sites in the BNP promoter. Thus, A-type natriuretic peptide regulation can be switched to B-type regulation by a short proximal BNP promoter element. In conclusion, these studies reveal certain basic differences in cardiac atrial and ventricular gene expression.

Conditions that lead to reversible growth arrest (quiescence), promote the expression of a set of genes called growth arrest specific (GAS) genes. GAS genes play a crucial role in initiating and maintaining the entry into quiescence, while also activating stress responses to help the cell overcome the effects of the stressors. Gene profiling study examining the transcriptome has shown a vast number of genes that are upregulated during quiescence, among them is GEM1 (GTP binding protein overexpressed in skeletal muscle). GEM1 transcripts were elevated 18-fold in response to quiescence. GEM1 is a small monomeric GTPase from the Ras superfamily. It is involved in regulation of cytoskeleton reorganization, and inhibition of voltage gated calcium channels that ultimately prevents hormone secretion. A preliminary study determined that GEM1 is packaged into extracellular vesicles (EV). GEM1 is also reported to promote lipid accumulation and adipogenesis in goat pre-adipocytes. GEM1 is also reported to bind transcription factors that are involved in lipid homeostasis pathways. Thus, it is probable that GEM1 may play a major role in EV formation and/or release, and lipid homeostasis. This study examined the expression of GEM1 at the protein level and validates its candidacy as a GAS gene. We also created two GEM1-shRNA retroviral constructs capable of partially downregulating GEM1 expression which can serve as a molecular tool for further characterizing the function of GEM1 in quiescent CEF. / Thesis / Bachelor of Science (BSc) / GEM1 is a small monomeric GTPase, implicated in a variety of roles in eukaryotes. It plays a role in regulating adipogenesis, and hormone secretion. Most notably it regulates cytoskeleton reorganization in response to changes in calcium concentrations. Gene profiling done by Bédard Lab identified that GEM1 transcripts were highly elevated in reversible growth arrested chicken embryo fibroblasts (CEF). In this study we further explore and characterize the protein expression of GEM1 in quiescent CEF. We also design and test shRNAi retroviral constructs to downregulate GEM1 in quiescent CEF.

No description available.

Em mamíferos a inativação do cromossomo X (ICX) consiste no silenciamento gênico de um dos dois X presentes nas células somáticas normais das fêmeas, garantindo a compensação de dose transcricional em relação aos machos. Existem duas formas de ICX: aleatória, na qual a escolha do cromossomo X inativado se dá ao acaso (X paterno ou materno); e de maneira completamente desviada, na qual a atividade do cromossomo X dependerá de sua origem parental. Nas fêmeas marsupiais a inativação ocorre de forma completamente desviada, sendo o X paterno preferencialmente inativado em todas as células, já nas células embrionárias de eutérios, o que se observa é a ICX aleatória. Entretanto, naquelas células que darão origem aos tecidos extra-embrionários, de camundongos e bovinos, a ICX se dá de forma equivalente à dos marsupiais, ou seja, o X paterno é preferencialmente inativado. Há mais de 30 anos o padrão de ICX em tecidos extra-embrionários humanos tem sido alvo de intenso debate. A crítica que se faz aqui é que tais estudos foram realizados com base na expressão de apenas um ou dois genes ligados ao X com amostras de tecidos extra-embrionários em diferentes idades gestacionais e, por vezes, em poucas amostras, o que deve ter levado às contradições entre as conclusões. O diferencial deste trabalho foi a utilização de técnicas de genotipagem de SNPs presentes em regiões codificadoras, para analisar o padrão de atividade alelo-específica de um grande número de genes presentes ao longo de todo o cromossomo X, gerando um panorama mais representativo da ICX em placenta humana. Neste estudo é comprovado o padrão aleatório de ICX em placenta humana a termo e demonstrado que este órgão se apresenta como um 65 mosaico em relação à escolha do X inativo. A análise global da atividade gênica no cromossomo X indicou ainda que a manutenção do estado epigenético do X inativo parece ser heterogêneo. Em conjunto, os dados gerados são capazes de explicar as incongruências entre as conclusões previamente publicadas. Este trabalho também ilustra as diferenças nos mecanismos de ICX entre humanos e camundongos e reforça a importância de se avaliar esse tema em outras espécies de mamíferos eutérios na tentativa de se elucidar os processos evolutivos envolvidos na compensação de dose em mamíferos / Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 23 X-linked genes, including XIST, using 28 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this chromosome-wide analysis indicated heterogeneous maintenance of the epigenetic state along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals

Em mamíferos a inativação do cromossomo X (ICX) consiste no silenciamento gênico de um dos dois X presentes nas células somáticas normais das fêmeas, garantindo a compensação de dose transcricional em relação aos machos. Existem duas formas de ICX: aleatória, na qual a escolha do cromossomo X inativado se dá ao acaso (X paterno ou materno); e de maneira completamente desviada, na qual a atividade do cromossomo X dependerá de sua origem parental. Nas fêmeas marsupiais a inativação ocorre de forma completamente desviada, sendo o X paterno preferencialmente inativado em todas as células, já nas células embrionárias de eutérios, o que se observa é a ICX aleatória. Entretanto, naquelas células que darão origem aos tecidos extra-embrionários, de camundongos e bovinos, a ICX se dá de forma equivalente à dos marsupiais, ou seja, o X paterno é preferencialmente inativado. Há mais de 30 anos o padrão de ICX em tecidos extra-embrionários humanos tem sido alvo de intenso debate. A crítica que se faz aqui é que tais estudos foram realizados com base na expressão de apenas um ou dois genes ligados ao X com amostras de tecidos extra-embrionários em diferentes idades gestacionais e, por vezes, em poucas amostras, o que deve ter levado às contradições entre as conclusões. O diferencial deste trabalho foi a utilização de técnicas de genotipagem de SNPs presentes em regiões codificadoras, para analisar o padrão de atividade alelo-específica de um grande número de genes presentes ao longo de todo o cromossomo X, gerando um panorama mais representativo da ICX em placenta humana. Neste estudo é comprovado o padrão aleatório de ICX em placenta humana a termo e demonstrado que este órgão se apresenta como um 65 mosaico em relação à escolha do X inativo. A análise global da atividade gênica no cromossomo X indicou ainda que a manutenção do estado epigenético do X inativo parece ser heterogêneo. Em conjunto, os dados gerados são capazes de explicar as incongruências entre as conclusões previamente publicadas. Este trabalho também ilustra as diferenças nos mecanismos de ICX entre humanos e camundongos e reforça a importância de se avaliar esse tema em outras espécies de mamíferos eutérios na tentativa de se elucidar os processos evolutivos envolvidos na compensação de dose em mamíferos / Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 23 X-linked genes, including XIST, using 28 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this chromosome-wide analysis indicated heterogeneous maintenance of the epigenetic state along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals

Conditions which promote reversible growth arrest, such as hypoxia and high cell density, lead to activation of a diverse network of proteins known as growth arrest specific (GAS) genes. Fatty acid binding protein 4 (FABP4), a lipid chaperone involved in the regulation of metabolic and inflammatory responses, has been shown to be part of the GAS program. While the induction of FABP4 in oxygen-deprived environments is well characterized, its functionality and regulation in such conditions remains unclear. In this study, we describe how mis-expression of FABP4 affects cell viability and survival within low oxygen conditions. Loss of FABP4 using shRNA was shown to be associated with a significant increase in oxidative stress and lipid peroxidation, a reduction in lipid droplet formation and a greater incidence of apoptosis. Hypoxia-mediated expression of FABP4 was also found to be positively correlated with cellular levels of C/EBP-beta, an essential activator of p20K in quiescence. FABP4 and p20K are both lipocalins that have been shown to share similar induction patterns and ability to assist in the maintenance of lipid trafficking in cellular stress circumstances. Unexpectedly, the depletion of FABP4 or p20K results in loss of the other in limited oxygen concentrations. This occurs independently of disruption to the broad GAS gene program, suggesting the two proteins may be co-regulated in a shared hypoxic-signalling pathway. C/EBP-beta appears to be the transcriptional activator shared by FABP4 and p20K in quiescence, and the three may be part of an intricate system to sense and respond to reactive oxygen species and lipid radicals. However, the forced expression of either FABP4 or p20K when the other is repressed only moderately restores cell survival through alleviating oxidative stress, indicating the two are both necessary for optimal response to hypoxia. In all, these studies suggest that analogous to the p20K lipocalin, FABP4 plays a critical role in lipid homeostasis and cell survival in conditions of limited oxygen concentrations, and its stimulation is dependent on C/EBP-beta activity. / Thesis / Master of Science (MSc) / A study investigating the role of FABP4 and p20K in conditions of reversible growth arrest with an emphasis on cell survival, lipid homeostasis and mitigating the effects of oxidative stress, and regulation of the two lipocalins by C/EBP-beta.