Peripheral nerves have demonstrated the ability to bridge gaps of up to 6 mm. Peripheral Nerve System injury sites beyond this range need autograft or allograft surgery. Central Nerve System cells do not allow spontaneous regeneration due to the intrinsic environmental inhibition. Although stem cell therapy seems to be a promising approach towards nerve repair, it is essential to use the distinct three-dimensional architecture of a cell scaffold with proper biomolecule embedding in order to ensure that the local environment can be controlled well enough for growth and survival. Many approaches have been developed for the fabrication of 3D scaffolds, and more recently, fiber-based scaffolds produced via the electrospinning have been garnering increasing interest, as it offers the opportunity for control over fiber composition, as well as fiber mesh porosity using a relatively simple experimental setup. All these attributes make electrospun fibers a new class of promising scaffolds for neural tissue engineering. Therefore, the purpose of this doctoral study is to investigate the use of the novel material PGD and its derivative PGDF for obtaining fiber scaffolds using the electrospinning. The performance of these scaffolds, combined with neural lineage cells derived from ESCs, was evaluated by the dissolvability test, Raman spectroscopy, cell viability assay, real time PCR, Immunocytochemistry, extracellular electrophysiology, etc. The newly designed collector makes it possible to easily obtain fibers with adequate length and integrity. The utilization of a solvent like ethanol and water for electrospinning of fibrous scaffolds provides a potentially less toxic and more biocompatible fabrication method. Cell viability testing demonstrated that the addition of gelatin leads to significant improvement of cell proliferation on the scaffolds. Both real time PCR and Immunocytochemistry analysis indicated that motor neuron differentiation was achieved through the high motor neuron gene expression using the metabolites approach. The addition of Fumaric acid into fiber scaffolds further promoted the differentiation. Based on the results, this newly fabricated electrospun fiber scaffold, combined with neural lineage cells, provides a potential alternate strategy for nerve injury repair.

Orientador: Henrique Marques Barbosa de Souza / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T10:31:42Z (GMT). No. of bitstreams: 1 Rosa_VivianedeSouza_M.pdf: 2727894 bytes, checksum: d0d5ab88ca9670f3109f39586f01a78c (MD5) Previous issue date: 2015 / Resumo: Células-tronco embrionárias (CTE) são células indiferenciadas que possuem a capacidade de (1) se proliferarem indefinidamente (auto-renovação) e, quando induzidas, (2) darem origem a qualquer tipo celular presente no embrião (pluripotência). Uma das abordagens mais comumente utilizadas para o estudo de diferenciação de CTE é através da formação de agregados multicelulares esféricos denominados corpos embrióides (CE). CE passam por um processo de morfogênese semelhante ao observado em embriões, originando derivados dos três folhetos germinativos. Durante o desenvolvimento embrionário, a formação e o posicionamento dos três folhetos ocorre por um processo altamente coordenado que culmina na formação de um embrião polarizado no eixo anteroposterior. Entretanto, um dos grandes desafios de pesquisas que envolvem o uso da diferenciação de CTE em CE é encontrar indícios de que esses processos são recapitulados in vitro e se entender como que células derivadas dos folhetos germinativos, que no embrião ocorrem de forma altamente organizada, são originadas em estruturas celulares sem nenhuma organização global evidente, como visto em CE. Coup-TFII (Chicken ovalbumin upstream promoter-transcription factor II) é um fator de transcrição o qual possui um papel fundamental na regulação do desenvolvimento embrionário e na aquisição de destinos celulares específicos durante a diferenciação de CTE. Utilizando CE como um modelo de estudo, caracterizamos a expressão de Coup-TFII e seu possível envolvimento durante a determinação de destinos celulares. Nossos resultados identificaram uma expressão hemisférica de Coup-TFII em CE em etapas inicias do processo de diferenciação. Esta observação nos levou a caracterizar a distribuição espacial de marcadores moleculares tecido-específicos nos CE em relação à expressão hemisférica de Coup-TFII. Interessantemente, praticamente todas as células identificadas como precursores mesodérmicos e precursores neuroectodérmicos, através da expressão de Brachyury-T e Nestin, respectivamente, estão contidas nas população de células Coup-TFII-positivas. Estes resultados sugerem a existência de um mecanismo de organização global intrínseco nas CTE, onde a expressão de Coup-TFII parece segregar os CE em dois hemisférios e, provavelmente de forma antagônica com Oct4, determinaria diferentes destinos celulares ainda em fases iniciais da diferenciação / Abstract: Embryonic stem cells (ESC) are undifferentiated cells that have the ability to (1) proliferate indefinitely (self-renewal) and when induced, (2) give rise to any cell type present in the embryo (pluripotency). One of the most commonly used approaches for the study of ESC differentiation is through the formation of spherical multicellular aggregates called embryoid bodies (EB). EB undergo a process similar to that observed in morphogenesis embryos, giving derivatives of three germ layers. During embryonic development, formation and placement of the three germ layers is a highly coordinated process by which culminates in the formation of a polarized embryo in the antero-posterior axis. However, one of the great challenges of research involving the use of ESC differentiation in EB is to find evidence that these processes are recapitulated in vitro and in understanding how to cells derived from the germ layers that occurs in the embryo highly organized manner originate on cellular structures with no apparent global organization, as seen in the EB. COUP-TFII (chicken ovalbumin promoter-upstream transcription factor II) is a transcription factor which plays a key role in the regulation of embryonic development and determination of specific cell fates during differentiation ESC. Using EB as a model system, we characterized the expression of Coup-TFII and its possible involvement in the determination of cell fates. Our results identified a hemispheric expression of Coup-TFII in EB at the onset of differentiation. This observation led us to characterize the spatial distribution of tissue-specific molecular markers in EB in relation the hemispheric expression of Coup-TFII. Interestingly, practically all cells identified as mesodermal and neuroectodermal precursors by the expression of Brachyury-T and Nestin, respectively, are contained in the COUP-TFII-positive cell population. These results suggest the existence of a mechanism of global organization intrinsic to ESC, where the expression of Coup-TFII segregates the EB into two hemispheres and probably antagonistically with Oct4, determine different cell fates still in early stages of differentiation / Mestrado / Biologia Tecidual / Mestra em Biologia Celular e Estrutural

A metilação do DNA em mamíferos é uma importante modificação epigenética, sendo essencial no silenciamento de DNAs repetitivos, de regiões que sofrem imprinting genômico e no estabelecimento do cromossomo X inativo em fêmeas. Existem 5 tipos de DNA Metiltransferases, tendo a DNMT3B um importante papel na metilação de novo. A MeCP2, por sua vez, é uma proteína capaz de reconhecer sítios de DNA metilados e recrutar proteínas responsáveis pela desacetilação das histonas. Isto provoca alterações na conformação da cromatina, impedindo a transcrição gênica. Alterações nos padrões de expressão de DNMT3B e na metilação do DNA encontradas em diferentes tipos de tumores, e a temporalidade de expressão de Dnmt3b e de Mecp2 durante ondas de desmetilação e de metilação que ocorrem no início do desenvolvimento embrionário, podem auxiliar na identificação de fatores envolvidos no estabelecimento e manutenção do padrão de metilação do DNA, os quais ainda são pouco conhecidos. Por sua vez, uma nova classe de pequenos RNAs, os microRNAs, envolvidos com a regulação da expressão gênica pós-transcricional, têm grande importância na manutenção do estado diferenciado de diferentes tipos celulares. Trabalhos recentes demonstram também que há alterações nos padrões de expressão de microRNAs entre tecidos normais e tumorais. Assim, é objetivo deste trabalho a identificação de possíveis miRNAs envolvidos na modulação da expressão dos genes DNMT3B/Dnmt3b e MeCP2/Mecp2 em diferentes linhagens de células normais e tumorais, bem como, em células tronco embrionárias humanas e murinas submetidas à diferenciação. / DNA methylation in mammals is an important epigenetic modification, playing an essential role in the silencing of repetitive DNA, in genomic imprinting and, in females, the establishment of X chromosome inactivation. There are 5 DNA metyhltransferases, and one of them, DNMT3B has an important role in de novo methylation. MeCP2, by its turn, is a protein capable of recognizing methylated DNA sites and of recruiting proteins responsible for histones deacetylation. This causes alterations in chromatin conformation, therefore inhibiting gene transcription. Changes in the expression patterns of DNMT3B and in DNA methylation are found in several types of tumors, and temporal expression of Dnmt3b and Mecp2 during global demetyhlation and de novo methylation waves, which occur in early embryonic development, could give a better understanding of the factors involved in the establishment and maintenance of DNA methylation patterns, which are still largely unkown. Additionally, a new class of small RNAs, the microRNAs, involved in the post-transcriptional gene silencing, has great importance in maintaining the differentiated state of several cell types. Recent studies have demonstrated alterations in miRNAs expression patterns between normal and tumor tissues. Thus, the aim of this work was to identify possible miRNAs involved in the modulation of Dnmt3b and Mecp2 RNAs in different normal and tumoral cell lines, as well as in human and murine embryonic stem cells and their respectively differentiated embryoid bodies.

Les complexes des pores nucléaires (NPCs) sont des assemblages protéiques ancrés dans l’enveloppe nucléaire (EN) qui permettent et régulent les échanges entre le cytoplasme et le noyau. Au-delà de leur fonction de transport, plusieurs sous unité des NPCs (les nucléoporines, Nups) jouent un rôle important dans d’autres processus cellulaire tels que la division cellulaire et la différenciation. Le complexe-Y, composé de 9 Nups distincte, dont Nup133, représente une sous unité structurale des NPCs. Cependant, une fraction de ce complexe est localisée aux kinétochores (KTs) durant la mitose, où il est requis pour la ségrégation des chromosomes. Cette localisation aux KTs dépend du complexe Ndc80 mais également de Cenp-F. Par ailleurs, l’interaction Nup133/Cenp-F s'effectue aussi au niveau de l'EN en prophase, ce qui permet le recrutement de la dynéine, étape requise pour l’ancrage des centrosomes à l’EN dans les cellules HeLa et pour la migration du noyau vers le centrosome dans les progéniteurs neuronaux de cerveau de rat. Des études développementales chez la souris ont précédemment identifié le mutant merm qui meurt en milieu de gestation (E10.5). Bien que la mutation merm entraine l’absence de Nup133, la prolifération des cellules souches embryonnaires (mESCs) dérivées de blastocystes merm (Nup133-/-) n’est pas altérée. Cependant l’absence de Nup133 altère la différenciation des mESCs, notamment en neurones post-mitotique. Ce projet de thèse visait à comprendre les mécanismes moléculaires par lesquels Nup133 contribue à la division et la différenciation cellulaire. Afin de caractériser le phénotype des mESCs Nup133-/-, nous avons utilisé deux protocoles de différenciation in vitro, vers une voie neuroectodermale ou mésoendodermale. Cette étude a montré que le nombre de cellules est fortement diminué chez le mutant Nup133-/- comparé aux cellules contrôles lors de la différenciation des mESCs. Cependant les mESCs Nup133-/- qui survivent montrent, comme les mESCs contrôles, une diminution de l’expression des marqueurs de pluripotence et une augmentation des marqueurs de différentiation. L’analyse par cytométrie de flux n’a pas révélé d'altération majeure dans la progression du cycle cellulaire mais à mis en évidence une augmentation de la mort cellulaire lors de la différenciation des mESCs Nup133-/-. Afin de déterminer les domaines de Nup133 requis pour la différenciation des mESCs, nous avons développé une stratégie de sauvetage en établissant des lignées mESCS Nup133-/- qui expriment de manière stable GFP-Nup133, différentes délétions de Nup133 qui n’altèrent pas sa localisation au NPCs (GFP-Nup133DN, DMid, et DC) ou la GFP seule comme contrôle. Des études fonctionnelles ont indiqué que le domaine N-ter (NTD) de Nup133 est requis pour la différenciation des mESCs.Le seul partenaire identifié de Nup133-NTD étant Cenp-F, j’ai décidé de déterminer si l’interaction Nup133/Cenp-F jouait un rôle dans la différenciation des mESCs. En collaboration avec l’équipe de R. Guerois, nous avons simulé in silico l’interaction de Nup133-NTD avec un peptide de Cenp-F que nous avions identifié dans des cribles en double hybride. Cette modélisaton nous a permis de concevoir des mutants affectant la surface d’interaction Nup133/Cenp-F. Nous avons montré que ces mutations empêchent la localisation de Cenp-F à l’EN sans altérer sa présence aux KTs. J’ai également utilisé la stratégie de sauvetage décrite plus haut, pour étudier un mutant de Nup133 qui empêche son interaction avec Cenp-F. Cette étude a montré que l’interaction Nup133/Cenp-F n'est pas requise pour la différenciation in vitro des mESCs. L’étude de Cenp-F a été complétée par la caractérisation d’une mutation de Cenp_F qui affecte sa localisation aux KTs. Nous avons montré que cette mutation altère l’interaction entre Cenp-F et Bub1 mais sans affecter celle avec Nup133. Cette étude a ainsi permis d'identifier Bub1 comme un partenaire direct de Cenp-F requis pour son ancrage aux KTs. / Nuclear pores complexes (NPCs) are macromolecular assemblies anchored in the nuclear envelope (NE) providing the gates that allow and regulate all exchanges between the nucleus and the cytoplasm. Beyond their function in transport, several NPC subunits, the nucleoporins (Nups), have been demonstrated to also play important roles in other cellular processes including cell division and differentiation.The Y-complex, composed of 9 distinct Nups, including Nup133, represents a major structural subunit stably bound to both the cytoplasmic and nuclear faces of the NPCs. Beyond its structural role at nuclear pores, the Y-complex localizes at kinetochores in mitosis, where it is required for chromosome segregation. This kinetochores localization relies on the Ndc80 complex, but also on Nup133/Cenp-F interaction. The Nup133/Cenp-F interaction also contributes to the recruitment of dynein to the NE, a process that is required for the correct centrosomes tethering at the NE in prophase HeLa and for the migration of the nucleus towards the centrosomes prior to mitotic entry in rat brain progenitor cells.Developmental studies previously identified the mouse merm mutant that dies in midgestation (E10.5). In collaboration with the team of E. Lacy, the team of V. Doye showed that the merm mutation leads to the absence of Nup133. Importantly this study further revealed that self-renewal is not impaired in embryonic stem cells (mESCs) derived from merm (Nup133-/-) blastocyst. However, the lack of Nup133 impairs mESC differentiation into postmitotic neurons. How Nup133 contributes to ESCs differentiation remains however unknown.This PhD project aimed at understanding the cellular mechanisms explaining Nup133 contribution to cell division and differentiation.To characterize Nup133-/- mESCs differentiation phenotype, we used two distinct in vitro differentiation protocols, towards either neuroectodermal or mesoendodermal fate. This study revealed that cell number was strongly decreased in Nup133-/- relative to WT in mESC differentiation. However, the few Nup133-/- mESCs that survived displayed, as WT mESCs, a decreased expression of pluripotency markers and acquired differentiated state based on marker expression. FACS analyses did not reveal any major alteration of cell cycle progression but showed increased cell death upon differentiation.To determine which domain of Nup133 is critical for mESC differentiation, we developed a “rescue strategy” using Nup133 alleles deleted for structurally defined domains. Therefore, we established Nup133-/- mESC lines stably expressing GFP-Nup133, GFP-Nup13-ΔN, different ΔC-ter domain (that did not impair the binding of Nup133 to the NPC) or GFP alone as control. Functional studies indicated that while full length and C-ter deleted Nup133 rescue Nup133-/- ESCs defect in differentiation, Nup133-ΔN does not.The only identified partner of Nup133-NTD is Cenp-F. In view of the role of Nup133-NTD in mESC differentiation, I decided to determine if Nup133/Cenp-F interaction contributes to mESC differentiation. In collaboration with R. Guerois' team we simulated in silico the interaction of Nup133-NTD with a short peptide of Cenp-F that we previously identified using yeast-2-hybrid (Y2H) screens. We could thereby design mutants affecting Nup133/Cenp-F contact and show that they prevent Cenp-F localization to the nuclear envelope without altering its kinetochore localization. I then used the “rescue strategy” described above to study a Nup133 mutant specifically impairing its interaction with Cenp-F. This analysis revealed that Nup133/Cenp-F interaction is dispensable for in vitro mESC differentiation. This study on Cenp-F was completed by the characterization of a mutation within an adjacent leucine zipper affecting Cenp-F targeting to kinetochores. We evidenced that this mutation impairs Cenp-F interaction with Bub1 but not with Nup133, identifying Bub1 as a direct kinetochore tether of Cenp-F.

The following work examines the mechanisms by which Tip60-p400 chromatin remodeling complex regulates gene expression in embryonic stem cells (ESCs). Tip60-p400 complex has distinct functions in undifferentiated and differentiated cells. While Tip60-p400 is often associated with gene activation in differentiated cells, its most prominent function in ESCs is to repress differentiation-related genes. I show that Tip60-p400 interacts with Hdac6 and other proteins to form a unique form of the complex in ESCs. Tip60-Hdac6 interaction is stem cell specific and is necessary for Tip60-p400 mediated gene regulation, indicating that Tip60- p400 function is controlled in part through the regulation of Hdac6 during development. Furthermore, I find that Hdac6 is required for the binding of Tip60- p400 to many of its target genes, indicating Hdac6 is necessary for the unique function of Tip60-p400 in ESCs. In addition to accessory proteins like Hdac6, Tip60-p400 also interacts with thousands of coding and noncoding RNAs in ESCs. I show that R-loops, DNA-RNA hybrids formed during transcription of many genes, are important for regulation of chromatin binding by at least two chromatin regulators (Tip60-p400 and PRC2). This finding suggests that transcripts produced by many genes in ESC may serve as a signal to modulate binding of chromatin regulators. However, R-loops might also function to regulate chromatin architecture in differentiated cells as well. Future studies based on this work will be necessary to understand the full repertoire of cell types and chromatin regulators regulated by these structures.

Cell proliferation and differentiation are tightly regulated processes required for the proper development of multi-cellular organisms. To understand the effects of cell proliferation on embryo patterning in mice, we inactivated Aurora A, a gene essential for completion of the cell cycle. We discovered that inhibiting cell proliferation leads to different outcomes depending on the tissue affected. If the epiblast, the embryonic component, is compromised, it leads to gastrulation failure. However, when Aurora A is inactivated in extra-embryonic tissues, mutant embryos fail to properly establish the anteroposterior axis. Ablation of Aurora A in the epiblast eventually leads to abnormal embryos composed solely of extra-embryonic tissues. We took advantage of this phenomenon to generate embryonic stem (ES) cell-derived mice. We successfully generated newborn pups using this epiblast ablation chimera strategy. Our results highlight the importance of coordinated cell proliferation events in embryo patterning. In addition, epiblast ablation chimeras provide a novel in vivo assay for pluripotency that is simpler and more amenable to use by stem cell researchers.

Indiana University-Purdue University Indianapolis (IUPUI) / CXXC finger protein 1 (Cfp1), a component of the Set1 histone methyltransferase complex, is a critical epigenetic regulator of both histone and cytosine methylation. Murine embryos lacking Cfp1 are unable to gastrulate and Cfp1-null embryonic stem (ES) cells fail to undergo cellular differentiation in vitro. However, expression of wild type Cfp1 in Cfp1-null ES cells rescues differentiation capacity, suggesting that dynamic epigenetic changes occurring during lineage specification require Cfp1. The domain structure of Cfp1 consists of a DNA binding CXXC domain and an N-terminal plant homeodomain (PHD). PHDs are frequently observed in chromatin remodeling proteins, functioning as reader modules for histone marks. However, the histone binding properties and underlying functional significance of Cfp1 PHD are largely unknown. My research revealed that Cfp1 PHD directly and specifically binds to histone H3K4me1/me2/me3 marks. A point mutation that abolishes binding to methylated H3K4 (W49A) does not affect rescue of cellular differentiation, but, point mutations that abolish both methylated H3K4 (W49A) and DNA (C169A) binding result in defective in vitro differentiation, indicating that PHD and CXXC exhibit redundant functions. The mammalian liver has the unique ability to regenerate following injury. Previous studies indicated that Cfp1 is essential for hematopoiesis in zebrafish and mice. I hypothesized that Cfp1 additionally plays a role in liver development and regeneration. To understand the importance of Cfp1 in liver development and regeneration, I generated a mouse line lacking Cfp1 specifically in the liver (Cfp1fl/fl Alb-Cre+). Around 40% of these mice display a wasting phenotype and die within a year. Livers of these mice have altered global H3K4me3 levels and often exhibit regenerative nodules. Most importantly, livers of these mice display an impaired regenerative response following partial hepatectomy. Collectively, these findings establish Cfp1 as an epigenetic regulator essential for ES cell function and liver homeostasis and regeneration.

Within many communities and religions, including the LDS community, there is some controversy surrounding the use of stem cells – particularly embryonic stem cells (ESC). Much of this controversy arises from confusion and misconceptions about what stem cells actually are, where they come from , and when life begins. The theology of the Church of Jesus Christ of Latter-day Saints has interesting implications for the last of these considerations, and it becomes less a question of “when does life begin” and more an exploration of “when does personhood begin” or “when does the spirit enter the body.” With no official Church stance, statements from Church leaders vary on this topic, and this first section of the thesis explores the philosophical and practical meaning of personhood with a biological background intended for those not familiar with the origin or uses of stem cells.The second portion of the thesis explores possible cloning technologies. Recent events and advances address the possibility of cloning endangered and extinct species. The ethics of these types of cloning have considerations uniquely different from the type of cloning commonly practiced. Cloning of cheetahs (and other endangered or vulnerable species) may be ethically appropriate, given certain constraints. However, the ethics of cloning extinct species varies; for example, cloning mammoths and Neanderthals is more ethically problematic than conservation cloning, and requires more attention. Cloning Neanderthals in particular is likely unethical and such a project should not be undertaken. It is important to discuss and plan for the constraints necessary to mitigate the harms of conservation and extinct cloning, and it is imperative that scientific and public discourse enlighten and guide actions in the sphere of cloning.

Die dreidimensionale Organisation des Chromatins verändert sich während der Zelldifferenzierung als Reaktion auf die Umgebung und ist bei Krankheiten oftmals verändert. Das Zusammenspiel zwischen Chromatinzustand, Chromatinorganisation und Genexpression ist insbesondere bei Neuronen nach wie vor nur geringfügig erforscht. In dieser Arbeit untersuchte ich die Organisation und den Zustand des Chromatins im Zusammenhang mit der Transkription in embryonalen Stammzellen (ESCs) und dopaminergen Neuronen (DNs) der Maus. Dazu habe ich die Organisation des Chromatins mittels Genome Architecture Mapping (GAM) bestimmt und zelltypspezifische Genexpressionsprofile zur Klassifizierungen von Promotoren, Enhancern und Super-Enhancern (SEs) erzeugt. Anschließend habe ich diese linearen Chromatinprofile mit den verschiedenen Stufen der Chromatinorganisation kombiniert und konnte so Unterschiede zwischen den 3D-Genomstrukturen von ESCs und DNs aufzeigen. Zudem konnte ich verstärkt Dreifach-Wechselwirkungen zwischen zelltypspezifischen SEs und/oder exprimierten Genen nachweisen, die bei DNs besonders oft neuronale Signalgene darstellen und oftmals bei neurologischen Störungen betroffen sind. Ich fand auch heraus, dass die Grenzen topologisch assoziierter Domänen (TADs) oft mit Genen zur zellulären Differenzierung zusammen fallen und zudem zelltyp-spezifische Eigenschaften aufweisen, was von Bedeutung für zukünftige funktionelle Untersuchungen solcher Grenzen sein dürfte. Schließlich konnte ich zeigen, dass Chromatinkompartimente zwischen ESCs und DNs in Abhängigkeit vom Chromatinzustands und der Chromatinexpression variieren und dass eine Gruppe transkriptionell aktiver DN Gene, die für die neuronale Aktivität wichtig sind, in B-Kompartimenten liegt. Mit diesen neuen Erkenntnissen erweitert meine Arbeit das Verständnis der Chromatinorganisation bei der Regulierung der Genexpression in Maus ESCs und DNs. / The three-dimensional organization of chromatin changes during cell differentiation, in response to the environment, and is often altered in disease. The interplay between chromatin state, chromatin organization and gene expression remains poorly understood, particularly in neurons. In this work, I examined the organization and state of chromatin associated with transcription in mouse embryonic stem cells (ESCs) and dopaminergic neurons (DNs). To do this, I determined the organization of chromatin using genome architecture mapping (GAM) and generated cell type-specific gene expression profiles to classify promoters, enhancers and super-enhancers (SEs). I then combined these linear chromatin profiles with the different levels of chromatin organization and was able to show differences between the 3D genome structures of ESCs and DNs. In addition, I was able to demonstrate increased triple interactions between cell type-specific SEs and/or expressed genes, which are often neuronal signalling genes in DNs and affected in neurological disorders. I also found that the boundaries of topologically associated domains (TADs) often coincide with cellular differentiation genes and also exhibit cell type-specific properties, which may be important for future functional studies of such boundaries. Finally, I was able to show that chromatin compartments between ESCs and DNs vary depending on chromatin state and chromatin expression, and that a group of transcriptionally active DN genes important for neuronal activity are located in B compartments. With these new findings, my work expands the understanding of chromatin organization in regulating gene expression in mouse ESCs and DNs.

No description available.