Identification of transcription factors that interact with Arid4b protein in mouse embryonic stem cells

Keskin, Ezgi Gül
Embryonic development is a process that is highly regulated at the level of gene expression. Throughout this process, the zygote divides and differentiates to form all cell types in the adult body. In the early stages of development, pluripotent embryonic stem cells (ESC) can be isolated and used to study cell fate mechanisms during development in vitro. The pluripotency of ESCs is governed by certain transcription factors (TF) (Oct4, Nanog, etc.). These TFs construct a transcription network specific to ESC and enable the high and stable expression of pluripotency genes. Chromatin factors work alongside TFs to maintain pluripotency. In our previous studies, we have identified Arid4b protein in the Sin3a corepressor complex is critical for proper ESC differentiation into mesoderm and endoderm lineages. Arid4b might direct the Sin3a complex to the ESC differentiation related genes with the aid of its histone modification and DNA binding domains. Histone deacetylases in the complex is critical for the suppression of gene expression. To better understand the role of Arid4b protein in ESC differentiation, we examined the histone 3 lysine 27 acetylation (H3K27Ac) genome-wide distribution in wildtype and arid4bΔ mesoderm or endoderm differentiated cells. H3K27Ac is a marker of active enhancer regions as well as active promotor regions. We found that the higher level of H3K27Ac in the arid4bΔ cells when compared to wildtype cells. Therefore, Sin3a complex may be required for the suppression of these genes during ESC differentiation. Upon bioinformatics analyses, we identified TF consensus binding sequences enriched in the regions with increased H3K27Ac levels in arid4bΔ cells. We analyzed the mRNA expression level of 10 such TFs in WT and arid4bΔ ESCs. We further validated the protein expression of selected TFs. Of these, we showed that Tfap2c physically interacts with Arid4b and Sin3a in ESCs through endogenous coimmunoprecipitation experiments.


Identification of protein partners of setd3 in mouse embryonic stem cells
Güven, Gözde; Terzi Çizmecioğlu, Nihal; Department of Molecular Biology and Genetics (2021-1-26)
Embryonic development is a highly coordinated process that contains rapid cell divisions. During this time, the cells also start differentiation, and at the end of development, the cells become fully differentiated. This differentiation commitment is regulated by epigenetic factors like histone modifiers, chromatin regulators. SETD3 is one of the histone methyltransferases that govern this pluripotency-differentiation balance. We have previously found that SETD3 is crucial for mesendoderm differentiation of...
Identification and analysis of genomic regions with large between-population differentiation in humans
Myles, S.; Tang, K.; Somel, Mehmet; Green, R. E.; Kelso, J.; Stoneking, M. (Wiley, 2008-01-01)
The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that...
Arid4b physically interacts with Tfap2c in mouse embryonic stem cells
Keskin, Ezgi Gul; Huang, Jialiang; Terzi Çizmecioğlu, Nihal (2021-01-01)
Precise regulation of gene expression is required for embryonic stem cell (ESC) differentiation. Transcription factor (TF) networks coordinate the balance of pluripotency and differentiation in response to extracellular and intracellular signals. Chromatin factors work alongside TFs to achieve timely regulation of gene expression for differentiation process. Our previous studies showed that a member of the Sin3a corepressor complex, Arid4b, is critical for proper mouse ESC differentiation into mesoderm and ...
Evaluating Oxygen Tensions Related to Bone Marrow and Matrix for MSC Differentiation in 2D and 3D Biomimetic Lamellar Scaffolds
Sayin, Esen; Baran, Erkan Turker; Elsheikh, Ahmed; Mudera, Vivek; Cheema, Umber; Hasırcı, Vasıf Nejat (2021-04-01)
The physiological O-2 microenvironment of mesenchymal stem cells (MSCs) and osteoblasts and the dimensionality of a substrate are known to be important in regulating cell phenotype and function. By providing the physiologically normoxic environments of bone marrow (5%) and matrix (12%), we assessed their potential to maintain stemness, induce osteogenic differentiation, and enhance the material properties in the micropatterned collagen/silk fibroin scaffolds that were produced in 2D or 3D. Expression of ost...
Ayaz, E. Serdar; Can, Tolga (2011-05-05)
RNAi system allows us to see the phenotypes when some genes are removed from living cells. By observing these phenotypes, we can build signaling pathways without dealing with the chemistry inside the cell. However it is costly in terms of time and space complexity. Furthermore, there are some interactions RNAi data cannot distinguish that results in many different signaling pathways all of which are consistent with the RNAi data. In this paper, we combine genetic algorithms with some greedy approaches to fi...
Citation Formats
E. G. Keskin, “Identification of transcription factors that interact with Arid4b protein in mouse embryonic stem cells,” Thesis (M.S.) -- Graduate School of Natural and Applied Sciences. Molecular Biology and Genetics, Middle East Technical University, 2019.