SETD3-dependent gene expression changes during endoderm differentiation of mouse embryonic stem cells

Balbaşı, Emre
Mouse embryonic stem cells (mESCs) are pluripotent cells that have self renewal capability. They can differentiate into all three primary germ layers: mesoderm, endoderm, and ectoderm during embryonic development. The embryonic development is controlled via spatiotemporal regulation of gene expression changes. The collaborative effects of Wnt, Nodal, BMP signaling pathways help form the primitive streak, and the subsequent definitive endoderm layer in the gastrulating embryo. Deactivation of core pluripotency network, and activation of germ layer specific transcription netwoks are required for this process. This is precisely achieved by chromatin-based regulation. SETD3 is a SET-domain containing methyltransferase that targets both histone and nonhistone proteins. An shRNA screen identified SETD3 as a key factor for mesendoderm commitment of mESCs. Setd3 knock-out mESC cannot upregulate pioneer transcription factors that initiate mesendoderm differentiation in vitro. In this project, we aimed to determine SETD3- dependent gene expression changes during the endoderm differentiation of mouse embyronic stem cells (mESCs) and we performed time-course endoderm differentiation experiments and employed RNA-sequencing to identify differentially expressed genes (DEGs) in the absence of SETD3. Our results indicate a role for SETD3 in timely downregulation of the pluripotent state, and response to key signaling pathways which leads to the delayed and defective differentiation in its absence.


Directed Differentiation of Mouse Embryonic Stem Cells to Mesoderm, Endoderm, and Neuroectoderm Lineages.
Balbasi, Emre; Sezginmert, Dersu; Alganatay, Ceren; Terzi Cizmecioglu, Nihal (2021-10-06)
The self-renewal and pluripotency features of mouse embryonic stem cells (mESCs) make them a great tool to study early mammalian development. Various signaling pathways that shape early mammalian development can be mimicked for in vitro mESC differentiation toward primitive lineages first and more specialized cell types later. Since the precise nature of the molecular mechanisms and the crosstalk between these signaling pathways is yet to be fully understood, there is a high level of variability in the effi...
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Bone marrow mesenchymal stem cells (BM-MSCs) are pluripotent cells that can differentiate into a variety of non-hematopoietic tissues. They also maintain healthy heamatopoiesis by providing supportive cellular microenvironment into BM. In this thesis, MSCs were characterized in terms of their morphological, immunophenotypical and differentiation properties. Then, they were examined by attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy together with hierarchical clustering, and FT...
Role of Vibrational Spectroscopy in Stem Cell Research
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Recent researches have mainly displayed the significant role of stem cells in tissue renewal and homeostasis with their unique capacity to develop different cell types. These findings have clarified the importance of stem cells to improve the effectiveness of any cell therapy for regenerative medicine. Identification of purity and differentiation stages of stem cells are the greatest challenges of stem cell biology and regenerative medicine. The existing methods to carefully monitor and characterize the ste...
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...
Citation Formats
E. Balbaşı, “SETD3-dependent gene expression changes during endoderm differentiation of mouse embryonic stem cells,” M.S. - Master of Science, Middle East Technical University, 2022.