2019-11-132019-11-13December 22016-12December 2Portions of this document appear in: Soibam, Benjamin, Ashley Benham, Jong Kim, Kuo‐Chan Weng, Litao Yang, Xueping Xu, Matthew Robertson et al. "Genome‐Wide Identification of MESP1 Targets Demonstrates Primary Regulation Over Mesendoderm Gene Activity." Stem Cells 33, no. 11 (2015): 3254-3265.https://hdl.handle.net/10657/5393MESP1 is a basic helix loop helix transcription factor that is essential for the survival and development of mouse embryogenesis. It is the earliest marker for identifying the nascent mesoderm that is fated to becoming the myocardium, head mesenchyme, and somites. In spite of the advancements in our knowledge of MESP1, it is, however, still very unclear how it directs the activation of the cardiac program. It is important to understand MESP1’s epigenetic, and transcriptional function during development to increase efficiency in somatic and stem cells cardiac reprogramming. ChIP-seq analysis of endogenous targets of endogenously expressed MESP1 affected neuro-ectoderm specific GO terms over mesendoderm specific terms predominantly. To analyze MESP1’s effect on target genes, a comparison to RNA-seq data of FACsorted YFP cells from ESC and day 5, 6, 7, and 8 was done. YFP protein marks endogenously activated MESP1 expressing cells during EB differentiation which resulted in identifying MESP1’s effect on target genes. Analysis of the transcriptome of YFP positive cells provided evidence that MESP1 is indirectly activating the core cardiac program and directly repressing the non-mesoderm program such as neuro-ectoderm. MESP1 directly represses the neuro-ectoderm developmental program by targeting, Sox2, Neurod1, Neurog1, Neurog2, and Neurog3 by reducing the expression levels within the first 12 hours of Dox induction. Meta-data analysis of MESP1-binding regions with H3K27acetylation and tri-methylation show strong overlap with H3K27acetyaltion favoring Mesendoderm specific genes and H3K27me3 favoring neuro-ectoderm target genes. H3K27acetylation suggest a potential mechanism in indirectly activating the core cardiac program. ChIP-qPCR of Neurog3 adjacent enhancers show that MESP1 guides the deposit of H3K27me3 through the PRC2 complex in an ebox variant-dependent manner. Analysis of MESP1 binding sites for potential bias in the ebox variant show that CACCTG variant is favored in regards to both repressive function and H3K27me3 marking,.application/pdfengThe author of this work is the copyright owner. UH Libraries and the Texas Digital Library have their permission to store and provide access to this work. UH Libraries has secured permission to reproduce any and all previously published materials contained in the work. Further transmission, reproduction, or presentation of this work is prohibited except with permission of the author(s).Helix loopMesendoderm2019-11-13Thesisborn digital