The major goal of this proposal is to reveal molecular mechanisms underlying formation and function of critical transcriptional assemblies essential to embryonic stem (ES) cells and cells with induced pluripotency (induced pluripotent stem (iPS) cells). Using bioinformatics and high throughput experimental methods, we will prepare defined domains of critical transcriptional factors controlling cell pluripotency and analyze them in their functional associations. Thousands of assemblies will be evaluated by biochemical and biophysical methods to identify the critical ones to be targeted by X-ray crystallography.
We aim for determination of three-dimensional structures for about 100 stable multi-component transcriptional assemblies. Each of them will represent a partial image of complicated transcriptional machinery controlling the specific transcriptional landscape of pluripotent cells. We expect that thoughtful analyses of these structures will enable us to establish the proper connections between these partial images and reconstruct a general model for function of critical participants of this transcriptional machinery. We will justify this model and the observed regulatory nteractions within identified transcriptional complexes in mutational and functional studies using iPS cells. The experiments are to be done at multiple sites: The Methodist Hospital Research Institute (Houston), Department of Biochemistry and Biophysics at UCSF, the Gladstone Institute of Cardiovascular Disease (UCSF) and X-ray crystallography by the PSI labs. The proposed structural and functional studies will propel our general knowledge ofthe basic mechanisms controlling cell fate, including those underlying self renewal, differentiation and pathogenesis of cancer. The results of this research will also provide more efficient molecular tools allowing precise control over cell programming and reprogramming. The accumulated structural and functional data would be immediately available to biochemical and clinical researchers, and therefore, would have a major impact on stem cell research as well as regenerative medicine.
The proposed studies on embryonic and reprogrammed stem cells will reveal parts of the complex mechanisms controlling cell fate, including those underlying self renewal, differentiation, and development of cancer. The results of our research will provide more efficient molecular tools allowing precise control over cell programming and reprogramming. The images and concepts that we produce will have immediate impact on regenerative medicine as well as stem cell and cancer research.
|Miyaoka, Yuichiro; Mayerl, Steven J; Chan, Amanda H et al. (2018) Detection and Quantification of HDR and NHEJ Induced by Genome Editing at Endogenous Gene Loci Using Droplet Digital PCR. Methods Mol Biol 1768:349-362|
|Cvoro, Aleksandra; Bajic, Aleksandar; Zhang, Aijun et al. (2016) Ligand Independent and Subtype-Selective Actions of Thyroid Hormone Receptors in Human Adipose Derived Stem Cells. PLoS One 11:e0164407|
|Benod, Cindy; Villagomez, Rosa; Webb, Paul (2016) TLX: An elusive receptor. J Steroid Biochem Mol Biol 157:41-7|
|Proudfoot, Andrew; Axelrod, Herbert L; Geralt, Michael et al. (2016) Dlx5 Homeodomain:DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome. J Mol Biol 428:1130-1141|
|Kime, Cody; Mandegar, Mohammad A; Srivastava, Deepak et al. (2016) Efficient CRISPR/Cas9-Based Genome Engineering in Human Pluripotent Stem Cells. Curr Protoc Hum Genet 88:Unit 21.4|
|Hayashi, Yohei; Caboni, Laura; Das, Debanu et al. (2015) Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells. Proc Natl Acad Sci U S A 112:4666-71|
|Cvoro, Aleksandra; Devito, Liani; Milton, Flora A et al. (2015) A thyroid hormone receptor/KLF9 axis in human hepatocytes and pluripotent stem cells. Stem Cells 33:416-28|
|Carruthers, Carl W; Suh, Ji Ho; Gustafsson, Jan-Ake et al. (2015) Phosphorylation of glucocorticoid receptor tau1c transactivation domain enhances binding to CREB binding protein (CBP) TAZ2. Biochem Biophys Res Commun 457:119-23|
|Sablin, Elena P; Blind, Raymond D; Uthayaruban, Rubatharshini et al. (2015) Structure of Liver Receptor Homolog-1 (NR5A2) with PIP3 hormone bound in the ligand binding pocket. J Struct Biol 192:342-348|
|Bhattacharya, Suparna; Lou, Xiaohua; Hwang, Peter et al. (2014) Structural and functional insight into TAF1-TAF7, a subcomplex of transcription factor II D. Proc Natl Acad Sci U S A 111:9103-8|
Showing the most recent 10 out of 18 publications