The long-term objective of this Program is to determine the fundamental mechanisms underlying the interplay between transcription factors, chromatin structure, and higher-order genomic organization during the cellular conversion to and maintenance of pluripotency. Despite the remarkable ability of transcription factors and miRNAs to convert cells to pluripotency, undefined stochastic parameters presently limit the efficiency of the process. In addition, different pluripotent lines have different capacities for terminal differentiation and we poorly understand parameters that determine how well in vitro differentiation compares to in vivo differentiation. Understanding the molecular mechanisms in pluripotency induction and maintenance as well as those limiting differentiation will allow enhancements of the process that, in turn, will facilitate the use of small human biopsy samples much more efficiently than present techniques allow. To this end, the four projects of the Program ask: 1) How is the differentiated cell genome reorganized within the nucleus, during reprogramming to pluripotency, what aspects of reorganization are important, and what controls genome organization in pluripotent cells? 2) How do ectopic pluripotency transcription factors gain access to silent, chromatinized target sites to activate the endogenous pluripotency network, and how can the process be enhanced? 3) What regulatory circuits need to be properly established within pluripotent cells to allow their subsequent differentiation to fully mature progeny? 4) What marks of the competence to differentiate exist in pluripotent cells and how do they get established? By seeking answers to these questions in a single Program, we can obtain a time-resolved, integrated view of the mechanisms by which different aspects of the nuclear genome change coordinately to properly convert a cell to pluripotency and the process by which cells return to the somatic state. We also anticipate that the coordinate mechanisms unveiled by our studies will provide insights into direct cell reprogramming, independent of pluripotency. Administrative and Bioinformatics Cores and a shared Web site will support the projects with integrated services for optimal quality, efficiency, and data-sharing. The Administrative Core leverages existing high throughput sequencing, microarray, and stem cell cores at the respective institutions. The Project and Core leaders have complementary expertise in the relevant areas of stem cell biology, differentiation, transcription and chromatin/ epigenetics and have a long-standing record of interactive collaborations and publications. The plan provides unique experimental synergies that address the objectives of the funding announcement.

Public Health Relevance

The information generated by these investigators will provide valuable knowledge to increase the efficiency and effectiveness of generating properly reprogrammed pluripotent stem cells from differentiated cells. Such increases will greatly facilitate the ability to generate reprogrammed cells to make autologous cells for transplantation and modeling of diseases, provide insights into other forms of cellular reprogramming, and further our understanding of basic mechanisms that control self-renewal and differentiation of stem cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM099134-04
Application #
8710262
Study Section
Special Emphasis Panel (ZGM1-GDB-8 (IP))
Program Officer
Haynes, Susan R
Project Start
2011-08-01
Project End
2016-07-31
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
4
Fiscal Year
2014
Total Cost
$2,221,650
Indirect Cost
$591,009
Name
University of California Los Angeles
Department
Biochemistry
Type
Schools of Medicine
DUNS #
092530369
City
Los Angeles
State
CA
Country
United States
Zip Code
90095
Traller, Jesse C; Cokus, Shawn J; Lopez, David A et al. (2016) Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnol Biofuels 9:258
Zaret, Kenneth S; Lerner, Jonathan; Iwafuchi-Doi, Makiko (2016) Chromatin Scanning by Dynamic Binding of Pioneer Factors. Mol Cell 62:665-7
Germanguz, I; Listgarten, J; Cinkornpumin, J et al. (2016) Identifying gene expression modules that define human cell fates. Stem Cell Res 16:712-24
Becker, Justin S; Nicetto, Dario; Zaret, Kenneth S (2016) H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes. Trends Genet 32:29-41
White, Andrew; Flores, Aimee; Ong, Jessica et al. (2016) Hmga2 is dispensable for cutaneous squamous cell carcinoma. Exp Dermatol 25:409-12
Famenini, Sam; Rigali, Elizabeth A; Olivera-Perez, Henry M et al. (2016) Increased intermediate M1-M2 macrophage polarization and improved cognition in mild cognitive impairment patients on ω-3 supplementation. FASEB J :
Zaret, Kenneth S; Mango, Susan E (2016) Pioneer transcription factors, chromatin dynamics, and cell fate control. Curr Opin Genet Dev 37:76-81
Patel, Sanjeet; Bonora, Giancarlo; Sahakyan, Anna et al. (2016) Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation. Cell Rep :
Pastor, William A; Chen, Di; Liu, Wanlu et al. (2016) Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell Stem Cell 18:323-9
Gu, Wen; Gaeta, Xavier; Sahakyan, Anna et al. (2016) Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State. Cell Stem Cell 19:476-490

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