Embryonic stem cells (ESCs) derived from the inner cell mass of blastocyst stage embryos are a powerful in vitro model for cellular differentiation and a potential source of cells for regenerative therapies. A better understanding of the factors controlling differentiation is necessary to robustly direct ESCs to produce mature cell types for therapeutic purposes. In addition, perturbations in differentiation in vivo lead to defects in early embryos and failed pregnancies. We are focusing on elucidating the components and wiring of the ESC gene regulatory network, in order to better control ESC differentiation and gain a more complete understanding of early development. Although three classes of regulatory factors comprise the ESC GRN?transcription factors, epigenetic regulators, and RNAs?the functions of only the first two classes are understood to a degree. We recently uncovered a key role for a structural feature of the ESC epigenome, RNA/DNA hybrids (RDHs), in cell fate. We found that RDHs are necessary to maintain the differentiation potential of ESCs?cells with reduced RDHs showed poor differentiation fidelity and a skewed differentiation profile. We recently found that RDHs play a key role in the ESC GRN, which likely accounts for these phenotypes. Depletion of RDHs leads to misregulation of thousands of genes. Interestingly, for a small fraction of these genes, we found that RDHs regulate the binding of two key epigenetic regulatory factors, PRC2 and Tip60-p400. However, most genes regulated by RDHs are neither direct nor indirect targets of these factors, raising the question of what other components of the GRN are modulated by RDHs. Here we propose to use epigenomic profiling and systems level approaches to comprehensively elucidate the roles of RDHs in the GRN. In addition, we will utilize a novel method for identification of new RDH-binding factors. Finally, we will use single cell profiling techniques to elucidate how RDHs regulate cell fate on a cell-by-cell basis. These studies will provide multiple new insights into how RNAs function within the ESC GRN. In addition, these studies will enhance our understanding of how cells acquire specific fates during ESC differentiation.

Public Health Relevance

In embryonic stem cells (ESCs) derived from early embryos, the gene regulatory network (GRN) controls when and how cells transform into any of the approximately two hundred mature cell types in the adult. Defects in this process lead to developmental defects early in gestation, resulting in failed pregnancies or birth defects. The proposed studies will elucidate unknown features of the ESC GRN, providing insight into cell fate decisions early in development, and facilitating use of ESCs in regenerative therapies.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Project (R01)
Project #
5R01HD072122-09
Application #
9932461
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Ravindranath, Neelakanta
Project Start
2012-08-15
Project End
2023-04-30
Budget Start
2020-05-01
Budget End
2021-04-30
Support Year
9
Fiscal Year
2020
Total Cost
Indirect Cost
Name
University of Massachusetts Medical School Worcester
Department
Genetics
Type
Schools of Medicine
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
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Ee, Ly-Sha; McCannell, Kurtis N; Tang, Yang et al. (2017) An Embryonic Stem Cell-Specific NuRD Complex Functions through Interaction with WDR5. Stem Cell Reports 8:1488-1496
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Hainer, Sarah J; McCannell, Kurtis N; Yu, Jun et al. (2016) DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. Elife 5:
Chen, Poshen B; Chen, Hsiuyi V; Acharya, Diwash et al. (2015) R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol 22:999-1007
Hainer, Sarah J; Fazzio, Thomas G (2015) Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome. Cell Rep 13:61-69
Hainer, Sarah J; Gu, Weifeng; Carone, Benjamin R et al. (2015) Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes Dev 29:362-78
Chen, Poshen B; Zhu, Lihua J; Hainer, Sarah J et al. (2014) Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics 15:1104
Carone, Benjamin R; Hung, Jui-Hung; Hainer, Sarah J et al. (2014) High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell 30:11-22

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