Embryonic stem cells maintain a delicate balance between pluripotent self-renewal and directed differentiation into any fetus cell type. Precise regulation of epigenetic state, particularly at lineage-specific developmental regulators which can induce differentiation, is crucial to maintaining this poised state during early development. Remarkably, these genes are often dually marked with both activating and repressive chromatin marks, a unique chromatin structure known as a bivalent domain. Understanding the biological mechanisms governing the setup and maintenance of bivalent domains however, has remained an elusive goal despite intense interest. The proposed research will discover the chromatin regulator circuitry operating at bivalent loci using high-throughput epigenomics technologies. I will identify chromatin regulators (CR) which bind to bivalent loci by using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). I will then perturb these enzymes in mouse embryonic stem cells and measure the resulting changes in both chromatin state and gene expression. Integrating these datasets together, I will apply probabilistic graphical modeling techniques to discover functional interdependencies relating chromatin regulators, histone modifications, and transcriptional output. This study will substantially enhance our understanding of the role CRs perform in early development, and in particular, the regulatory mechanisms responsible for establishing, maintaining, and resolving bivalent domains.

Public Health Relevance

Embryonic stem cells hold immense therapeutic promise due to their unique abilities. These cells are capable of replicating indefinitely, but also can give rse to any adult cell type under the proper conditions. My research will explore the molecular causes and consequences of these two opposing properties, potentially paving the way for new regenerative therapies.

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
5F32HD075541-02
Application #
8654493
Study Section
Special Emphasis Panel (ZRG1-F05-R (20))
Program Officer
Mukhopadhyay, Mahua
Project Start
2013-02-01
Project End
2016-01-31
Budget Start
2014-02-01
Budget End
2015-01-31
Support Year
2
Fiscal Year
2014
Total Cost
$53,282
Indirect Cost
Name
Broad Institute, Inc.
Department
Type
DUNS #
623544785
City
Cambridge
State
MA
Country
United States
Zip Code
02142
Trombetta, John J; Gennert, David; Lu, Diana et al. (2014) Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. Curr Protoc Mol Biol 107:4.22.1-4.22.17
Schwartz, Schraga; Bernstein, Douglas A; Mumbach, Maxwell R et al. (2014) Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159:148-62
Kumar, Roshan M; Cahan, Patrick; Shalek, Alex K et al. (2014) Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516:56-61
Shalek, Alex K; Satija, Rahul; Shuga, Joe et al. (2014) Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510:363-9
Satija, Rahul; Shalek, Alex K (2014) Heterogeneity in immune responses: from populations to single cells. Trends Immunol 35:219-29
Shalek, Alex K; Satija, Rahul; Adiconis, Xian et al. (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498:236-40