Understanding the molecular logic of regulatory strategies that control genome-wide patterns of transcriptional response to regulatory signals, development and human disease remains a key, unresolved issue. Under this Grant, we have investigated the integration of transcriptional programs by coactivators and corepressors and have established their role in regulated gene transcription by DNA binding transcription factors. Furthermore, we have established the critical role of specific corepressor complex components in cofactor exchange in ligand-dependent gene activation. We have investigated the effects of ligands on long-distance interactions in normal cells and as a component of tumor biology, including translocation events. Investigation of pituitary gland development as a model has permitted the in vivo characterization of new aspects of the Notch pathway and the role of Wnt pituitary/2-catenin POU domain interactions in cell type-specific gene activation events. In this competitive renewal, based on preliminary data obtained under this Grant, we will focus on the role of nuclear receptor-mediated transcriptional activation driven by specific response elements in a large number of DNA repeats resulting in novel small regulatory RNAs and ligand-regulated ncRNAs. We will develop and apply genome-wide location analysis 3-D interaction methods to explore new aspects of gene regulation and control of transcriptional activation programs aimed at identifying specific strategies of enhancers and regulation of subnuclear location events during development and in control of proliferation. We also propose a novel non-histone methylation strategy, which is critical for the movement of transcription units between the nuclear architecture regions that underlie growth control gene regulation. Our studies will link non-histone protein modifications, ncRNAs and nuclear architecture as an integrating strategy for regulated mammalian transcriptional programs.

Public Health Relevance

The experiments proposed in this competitive renewal will provide novel insights into regulated patterns of gene transcription, focusing on new technologies to investigate the role of ligand-dependent induction of DNA repeats and gene enhancers in gene expression programs and in ncRNAs and nuclear architecture strategies critical for integrating gene transcriptional programs. The proposed studies have particular relevance in uncovering the molecular basis of growth control and nuclear receptor actions in normal and cancer cells. Understanding these new strategies underlying regulation of gene expression is likely to translate into new types of therapeutic modalities.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Research Project (R01)
Project #
2R01DK018477-36A1
Application #
8188155
Study Section
Molecular and Cellular Endocrinology Study Section (MCE)
Program Officer
Margolis, Ronald N
Project Start
1998-10-01
Project End
2016-06-30
Budget Start
2011-09-01
Budget End
2012-06-30
Support Year
36
Fiscal Year
2011
Total Cost
$546,606
Indirect Cost
Name
University of California San Diego
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Cardamone, Maria Dafne; Tanasa, Bogdan; Cederquist, Carly T et al. (2018) Mitochondrial Retrograde Signaling in Mammals Is Mediated by the Transcriptional Cofactor GPS2 via Direct Mitochondria-to-Nucleus Translocation. Mol Cell 69:757-772.e7
Kim, Hong Sook; Tan, Yuliang; Ma, Wubin et al. (2018) Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells. Nature 556:510-514
Wang, Jianxun; Saijo, Kaoru; Skola, Dylan et al. (2018) Histone demethylase LSD1 regulates hematopoietic stem cells homeostasis and protects from death by endotoxic shock. Proc Natl Acad Sci U S A 115:E244-E252
Tan, Yuliang; Jin, Chunyu; Ma, Wubin et al. (2018) Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program. Mol Cell 71:526-539.e8
Yang, Feng; Ma, Qi; Liu, Zhijie et al. (2017) Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ER?-Regulated Transcriptional Program. Mol Cell 66:321-331.e6
Puc, Janusz; Aggarwal, Aneel K; Rosenfeld, Michael G (2017) Physiological functions of programmed DNA breaks in signal-induced transcription. Nat Rev Mol Cell Biol 18:471-476
Puc, Janusz; Kozbial, Piotr; Li, Wenbo et al. (2015) Ligand-dependent enhancer activation regulated by topoisomerase-I activity. Cell 160:367-80
Li, Wenbo; Hu, Yiren; Oh, Soohwan et al. (2015) Condensin I and II Complexes License Full Estrogen Receptor ?-Dependent Enhancer Activation. Mol Cell 59:188-202
Wang, Jianxun; Telese, Francesca; Tan, Yuliang et al. (2015) LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control. Nat Neurosci 18:1256-64
Telese, Francesca; Ma, Qi; Perez, Patricia Montilla et al. (2015) LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation. Neuron 86:696-710

Showing the most recent 10 out of 61 publications