Mammalian cells exhibit a precise gene regulation process, during which enhancers play critical roles in mediating rapid gene activation in response to different signals. Indeed, much of our knowledge about gene transcriptional control comes from the long-standing investigation of the actions of nuclear receptors, well exemplified by estrogen 17?-estradiol (E2)-dependent activation of transcriptional programs. This program is controlled virtually entirely by activation of a cohort of ~1000 robustly activated ER?-bound enhancers. Under physiological conditions, many signals are pulsatile, including ligands for nuclear receptors such as ER?, representing a continuum from transient, acute stimulation to chronic stimulation. We have found that the acute 17?-estradiol (E2)-dependent activation of functional enhancers requires assembly of an eRNA-dependent ribonucleoprotein (eRNP) complex, referred to as the MegaTrans complex. A transformative, newly emerging concept, to which we are pleased to have contributed, is that acute signal of ligand-dependent activation of target enhancers causes them to form an RNA-protein condensate, with features of phase separation, that results in cooperative activation of other homotypic enhancers separated by multiple TADs and, even in other chromosomes. In contrast, chronic signal/ligand activation results in loss of the dynamic RNP condensate at the enhancers, loss of induced proximity of homotypic enhancers observed with acute activation, with enhancer activation function now confined to the nearby cognate target gene promoters. We will use global genomic, proteomic, and real time, single nucleus approaches, with appropriate informatics, to examine the patterns of enhancer activation, potential interactions in acute vs chronic ligand-dependent activation, relationship to localization in phase-separated subnuclear architectural structures and patterns of movement by single molecule imaging. Our goal is to provide a paradigm-shifting insight into ligand/hormone-regulated transcriptional programs, based on this multidisciplinary approach.

Public Health Relevance

Our data suggest that acute signal or ligand-dependent activation of target enhancers causes them to form an RNA-protein condensate, with features of phase separation, resulting in in induced proximity and cooperative activation of other homotypic enhancers, although separated by multiple TADs and, potentially, even in other chromosomes. In contrast, chronic signal/ligand activation results in loss of the dynamic RNP condensate at the enhancers, loss of induced proximity of homotypic enhancers observed with acute activation, with enhancer activation function now confined to the nearby cognate target gene promoters. We will use global genomic, proteomic, and real time, single nucleus approaches with the goal of providing a paradigm-shifting insight into hormone-regulated transcriptional programs.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Research Project (R01)
Project #
2R01DK039949-39
Application #
10051218
Study Section
Molecular and Cellular Endocrinology Study Section (MCE)
Program Officer
Silva, Corinne M
Project Start
1982-08-01
Project End
2025-02-28
Budget Start
2021-03-15
Budget End
2022-02-28
Support Year
39
Fiscal Year
2021
Total Cost
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
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
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
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
Depledge, Daniel P; Yamanishi, Koichi; Gomi, Yasuyuki et al. (2016) Deep Sequencing of Distinct Preparations of the Live Attenuated Varicella-Zoster Virus Vaccine Reveals a Conserved Core of Attenuating Single-Nucleotide Polymorphisms. J Virol 90:8698-704
Belinson, H; Nakatani, J; Babineau, B A et al. (2016) Prenatal ?-catenin/Brn2/Tbr2 transcriptional cascade regulates adult social and stereotypic behaviors. Mol Psychiatry 21:1417-33
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

Showing the most recent 10 out of 41 publications