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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2018)

This dissertation, by Yiren Hu, discusses how enhancer activity is regulated to drive rapid, coordinated transcriptional response to signals like estrogen and inflammatory stimuli. Enhancer elements play a central role in instructing precise spatiotemporal gene expression and are capable of activating target gene transcription from a long distance. How do enhancers achieve these functions? And how are enhancers regulated in response to multiple signals at the same time? To answer these questions, we took a high-throughput approach with the power of next-generation sequencing technologies to study the genome wide transcription landscape changes of human breast cancer cells as well as mouse immune cells in response to stimuli like estradiol and TNFα. We tackled enhancer regulatory mechanisms from three aspects and found that: 1) chromatin structure regulators Condensin Complex I and II play essential roles in activating Estrogen Receptor α-bound enhancers by balancing transcription co-activators versus co-repressors homeostasis (see Chapter 1) 2) histone demethylase JMJD6 activates Estrogen Receptor α-bound enhancers and controls coding gene Pol II pausing release by modulating mediator complex protein MED12 chromatin loading (see Chapter 2) 3) Estrogen Receptor α and histone demethylase KDM2B form a two-layer restriction mechanism to repress NFκB enhancers and corresponding pro-inflammatory genes (see Chapter 3 and 4).

    Cover page: Dissecting Enhancer Functions in Signal Induced Transcription Programs
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2017)
    The molecular mechanisms underlying the opposing functions of glucocorticoid receptors (GRs) and estrogen receptor α (ERα) in breast cancer development remain poorly understood. Here we report that, in breast cancer cells, liganded GR represses a large ERα-activated transcriptional program by binding, in trans, to ERα-occupied enhancers. This abolishes effective activation of these enhancers and their cognate target genes, and it leads to the inhibition of ERα-dependent binding of components of the MegaTrans complex. Consistent with the effects of SUMOylation on other classes of nuclear receptors, dexamethasone (Dex)-induced trans-repression of the estrogen E2 program appears to depend on GR SUMOylation, which leads to stable trans-recruitment of the GR-N-CoR/SMRT-HDAC3 corepressor complex on these enhancers. Together, these results uncover a mechanism by which competitive recruitment of DNA-binding nuclear receptors/transcription factors in trans to hot spot enhancers serves as an effective biological strategy for trans-repression, with clear implications for breast cancer and other diseases.
      Cover page: Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program.
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2015)
      Enhancers instruct spatio-temporally specific gene expression in a manner tightly linked to higher-order chromatin architecture. Critical chromatin architectural regulators condensin I and condensin II play non-redundant roles controlling mitotic chromosomes. But the chromosomal locations of condensins and their functional roles in interphase are poorly understood. Here we report that both condensin complexes exhibit an unexpected, dramatic estrogen-induced recruitment to estrogen receptor α (ER-α)-bound eRNA(+) active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-α via its DNA-binding domain (DBD). Condensins positively regulate ligand-dependent enhancer activation at least in part by recruiting an E3 ubiquitin ligase, HECTD1, to modulate the binding of enhancer-associated coactivators/corepressors, including p300 and RIP140, permitting full eRNA transcription, formation of enhancer:promoter looping, and the resultant coding gene activation. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating estrogen-regulated enhancer activation and coding gene transcriptional program.
        Cover page: Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2018)
        Nuclear receptors induce both transcriptional activation and repression programs responsible for development, homeostasis, and disease. Here, we report a previously overlooked enhancer decommissioning strategy underlying a large estrogen receptor alpha (ERα)-dependent transcriptional repression program. The unexpected signature for this E2-induced program resides in indirect recruitment of ERα to a large cohort of pioneer factor basally active FOXA1-bound enhancers that lack cognate ERα DNA-binding elements. Surprisingly, these basally active estrogen-repressed (BAER) enhancers are decommissioned by ERα-dependent recruitment of the histone demethylase KDM2A, functioning independently of its demethylase activity. Rather, KDM2A tethers the E3 ubiquitin-protein ligase NEDD4 to ubiquitylate/dismiss Pol II to abrogate eRNA transcription, with consequent target gene downregulation. Thus, our data reveal that Pol II ubiquitylation/dismissal may serve as a potentially broad strategy utilized by indirectly bound nuclear receptors to abrogate large programs of pioneer factor-mediated, eRNA-producing enhancers.
          Cover page: Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2019)
          A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. The potential contributions of physicochemical properties of enhancer assembly in signaling events remain poorly understood. Here we report that in human breast cancer cells, the acute 17β-estradiol-dependent activation of functional enhancers requires assembly of an enhancer RNA-dependent ribonucleoprotein (eRNP) complex exhibiting properties of phase-separated condensates. Unexpectedly, while acute ligand-dependent assembly of eRNPs resulted in enhancer activation sensitive to chemical disruption of phase separation, chronically activated enhancers proved resistant to such disruption, with progressive maturation of eRNPs to a more gel-like state. Acute, but not chronic, stimulation resulted in ligand-induced, condensin-dependent changes in spatial chromatin conformation based on homotypic enhancer association, resulting in cooperative enhancer-activation events. Thus, distinct physicochemical properties of eRNP condensates on enhancers serve as determinants of rapid ligand-dependent alterations in chromosomal architecture and cooperative enhancer activation.
            Cover page: Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly
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