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Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2019)

ABSTRACT OF THE DISSERTATION

Functional Characterization of Human LncRNA JPX

By

Heather Karner

Doctor of Philosophy in Biological Sciences

University of California, Irvine, 2019

Assistant Professor Sha Sun, Chair

Long noncoding RNAs are present in all eukaryotes, but knowledge of their function and mechanisms are lacking. In this dissertation, I have worked toward characterizing a human lncRNA known as JPX. In mice, this lncRNA has been proposed to be the activator of the master regulator of X chromosome inactivation, lncRNA Xist. My research provides evidence that human lncRNA JPX is capable of this function as well, through comparative sequence, structural, and functional analyses. Human JPX, despite sequence and structural divergence from its mouse homolog, robustly binds CTCF—a protein that is known to sit on the Xist promoter and inhibit expression. Most interestingly, the human JPX complemented the deleterious effect of a heterozygous loss of Jpx in mouse embryonic stem cells and returned these cells to wild type viability and morphology, as well as increased Xist expression. The differences between the two lncRNAs begs the question of whether lncRNA JPX has gained new functions in humans. To study this, I investigated JPX and XIST in ovarian cancer. This cancer tends to be discovered at later, more aggressive stages. It was found that these later stages also tend to have decreased expression of JPX and XIST in patients. So far, my research indicates that these lncRNAs may be engaged in biological pathways involved in tumor suppression, and their loss could lead to the progression and metastasis of ovarian cancer.

    Cover page: Functional Characterization of Human LncRNA JPXCreative Commons 'BY-NC-ND' version 4.0 license
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2016)
    X-chromosome inactivation (XCI) is the mammalian dosage compensation strategy for balancing sex chromosome content between females and males. While works exist on initiation of symmetric breaking, the underlying allelic choice mechanisms and dynamic regulation responsible for the asymmetric fate determination of XCI remain elusive. Here we combine mathematical modeling and experimental data to examine the mechanism of XCI fate decision by analyzing the signaling regulatory circuit associated with long noncoding RNAs (lncRNAs) involved in XCI. We describe three plausible gene network models that incorporate features of lncRNAs in their localized actions and rapid transcriptional turnovers. In particular, we show experimentally that Jpx (a lncRNA) is transcribed biallelically, escapes XCI, and is asymmetrically dispersed between two X's. Subjecting Jpx to our test of model predictions against previous experimental observations, we identify that a self-enhanced transport feedback mechanism is critical to XCI fate decision. In addition, the analysis indicates that an ultrasensitive response of Jpx signal on CTCF is important in this mechanism. Overall, our combined modeling and experimental data suggest that the self-enhanced transport regulation based on allele-specific nature of lncRNAs and their temporal dynamics provides a robust and novel mechanism for bi-directional fate decisions in critical developmental processes.
      Cover page: A self-enhanced transport mechanism through long noncoding RNAs for X chromosome inactivation
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2024)
      Plasticity, a key hallmark of cancer, enables cells to transition into different states, driving tumor heterogeneity. This cellular plasticity is associated with cancer progression, treatment resistance, and relapse. Cancer stem cells (CSCs) play a central role in this process, yet the molecular factors underlying cancer cell stemness remain poorly understood. In this study, we explored the role of XIST (X-inactive specific transcript) long noncoding RNA in ovarian cancer stemness and plasticity through in silico and in vitro analyses. We found that XIST is significantly down-regulated in ovarian tumors, with low XIST expression linked to a higher stemness index and lower overall survival. Knocking down XIST in ovarian cancer cells enhanced stemness, particularly increasing mesenchymal-like CSCs, and under hypoxic conditions, it promoted epithelial-like CSC markers. Our findings suggest that XIST loss leads to CSC enrichment and cellular plasticity in ovarian cancer, pointing to potential therapeutic targets for patients with low XIST expression.
        Cover page: Loss of XIST lncRNA unlocks stemness and cellular plasticity in ovarian cancer
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2024)
        Large-scale sequencing efforts have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of variants occur within non-coding genomic regions. We designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Applying this framework to sequencing data from a large prostate cancer patient cohort revealed a large set of candidate drivers. We used (1) in silico analyses, (2) massively parallel reporter assays, and (3) in vivo CRISPR interference screens to systematically validate metastatic castration-resistant prostate cancer (mCRPC) drivers. One identified enhancer region, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of the U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. SF3A1 and CCDC157 promote tumor growth in vivo. We nominated a number of transcription factors, notably SOX6, to regulate expression of SF3A1 and CCDC157. Our integrative approach enables the systematic detection of non-coding regulatory regions that drive human cancers.
          Cover page: Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.
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