Browsing by Subject "Genomic Instability"
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Item Discovering GCNA: A Novel Regulator of Germline Genomic Stability(2018-10-15) Bhargava, Varsha; Mendell, Joshua T.; Buszczak, Michael; Olson, Eric N.; Tu, BenjaminGerm cells transfer genetic information across generations. Any change in germ line DNA is inherited by succeeding generations. Therefore, germ cell DNA must be protected from both internal and external assault. An advantage of sexual reproduction stems from the ability to generate variation by exchange of chromosomal segments during meiosis. During meiosis, hundreds of double-stranded DNA breaks are initiated at once, which if generated in most other cell types would introduce chromosomal aberrations. Germ cells, however, execute the formation of these breaks while preventing their deleterious effects from becoming pervasive throughout the genome. The mechanisms underlying the robustness of germ cells in the face of DNA damage, however, are poorly understood. We initiated an in vivo CRISPR-Cas9 knockout screen for genes highly enriched in the Drosophila female germ line. From this screen, we identified Germ Cell Nuclear Acidic Peptidase (GCNA) as a conserved regulator of genome stability across multiple species. Loss of GCNA results in replication stress, chromosomal instability, and an accumulation of DNA-protein crosslinks (DPCs). Disruption of GCNA leads to an accumulation of nuclear Top2 and Top2 DPCs. This work shows GCNA protects germ cells from damage and provides novel insights into the conserved networks that promote genome integrity across generations.Item GCNA: Guardian of the Genome(2020-05-01T05:00:00.000Z) Goldstein, Courtney DaVee; Abrams, John M.; Buszczak, Michael; Brekken, Rolf A.; Olson, Eric N.The propagation of species depends on the ability of germ cells to protect their genome in the face of numerous exogenous and endogenous threats. While germ cells employ a number of know repair pathways, specialized mechanisms that ensure high-fidelity replication, chromosome segregation, and repair of germ cell genomes remain incompletely understood. Here, we identify Germ cell nuclear acidic peptidase (GCNA) as a conserved regulator of genome stability in flies, worms, zebrafish and human germ cell tumors. GCNA contains an acidic intrinsically disordered region (IDR) and a protease-like SprT domain. In addition to chromosomal instability and replication stress, Gcna mutants accumulate DNA-protein crosslinks (DPCs). GCNA acts in parallel with a second SprT domain protein Spartan. Structural analysis reveals that while the SprT domain is needed to limit meiotic and replicative damage, much of GCNA's function maps to its IDR. This work shows GCNA protects germ cells from various sources of damage, providing novel insights into conserved mechanisms that promote genome integrity across generations.Item Regulation of Pumilio RNA Binding Proteins by Long Noncoding RNA NORAD(August 2021) Elguindy, Mahmoud Mohamed; Zhu, Hao; Buszczak, Michael; Sabari, Benjamin; Mendell, Joshua T.The mammalian genome is extensively transcribed and encodes thousands of long noncoding RNAs (lncRNAs). Defining the mechanism of action of lncRNAs has been a critical challenge and priority for understanding their biological functions. An important example of this is the lncRNA NORAD, which is a highly conserved lncRNA that is required for maintaining genome stability in mammals. Work in this thesis begins by examining the physiologic function and molecular mechanism of NORAD in human cells. We clearly demonstrate that NORAD localizes predominantly to the cytoplasm where it functions by binding to and inhibiting PUMILIO (PUM1 and PUM2) RNA binding proteins (RBPs). Thorough dissection of the functional domains of NORAD establish the essentiality of PUM binding to NORAD for its function in maintaining genome stability. We further examine the mechanism by which NORAD is able to efficiently sequester and regulate PUM proteins. Through a multidisciplinary approach involving biochemical, microscopy, and mutational analysis experiments, we uncover how NORAD sequesters a super-stoichiometric amount of PUM proteins into novel liquid-like membraneless organelles through a multivalency-induced phase separation mechanism. Moreover, we provide a molecular understanding of the properties of NORAD that promote PUM phase separation, revealing new principles of lncRNA function and demonstrating the physiologic importance of RNA-driven phase separation as a regulatory mechanism in mammalian biology. Our findings, together with the widespread repetitive architecture of lncRNAs, suggest that the phase separation principles we establish may be broadly utilized for lncRNA-mediated regulation.Item Regulation of the Insulin-like Growth Factor 1-Secretory Clusterin Expression Axis in Genomic Instability and Cell Stress(2009-09-04) Goetz, Eva Marie; Boothman, David A.Secretory clusterin (sCLU) is a pro-survival factor that is up-regulated in human tumors and after exposure to cell stress. Understanding the regulation of sCLU expression in cancer, and after exposure to therapeutic agents, could reveal new therapeutic targets for cancer treatment. A DNA damage induced signaling cascade leading from ATM to sCLU expression mediated by IGF-1/IGF-1R/MAPK activation was uncovered. IGF-1 ligand promoter activity, mRNA, and protein expression induced after exposure to ionizing radiation (IR), hydrogen peroxide, or topoisomerase I and II-alpha poisons matched sCLU expression. Elevated basal IGF-1-sCLU signaling was noted in genomically unstable cells, whether they were deficient in DNA repair factors or telomerase function. ATM function was necessary for induction of sCLU after IR, and for maintaining elevated expression of sCLU in genomically unstable cells. p53 suppressed IGF-1 promoter activity, leading to decreased mRNA and protein expression, and abrogated induction of IGF-1 and sCLU by IR. Loss of p53 by knockdown or knockout enhanced IGF-1 and sCLU induction. Mutations in the p53 DNA binding domain found in cancer did not repress IGF-1 and sCLU. An NF-Y binding site in the IGF-1 promoter was essential for p53 suppression, and both p53 and NF-YA bound to the IGF-1 promoter. Nutlin-3, an Mdm2-p53 inhibitor, stabilized p53 expression, leading to dramatically decreased sCLU expression. Nutlin-3 treatment sensitized wild-type p53 cells to IR exposure. Finally, exogenous IGF-1 exposure led to serine 1981 auto-phosphorylation of ATM, and enhanced DNA damage repair and abrogated cell death after IR exposure. These studies uncovered key molecules important for the regulation of IGF-1-sCLU expression axis after IR exposure, and supported the use of IGF-1 or sCLU expression inhibitors for cancer chemotherapy.Item The Sec6/8 (a.k.a. Exocyst) Complex Supports DNA Repair Fidelity(2014-04-14) Torres, Michael Jason 1982-; Brekken, Rolf A.; Cobb, Melanie H.; Burma, SandeepThe exocyst complex, first described in yeast, is a heterooctomeric complex that serves as a signaling platform to mediate cellular responses to diverse spatial and temporal cues. Evidence suggests that the exocyst might contribute to oncogenesis, potentially by disrupting spatial and temporal regulation of pathways critical to determining cell survival vs. apoptosis. Our work investigated how cancer cells subvert the exocyst to upregulate the AKT (v-akt murine thymoma viral oncogene) pro-survival pathway through the innate immune protein TBK1 (TANK-binding kinase 1). siRNA-mediated depletion of TBK1 in pancreatic and breast cancer cell lines results in apoptosis, which is mediated through the AKT pathway. Pharmacological inhibition of TBK1 recapitulates the apoptotic phenotype in mouse orthotopic models. Additionally, my work uncovered exocyst participation in the regulation of DNA repair. The isolation of multiple components of the DNA damage response (DDR) within the human exocyst protein-protein interaction network, together with the identification of Sec8 as a suppressor of the p53 response, prompted an investigation of functional interactions between the exocyst and the DDR. We found that exocyst perturbation resulted in a radioresistance phenotype to ionizing radiation (IR) that was associated with accelerated resolution of DNA damage. This occurred at the expense of genomic integrity, as enhanced recombination frequencies correlated with the accumulation of aberrant chromatid exchanges. Exocyst-dependent modulation of the DDR is, at least in part, through restraint of the associated chromatin modifiers ATF2 and RNF20. Exocyst perturbation resulted in aberrant accumulation of ATF2 and RNF20; the promiscuous accumulation of DDR-associated chromatin marks; and IR-induced increased Rad51 repairosomes. Thus, the exocyst indirectly supports DNA repair fidelity by limiting formation of repair chromatin in the absence of a DNA damage signal. This newly revealed regulation of DNA repair by the exocyst may provide additional insight into the emerging observations of DNA damage protein involvement in pathways not canonically associated DNA repair, such as the host cytokinesis, host defense response, and maintenance of cilia. This work further substantiates the importance of the exocyst in normal cell biology and gives insight into how disruption of exocyst function can result in disease.