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Mechanisms and Functional Roles of Nuclear Respiratory Factor 1 (NRF1) Binding Sites in the Human Genome

Zhu, Wan (2011) Mechanisms and Functional Roles of Nuclear Respiratory Factor 1 (NRF1) Binding Sites in the Human Genome. Doctoral Dissertation, University of Pittsburgh.

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    Abstract

    Genome-wide studies have suggested that NRF1 regulates transcription of ~5-6% of human genes, including nuclear genes encoding mitochondrial products. My thesis focus is in neural systems in which NRF1 is a master regulator.Prader-Willi syndrome (PWS) results from genetic loss of function of an imprinted domain in human chromosome 15q11.2. I confirmed NRF1 regulation of ~83% of PWS-region genes using chromatin immunoprecipitation (ChIP). Further studies focused on evolution of this region. Uniquely in marsupials, SNRPN and the ancestral SNRPB' gene are adjacent each with an intronic snoRNA paralog. Based on molecular phylogenetics, a model is proposed for origin of each PWS snoRNA from a single ancestral snoRNA. Thus, most extant eutherian PWS genes originated by stepwise duplication and divergence over the past ~180 million years.Circadian rhythms regulate organismal physiology in a 24 hour day-night cycle. Functional NRF1 binding sites in promoters/enhancers were found for ~56% of circadian regulatory genes using bioinformatics, ChIP, NRF1 siRNA assays, and luciferase reporter constructs having significantly reduced transcriptional activity on mutation of NRF1 sites. Further, co-immunoprecipitation showed that NRF1 and the phosphorylated, active form of CLOCK interact in a molecular complex. In serum-induced NIH3T3 cells with circadian oscillations of Dbp and Nr1d1 mRNA, Nrf1 mRNA and protein levels show ultradian oscillations. Hence, NRF1 regulates numerous circadian regulatory genes and interacts with CLOCK, suggesting multiple roles in circadian biology. Additional studies included finding that NRF1 regulates ~45% known hereditary spastic paraplegia (HSP) genes, that NRF1 activates its own transcription, and that the number of NRF1 sites determine the degree of transcriptional activation. In summary, NRF1 is a master regulator in PWS, circadian rhythms, and HSP. Identification of NRF1 target genes and mechanisms will lead to an understanding of the evolution, functions, disease processes, and therapeutic targets within gene regulatory networks involving NRF1. Circadian rhythms are disrupted by travel, shift-work, and in illness, including infection, psychiatric and sleep disorders, obesity, diabetes, and cancer. Consequently, understanding body clocks will provide insights into the pathogenesis of these disorders and potentially lead to improved treatment and prevention options, which will have enormous public health impact.


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    Item Type: University of Pittsburgh ETD
    ETD Committee:
    ETD Committee TypeCommittee MemberEmailORCID
    Committee ChairNicholls, Robert D.robert.nicholls@chp.edu
    Committee MemberFeingold , Eleanorfeingold@pitt.edu
    Committee MemberFerrell, Robert E.rferrell@pitt.edu
    Committee MemberGollin, Susanne M.gollin@pitt.edu
    Title: Mechanisms and Functional Roles of Nuclear Respiratory Factor 1 (NRF1) Binding Sites in the Human Genome
    Status: Unpublished
    Abstract: Genome-wide studies have suggested that NRF1 regulates transcription of ~5-6% of human genes, including nuclear genes encoding mitochondrial products. My thesis focus is in neural systems in which NRF1 is a master regulator.Prader-Willi syndrome (PWS) results from genetic loss of function of an imprinted domain in human chromosome 15q11.2. I confirmed NRF1 regulation of ~83% of PWS-region genes using chromatin immunoprecipitation (ChIP). Further studies focused on evolution of this region. Uniquely in marsupials, SNRPN and the ancestral SNRPB' gene are adjacent each with an intronic snoRNA paralog. Based on molecular phylogenetics, a model is proposed for origin of each PWS snoRNA from a single ancestral snoRNA. Thus, most extant eutherian PWS genes originated by stepwise duplication and divergence over the past ~180 million years.Circadian rhythms regulate organismal physiology in a 24 hour day-night cycle. Functional NRF1 binding sites in promoters/enhancers were found for ~56% of circadian regulatory genes using bioinformatics, ChIP, NRF1 siRNA assays, and luciferase reporter constructs having significantly reduced transcriptional activity on mutation of NRF1 sites. Further, co-immunoprecipitation showed that NRF1 and the phosphorylated, active form of CLOCK interact in a molecular complex. In serum-induced NIH3T3 cells with circadian oscillations of Dbp and Nr1d1 mRNA, Nrf1 mRNA and protein levels show ultradian oscillations. Hence, NRF1 regulates numerous circadian regulatory genes and interacts with CLOCK, suggesting multiple roles in circadian biology. Additional studies included finding that NRF1 regulates ~45% known hereditary spastic paraplegia (HSP) genes, that NRF1 activates its own transcription, and that the number of NRF1 sites determine the degree of transcriptional activation. In summary, NRF1 is a master regulator in PWS, circadian rhythms, and HSP. Identification of NRF1 target genes and mechanisms will lead to an understanding of the evolution, functions, disease processes, and therapeutic targets within gene regulatory networks involving NRF1. Circadian rhythms are disrupted by travel, shift-work, and in illness, including infection, psychiatric and sleep disorders, obesity, diabetes, and cancer. Consequently, understanding body clocks will provide insights into the pathogenesis of these disorders and potentially lead to improved treatment and prevention options, which will have enormous public health impact.
    Date: 23 September 2011
    Date Type: Completion
    Defense Date: 14 July 2011
    Approval Date: 23 September 2011
    Submission Date: 25 July 2011
    Access Restriction: 5 year -- Restrict access to University of Pittsburgh for a period of 5 years.
    Patent pending: No
    Institution: University of Pittsburgh
    Thesis Type: Doctoral Dissertation
    Refereed: Yes
    Degree: PhD - Doctor of Philosophy
    URN: etd-07252011-180258
    Uncontrolled Keywords: circadian rhythms; NRF1; prader-willi syndrome; transcription factor
    Schools and Programs: Graduate School of Public Health > Human Genetics
    Date Deposited: 10 Nov 2011 14:53
    Last Modified: 11 Jan 2012 16:54
    Other ID: http://etd.library.pitt.edu/ETD/available/etd-07252011-180258/, etd-07252011-180258

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