메뉴 건너뛰기




Volumn 2013, Issue 7, 2013, Pages 139-152

Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the pathogenesis of Neurodegenerative Diseases

Author keywords

Alzheimer's disease; Binding sites; ChIP seq; Genomejack; NRF1; Parkinson's disease

Indexed keywords

ARGONAUTE 1 PROTEIN; DJ 1 PROTEIN; MITOCHONDRIAL DNA; NUCLEAR RESPIRATORY FACTOR 1; PARKIN; UBIQUITIN;

EID: 84887149480     PISSN: None     EISSN: 11776250     Source Type: Journal    
DOI: 10.4137/GRSB.S13204     Document Type: Article
Times cited : (120)

References (39)
  • 1
    • 33750347347 scopus 로고    scopus 로고
    • Mitochondrial dysfunction and oxidative stress in neuro-degenerative diseases
    • Lin MT, Beal MF. Mitochondrial dysfunction and oxidative stress in neuro-degenerative diseases. Nature. 2006;443(7113):787-795.
    • (2006) Nature , vol.443 , Issue.7113 , pp. 787-795
    • Lin, M.T.1    Beal, M.F.2
  • 2
    • 84883605293 scopus 로고    scopus 로고
    • Insights on altered mitochondrial function and dynamics in the pathogenesis of neurodegeneration
    • McInnes J. Insights on altered mitochondrial function and dynamics in the pathogenesis of neurodegeneration. Transl Neurodegener. 2013;2(1):12.
    • (2013) Transl Neurodegener , vol.2 , Issue.1 , pp. 12
    • McInnes, J.1
  • 3
    • 42049114034 scopus 로고    scopus 로고
    • Transcriptional paradigms in mammalian mitochondrial biogenesis and function
    • Scarpulla RC. Transcriptional paradigms in mammalian mitochondrial biogenesis and function. Physiol Rev. 2008;88(2):611-638.
    • (2008) Physiol Rev , vol.88 , Issue.2 , pp. 611-638
    • Scarpulla, R.C.1
  • 4
    • 0030818689 scopus 로고    scopus 로고
    • Serine phosphorylation within a concise amino-terminal domain in nuclear respiratory factor 1 enhances DNA binding
    • Gugneja S, Scarpulla RC. Serine phosphorylation within a concise amino-terminal domain in nuclear respiratory factor 1 enhances DNA binding. J Biol Chem. 1997;272(30):18732-18739.
    • (1997) J Biol Chem , vol.272 , Issue.30 , pp. 18732-18739
    • Gugneja, S.1    Scarpulla, R.C.2
  • 5
    • 0027135555 scopus 로고
    • NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA-binding domain conserved in a family of developmental regulators
    • Virbasius CA, Virbasius JV, Scarpulla RC. NRF-1, an activator involved in nuclear-mitochondrial interactions, utilizes a new DNA-binding domain conserved in a family of developmental regulators. Genes Dev. 1993;7(12A): 2431-2445.
    • (1993) Genes Dev , vol.7 , Issue.12 A , pp. 2431-2445
    • Virbasius, C.A.1    Virbasius, J.V.2    Scarpulla, R.C.3
  • 6
    • 0031647714 scopus 로고    scopus 로고
    • Not really finished is crucial for development of the zebrafish outer retina and encodes a transcription factor highly homologous to human Nuclear Respiratory Factor-1 and avian Initiation Binding Repressor
    • Becker TS, Burgess SM, Amsterdam AH, Allende ML, Hopkins N. Not really finished is crucial for development of the zebrafish outer retina and encodes a transcription factor highly homologous to human Nuclear Respiratory Factor-1 and avian Initiation Binding Repressor. Development. 1998;125(22):4369-4378.
    • (1998) Development , vol.125 , Issue.22 , pp. 4369-4378
    • Becker, T.S.1    Burgess, S.M.2    Amsterdam, A.H.3    Allende, M.L.4    Hopkins, N.5
  • 7
    • 0035169827 scopus 로고    scopus 로고
    • Mitochondrial DNA instability and peri-implantation lethality associated with targeted disruption of nuclear respiratory factor 1 in mice
    • Huo L, Scarpulla RC. Mitochondrial DNA instability and peri-implantation lethality associated with targeted disruption of nuclear respiratory factor 1 in mice. Mol Cell Biol. 2001;21(2):644-654.
    • (2001) Mol Cell Biol , vol.21 , Issue.2 , pp. 644-654
    • Huo, L.1    Scarpulla, R.C.2
  • 8
    • 0027240848 scopus 로고
    • The Drosophila erect wing gene, which is important for both neuronal and muscle development, encodes a protein which is similar to the sea urchin P3A2 DNA binding protein
    • DeSimone SM, White K. The Drosophila erect wing gene, which is important for both neuronal and muscle development, encodes a protein which is similar to the sea urchin P3A2 DNA binding protein. Mol Cell Biol. 1993;13(6):3641-3649.
    • (1993) Mol Cell Biol , vol.13 , Issue.6 , pp. 3641-3649
    • Desimone, S.M.1    White, K.2
  • 9
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009;10(10):669-680.
    • (2009) Nat Rev Genet , vol.10 , Issue.10 , pp. 669-680
    • Park, P.J.1
  • 10
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • Gerstein MB, Kundaje A, Hariharan M, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012;489(7414): 91-100.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 91-100
    • Gerstein, M.B.1    Kundaje, A.2    Hariharan, M.3
  • 11
    • 79952049316 scopus 로고    scopus 로고
    • Bioinformatics approach to identifying molecular biomarkers and networks in multiple sclerosis
    • Satoh J. Bioinformatics approach to identifying molecular biomarkers and networks in multiple sclerosis. Clin Exp Neuroimmunol. 2010;1(3): 127-140.
    • (2010) Clin Exp Neuroimmunol , vol.1 , Issue.3 , pp. 127-140
    • Satoh, J.1
  • 12
    • 8644281106 scopus 로고    scopus 로고
    • A common set of gene regulatory networks links metabolism and growth inhibition
    • Cam H, Balciunaite E, Blais A, et al. A common set of gene regulatory networks links metabolism and growth inhibition. Mol Cell. 2004;16(3): 399-411.
    • (2004) Mol Cell , vol.16 , Issue.3 , pp. 399-411
    • Cam, H.1    Balciunaite, E.2    Blais, A.3
  • 13
    • 79955550445 scopus 로고    scopus 로고
    • A user's guide to the Encyclopedia of DNA Elements (ENCODE)
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. A user's guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol. 2011;9(4):e1001046.
    • (2011) PLoS Biol , vol.9 , Issue.4
  • 14
    • 77956885532 scopus 로고    scopus 로고
    • Defned genome-wide map of vitamin D receptor binding: Associations with disease and evolution
    • Ramagopalan SV, Heger A, Berlanga AJ, et al. defned genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res. 2010;20(10):1352-1360.
    • (2010) Genome Res , vol.20 , Issue.10 , pp. 1352-1360
    • Ramagopalan, S.V.1    Heger, A.2    Berlanga, A.J.3
  • 15
    • 84875663378 scopus 로고    scopus 로고
    • A comprehensive profle of ChIP-Seq-based STAT1 target genes suggests the complexity of STAT1-mediated gene regulatory mechanisms
    • Satoh J, Tabunoki H. A comprehensive profle of ChIP-Seq-based STAT1 target genes suggests the complexity of STAT1-mediated gene regulatory mechanisms. Gene Regul Syst Bio. 2013;7:41-56.
    • (2013) Gene Regul Syst Bio , vol.7 , pp. 41-56
    • Satoh, J.1    Tabunoki, H.2
  • 16
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57.
    • (2009) Nat Protoc , vol.4 , Issue.1 , pp. 44-57
    • da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 17
    • 84871857327 scopus 로고    scopus 로고
    • Molecular network analysis of diseases and drugs in KEGG
    • Kanehisa M. Molecular network analysis of diseases and drugs in KEGG. Methods Mol Biol. 2013;939:263-275.
    • (2013) Methods Mol Biol , vol.939 , pp. 263-275
    • Kanehisa, M.1
  • 18
    • 0035830879 scopus 로고    scopus 로고
    • Interaction of the transcription factors USF1, USF2, and α-Pal/Nrf-1 with the FMR1 promoter. Implications for Fragile X mental retardation syndrome
    • Kumari D, Usdin K. Interaction of the transcription factors USF1, USF2, and α-Pal/Nrf-1 with the FMR1 promoter. Implications for Fragile X mental retardation syndrome. J Biol Chem. 2001;276(6):4357-4364.
    • (2001) J Biol Chem , vol.276 , Issue.6 , pp. 4357-4364
    • Kumari, D.1    Usdin, K.2
  • 19
    • 0024355576 scopus 로고
    • Identifcation and characterization of a novel transcription factor participating in the expression of eukaryotic initiation factor 2α
    • Jacob WF, Silverman TA, Cohen RB, Safer B. Identifcation and characterization of a novel transcription factor participating in the expression of eukaryotic initiation factor 2α. J Biol Chem. 1989;264(34): 20372-20384.
    • (1989) J Biol Chem , vol.264 , Issue.34 , pp. 20372-20384
    • Jacob, W.F.1    Silverman, T.A.2    Cohen, R.B.3    Safer, B.4
  • 20
    • 0033548192 scopus 로고    scopus 로고
    • Genomic cloning and characterization of the human eukaryotic initiation factor-2β promoter
    • Chiorini JA, Miyamoto S, Harkin SJ, Safer B. Genomic cloning and characterization of the human eukaryotic initiation factor-2β promoter. J Biol Chem. 1999;274(7):4195-4201.
    • (1999) J Biol Chem , vol.274 , Issue.7 , pp. 4195-4201
    • Chiorini, J.A.1    Miyamoto, S.2    Harkin, S.J.3    Safer, B.4
  • 21
    • 0024358781 scopus 로고
    • Interaction of nuclear factors with multiple sites in the somatic cytochrome c promoter. Characterization of upstream NRF-1, ATF, and intron Sp1 recognition sequences
    • Evans MJ, Scarpulla RC. Interaction of nuclear factors with multiple sites in the somatic cytochrome c promoter. Characterization of upstream NRF-1, ATF, and intron Sp1 recognition sequences. J Biol Chem. 1989;264(24):14361-14368.
    • (1989) J Biol Chem , vol.264 , Issue.24 , pp. 14361-14368
    • Evans, M.J.1    Scarpulla, R.C.2
  • 22
    • 33845227580 scopus 로고    scopus 로고
    • NF-Y, AP2, Nrf1 and Sp1 regulate the fragile X-related gene 2 (FXR2)
    • Mahishi L, Usdin K. NF-Y, AP2, Nrf1 and Sp1 regulate the fragile X-related gene 2 (FXR2). Biochem J. 2006;400(2):327-335.
    • (2006) Biochem J , vol.400 , Issue.2 , pp. 327-335
    • Mahishi, L.1    Usdin, K.2
  • 23
    • 9144241740 scopus 로고    scopus 로고
    • The NRF-1/α-PAL transcription factor regulates human E2F6 promoter activity
    • Kherrouche Z, De Launoit Y, Monte D. The NRF-1/α-PAL transcription factor regulates human E2F6 promoter activity. Biochem J. 2004;383(Pt 3): 529-536.
    • (2004) Biochem J , vol.383 , Issue.PART 3 , pp. 529-536
    • Kherrouche, Z.1    de Launoit, Y.2    Monte, D.3
  • 24
    • 2442442937 scopus 로고    scopus 로고
    • α-Pal/NRF-1 regulates the promoter of the human integrin-associated protein/CD47 gene
    • Chang WT, Huang AM. α-Pal/NRF-1 regulates the promoter of the human integrin-associated protein/CD47 gene. J Biol Chem. 2004;279(15): 14542-14550.
    • (2004) J Biol Chem , vol.279 , Issue.15 , pp. 14542-14550
    • Chang, W.T.1    Huang, A.M.2
  • 26
    • 79956205888 scopus 로고    scopus 로고
    • DNA repair defciency in neurodegeneration
    • Jeppesen DK, Bohr VA, Stevnsner T. DNA repair defciency in neurodegeneration. Prog Neurobiol. 2011;94(2):166-200.
    • (2011) Prog Neurobiol , vol.94 , Issue.2 , pp. 166-200
    • Jeppesen, D.K.1    Bohr, V.A.2    Stevnsner, T.3
  • 27
    • 79151485014 scopus 로고    scopus 로고
    • Role of ubiquitin-proteasome-mediated proteolysis in nervous system disease
    • Hegde AN, Upadhya SC. Role of ubiquitin-proteasome-mediated proteolysis in nervous system disease. Biochim Biophys Acta. 2011;1809(2):128-40.
    • (2011) Biochim Biophys Acta , vol.1809 , Issue.2 , pp. 128-140
    • Hegde, A.N.1    Upadhya, S.C.2
  • 28
    • 22144443868 scopus 로고    scopus 로고
    • A novel function of transcription factor α-Pal/NRF-1: Increasing neurite outgrowth
    • Chang WT, Chen HI, Chiou RJ, Chen CY, Huang AM. A novel function of transcription factor α-Pal/NRF-1: increasing neurite outgrowth. Biochem Biophys Res Commun. 2005;334(1):199-206.
    • (2005) Biochem Biophys Res Commun , vol.334 , Issue.1 , pp. 199-206
    • Chang, W.T.1    Chen, H.I.2    Chiou, R.J.3    Chen, C.Y.4    Huang, A.M.5
  • 29
    • 0028305728 scopus 로고
    • A key transcription factor for eukaryotic initiation factor-2α is strongly homologous to developmental transcription factors and may link metabolic genes to cellular growth and development
    • Efok BJ, Chiorini JA, Safer B. A key transcription factor for eukaryotic initiation factor-2α is strongly homologous to developmental transcription factors and may link metabolic genes to cellular growth and development. J Biol Chem. 1994;269(29):18921-18930.
    • (1994) J Biol Chem , vol.269 , Issue.29 , pp. 18921-18930
    • Efok, B.J.1    Chiorini, J.A.2    Safer, B.3
  • 30
    • 84865864065 scopus 로고    scopus 로고
    • The genetics and neuropathology of Parkinson's disease
    • Houlden H, Singleton AB. The genetics and neuropathology of Parkinson's disease. Acta Neuropathol. 2012;124(3):325-338.
    • (2012) Acta Neuropathol , vol.124 , Issue.3 , pp. 325-338
    • Houlden, H.1    Singleton, A.B.2
  • 32
    • 75749156257 scopus 로고    scopus 로고
    • PINK1 is selectively stabilized on impaired mitochondria to activate Parkin
    • Narendra DP, Jin SM, Tanaka A, et al. PINK1 is selectively stabilized on impaired mitochondria to activate Parkin. PLoS Biol. 2010;8(1):e1000298.
    • (2010) PLoS Biol , vol.8 , Issue.1
    • Narendra, D.P.1    Jin, S.M.2    Tanaka, A.3
  • 33
    • 20144389422 scopus 로고    scopus 로고
    • Hypersensitivity of DJ-1-defcient mice to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrindine (MPTP) and oxida-tive stress
    • Kim RH, Smith PD, Aleyasin H, et al. Hypersensitivity of DJ-1-defcient mice to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrindine (MPTP) and oxida-tive stress. Proc Natl Acad Sci U S A. 2005;102(14):5215-5220.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.14 , pp. 5215-5220
    • Kim, R.H.1    Smith, P.D.2    Aleyasin, H.3
  • 34
    • 0035967883 scopus 로고    scopus 로고
    • An unfolded putative transmembrane polypeptide, which can lead to endoplasmic reticu-lum stress, is a substrate of Parkin
    • Imai Y, Soda M, Inoue H, Hattori N, Mizuno Y, Takahashi R. An unfolded putative transmembrane polypeptide, which can lead to endoplasmic reticu-lum stress, is a substrate of Parkin. Cell. 2001;105(7):891-902.
    • (2001) Cell , vol.105 , Issue.7 , pp. 891-902
    • Imai, Y.1    Soda, M.2    Inoue, H.3    Hattori, N.4    Mizuno, Y.5    Takahashi, R.6
  • 35
    • 33646152108 scopus 로고    scopus 로고
    • Mitochondria are a direct site of Aβ accumulation in Alzheimer's disease neurons: Implications for free radical generation and oxidative damage in disease progression
    • Manczak M, Anekonda TS, Henson E, Park BS, Quinn J, Reddy PH. Mitochondria are a direct site of Aβ accumulation in Alzheimer's disease neurons: implications for free radical generation and oxidative damage in disease progression. Hum Mol Genet. 2006;15(9):1437-1449.
    • (2006) Hum Mol Genet , vol.15 , Issue.9 , pp. 1437-1449
    • Manczak, M.1    Anekonda, T.S.2    Henson, E.3    Park, B.S.4    Quinn, J.5    Reddy, P.H.6
  • 36
    • 84883453343 scopus 로고    scopus 로고
    • Suppression of eIF2α kinases alleviates Alzheimer's disease-related plasticity and memory defcits
    • Ma T, Trinh MA, Wexler AJ, et al. Suppression of eIF2α kinases alleviates Alzheimer's disease-related plasticity and memory defcits. Nat Neurosci. 2013;16(9):1299-1305.
    • (2013) Nat Neurosci , vol.16 , Issue.9 , pp. 1299-1305
    • Ma, T.1    Trinh, M.A.2    Wexler, A.J.3
  • 38
    • 0037150687 scopus 로고    scopus 로고
    • Sp1 and TAFII130 transcriptional activity disrupted in early Huntington's disease
    • Dunah AW, Jeong H, Griffn A, et al. Sp1 and TAFII130 transcriptional activity disrupted in early Huntington's disease. Science. 2002;296(5576): 2238-2243.
    • (2002) Science , vol.296 , Issue.5576 , pp. 2238-2243
    • Dunah, A.W.1    Jeong, H.2    Griffn, A.3
  • 39
    • 33749042331 scopus 로고    scopus 로고
    • Transcriptional repression of PGC-1α by mutant huntingtin leads to mito-chondrial dysfunction and neurodegeneration
    • Cui L, Jeong H, Borovecki F, Parkhurst CN, Tanese N, Krainc D. Transcriptional repression of PGC-1α by mutant huntingtin leads to mito-chondrial dysfunction and neurodegeneration. Cell. 2006;127(1):59-69.
    • (2006) Cell , vol.127 , Issue.1 , pp. 59-69
    • Cui, L.1    Jeong, H.2    Borovecki, F.3    Parkhurst, C.N.4    Tanese, N.5    Krainc, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.