Novel genes that mediate nuclear respiratory factor 1-regualted neurite outgrowth in neuroblastoma IMR-32 cells

Gene

Volumn 515, Issue 1, 2013, Pages 62-70

  Tong, Chih Wei ^a   Wang, Jen Ling ^a   Jiang, Mei Sian ^a   Hsu, Chia Hao ^a   Chang, Wen Teng ^b   Huang, A Min ^a  

^a NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^b CHUNG HWA UNIVERSITY OF MEDICAL TECHNOLOGY   (Taiwan)

Author keywords

Bioinformatics; Neurite outgrowth; Neuroblastoma cells; NRF 1; NRF 1 response element

Indexed keywords

MESSENGER RNA; NUCLEAR RESPIRATORY FACTOR 1; RHOA GUANINE NUCLEOTIDE BINDING PROTEIN; SMAD5 PROTEIN; SPROUTY PROTEIN;

ARTICLE; BIOINFORMATICS; CELL DIFFERENTIATION; CHROMATIN IMMUNOPRECIPITATION; GEL MOBILITY SHIFT ASSAY; GENE CONTROL; GENE LOCATION; GENE OVEREXPRESSION; GENE SILENCING; GENE TARGETING; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; IN VIVO STUDY; NERVE FIBER GROWTH; NEUROBLASTOMA CELL; PRIORITY JOURNAL; PROTEIN BINDING; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE KNOCKDOWN TECHNIQUES; HUMANS; NEURITES; NEUROBLASTOMA; NF-E2-RELATED FACTOR 1; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; RESPONSE ELEMENTS; RNA, MESSENGER; TRANSCRIPTION FACTORS;

EID: 84872272608     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.11.026     Document Type: Article

References (45)

1. Albertinazzi C. ADP-ribosylation factor 6 and a functional PIX/p95-APP1 complex are required for Rac1B-mediated neurite outgrowth. Mol. Biol. Cell 2003, 14:1295-1307.
2. Asangani I.A., Rasheed S.A., Leupold J.H., Post S., Allgayer H. NRF-1, and AP-1 regulate the promoter of the human calpain small subunit 1 (CAPNS1) gene. Gene 2008, 410:197-206.
3. Becker T.S., Burgess S.M., Amsterdam A.H., Allende M.L., 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, 125:4369-4378.
4. Cam H., et al. A common set of gene regulatory networks links metabolism and growth inhibition. Mol. Cell 2004, 16:399-411.
5. Chan C.H., et al. Deciphering the transcriptional complex critical for RhoA gene expression and cancer metastasis. Nat. Cell Biol. 2010, 12:457-467.
6. Chang W.T., Huang A.M. Alpha-Pal/NRF-1 regulates the promoter of the human integrin-associated protein/CD47 gene. J. Biol. Chem. 2004, 279:14542-14550.
7. Chang W.T., Chen H.I., Chiou R.J., Chen C.Y., Huang A.M. A novel function of transcription factor alpha-Pal/NRF-1: increasing neurite outgrowth. Biochem. Biophys. Res. Commun. 2005, 334:199-206.
8. Chau C.M., Evans M.J., Scarpulla R.C. Nuclear respiratory factor 1 activation sites in genes encoding the gamma-subunit of ATP synthase, eukaryotic initiation factor 2 alpha, and tyrosine aminotransferase. Specific interaction of purified NRF-1 with multiple target genes. J. Biol. Chem. 1992, 267:6999-7006.
9. Conaway R.C., Conaway J.W. General initiation factors for RNA polymerase II. Annu. Rev. Biochem. 1993, 62:161-190.
10. DeSimone S.M., 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, 13:3641-3649.
11. Ding W., Bellusci S., Shi W., Warburton D. Genomic structure and promoter characterization of the human Sprouty4 gene, a novel regulator of lung morphogenesis. Am. J. Physiol. Lung Cell Mol. Physiol. 2004, 287:L52-L59.
12. Eddy S.R. Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
13. Efiok B.J., Safer B. Transcriptional regulation of E2F-1 and eIF-2 genes by alpha-pal: a potential mechanism for coordinated regulation of protein synthesis, growth, and the cell cycle. Biochim. Biophys. Acta 2000, 1495:51-68.
14. Evans M.J., Scarpulla R.C. NRF-1: a trans-activator of nuclear-encoded respiratory genes in animal cells. Genes Dev. 1990, 4:1023-1034.
15. Evans M.J., Scarpullas R.C. Interaction of nuclear factors with multiple sites in the somatic cytochrome c promoter. J. Biol. Chem. 1989, 264:14361-14368.
16. Evrard C., Caron S., Rouget P. Functional analysis of the NPDC-1 gene. Gene 2004, 343:153-163.
17. FitzGerald P.C., Shlyakhtenko A., Mir A.A., Vinson C. Clustering of DNA sequences in human promoters. Genome Res. 2004, 14:1562-1574.
18. Gaitanos T.N., Santamaria A., Jeyaprakash A.A., Wang B., Conti E., Nigg E.A. Stable kinetochore-microtubule interactions depend on the Ska complex and its new component Ska3/C13Orf3. EMBO J. 2009, 28:1442-1452.
19. Gallo G., Letourneau P.C. Regulation of growth cone actin filaments by guidance cues. J. Neurobiol. 2004, 58:92-102.
20. Gonen N., Assaraf Y.G. The obligatory intestinal folate transporter PCFT (SLC46A1) is regulated by nuclear respiratory factor 1. J. Biol. Chem. 2010, 285:33602-33613.
21. Gottlieb E., et al. Transgenic mouse model for studying the transcriptional activity of the p53 protein: age- and tissue-dependent changes in radiation-induced activation during embryogenesis. EMBO J. 1997, 16:1381-1390.
22. Hausott B., et al. Sprouty2 and -4 regulate axon outgrowth by hippocampal neurons. Hippocampus 2012, 22:434-441.
23. Hernandez-Deviez D.J. ARNO and ARF6 regulate axonal elongation and branching through downstream activation of phosphatidylinositol 4-phosphate 5-kinase. Mol. Biol. Cell 2003, 15:111-120.
24. Huo L., Scarpulla R.C. Mitochondrial DNA instability and peri-implantation lethality associated with targeted disruption of nuclear respiratory factor 1 in mice. Mol. Cell. Biol. 2001, 21:644-654.
25. Johnson D.G., Schwarz J.K., Cress W.D., Nevins J.R. Expression of transcription factor E2F1 induces quiescent cells to enter S phase. Nature 1993, 365:349-352.
26. Jordan M., Schallhorn A., Wurm F.M. Transfecting mammalian cells: optimization of critical parameters affecting calcium-phosphate precipitate formation. Nucleic Acids Res. 1996, 24:596-601.
27. Kerppola T.K., Kane C.M. RNA polymerase: regulation of transcript elongation and termination. FASEB J. 1991, 5:2833-2842.
28. Kherrouche Z., De Launoit Y., Monte D. The NRF-1/alpha-PAL transcription factor regulates human E2F6 promoter activity. Biochem. J. 2004, 383:529-536.
29. Komarova Y., et al. Mammalian end binding proteins control persistent microtubule growth. J. Cell Biol. 2009, 184:691-706.
30. Kuiperij H.B., et al. Characterisation of PDZ-GEFs, a family of guanine nucleotide exchange factors specific for Rap1 and Rap2. Biochim Biophys Acta 2003, 1593:141-149.
31. Nakagawa H., Koyama K., Murata Y., Morito M., Akiyama T., Nakamura Y. EB3, a novel member of the EB1 family preferentially expressed in the central nervous system, binds to a CNS-specific APC homologue. Oncogene 2000, 19:210-216.
32. Nusser N., Gosmanova E., Zheng Y., Tigyi G. Nerve growth factor signals through TrkA, phosphatidylinositol 3-kinase, and Rac1 to inactivate RhoA during the initiation of neuronal differentiation of PC12 cells. J. Biol. Chem. 2002, 277:35840-35846.
33. Rios I., Alvarez-Rodriguez R., Marti E., Pons S. Bmp2 antagonizes sonic hedgehog-mediated proliferation of cerebellar granule neurones through Smad5 signalling. Development 2004, 131:3159-3168.
34. Sansal I., Dupont E., Toru D., Evrard C., Rouget P. NPDC-1, a regulator of neural cell proliferation and differentiation, interacts with E2F-1, reduces its binding to DNA and modulates its transcriptional activity. Oncogene 2000, 19:5000-5009.
35. Sasaki A., et al. Mammalian Sprouty4 suppresses Ras-independent ERK activation by binding to Raf1. Nat. Cell Biol. 2003, 5:427-432.
36. Scarpulla R.C. Nulear control of respiratory chain expression in mammalian cells. J. Bioenerg. Biomembr. 1997, 29:109-119.
37. Scarpulla R.C. Nuclear control of respiratory chain expression by nuclear respiratory factors and PGC-1-related coactivator. Ann. N. Y. Acad. Sci. 2008, 1147:321-334.
38. Stradal T.E., Scita G. Protein complexes regulating Arp2/3-mediated actin assembly. Curr. Opin. Cell Biol. 2006, 18:4-10.
39. Suzuki Y., Yamashita R., Nakai K., Sugano S. DBTSS: DataBase of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 2002, 30:328-331.
40. Tanabe K., Torii T., Natsume W., Braesch-Andersen S., Watanabe T., Satake M. A novel GTPase-activating protein for ARF6 directly interacts with clathrin and regulates clathrin-dependent endocytosis. Mol. Biol. Cell 2005, 16:1617-1628.
41. Virbasius J.V., Scarpulla R.C. Activation of the human mitochondrial transcription factor A gene by nuclear respiratory factors: a potential regulatory link between nuclear and mitochondrial gene expression in organelle biogenesis. Proc. Natl. Acad. Sci. U. S. A. 1994, 91:1309-1313.
42. Wang J.L., Chang W.T., Tong C.W., Kohno K., Huang A.M. Human synapsin I mediates the function of nuclear respiratory factor 1 in neurite outgrowth in neuroblastoma IMR-32 cells. J. Neurosci. Res. 2009, 87:2255-2263.
43. Xie X., et al. Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 2005, 434:338-345.
44. Yamamoto N., Akiyama S., Katagiri T., Namiki M., Kurokawa T., Suda T. Smad1 and smad5 act downstream of intracellular signalings of BMP-2 that inhibits myogenic differentiation and induces osteoblast differentiation in C2C12 myoblasts. Biochem. Biophys. Res. Commun. 1997, 238:574-580.
45. Yuan J., Luo K., Zhang L., Cheville J.C., Lou Z. USP10 regulates p53 localization and stability by deubiquitinating p53. Cell 2010, 140:384-396.