The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y

Nucleic Acids Research

Volumn 35, Issue 2, 2007, Pages 664-677

  Zanotto, Ernesto ^a   Shah, Zahid H ^a   Jacobs, Howard T ^a,b  

^a TAMPERE UNIVERSITY HOSPITAL   (Finland)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CCAAT BINDING FACTOR; MITOCHONDRIAL DNA; MITORIBOSOMAL PROTEIN S12; NUCLEAR FACTOR Y; PROTEIN SARS2; PROTEIN SARSM; RIBOSOME PROTEIN; SERINE TRANSFER RNA LIGASE; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BINDING SITE; CELL CULTURE; CELL PROLIFERATION; CELL STRAIN 3T3; CHROMATIN IMMUNOPRECIPITATION; DNA FOOTPRINTING; ELECTROPHORETIC MOBILITY; GEL MOBILITY SHIFT ASSAY; GENE VECTOR; GENETIC TRANSCRIPTION; IN VIVO STUDY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA TRANSLATION; TRANSLATION REGULATION;

ANIMALS; BINDING SITES; CCAAT-BINDING FACTOR; DNA, INTERGENIC; ELECTROPHORETIC MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION; GENES, MITOCHONDRIAL; GENES, REPORTER; MICE; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; NIH 3T3 CELLS; PROMOTER REGIONS (GENETICS); PROTEIN BIOSYNTHESIS; RIBOSOMAL PROTEINS; SERINE-TRNA LIGASE;

EID: 33846912237     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1037     Document Type: Article

References (49)

1. Taanman,J.W. (1999) The mitochondrial genome: Structure, transcription, translation and replication. Biochim. Biophys. Acta, 1410, 103-123.
2. Yokogawa,T., Shimada,N., Takeuchi,N., Benkowski,L., Suzuki,T., Omori,A., Ueda,T., Nishikawa,K., Spremulli,L.L. and Watanabe,K. (2000) Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase. J. Biol. Chem., 275, 19913-19920.
3. Shah,Z.H., Toompuu,M., Hakkinen,T., Rovio,A.T., van Ravenswaay,C., De Leenheer,E.M., Smith,R.J., Cremers,F.P., Cremers,C.W. and Jacobs,H.T. (2001) Novel coding-region polymorphisms in mitochondrial seryl-tRNA synthetase (SARSM) and mitoribosomal protein S12 (RPMS12) genes in DFNA4 autosomal dominant deafness families. Hum. Mutat., 17, 433-434.
4. Gibbons,W.J., Jr, Yan,Q., Li,R., Li,X. and Guan,M.X. (2004) Genomic organization, expression, and subcellular localization of mouse mitochondrial seryl-tRNA synthetase. Biochem. Biophys. Res. Commun., 317, 774-778.
5. Trinklein,N.D., Aldred,S.F., Hartman,S.J., Schroeder,D.I., Otillar,R.P. and Myers,R.M. (2004) An abundance of bidirectional promoters in the human genome. Genome Res., 14, 62-66.
6. Engstrom,P.G., Suzuki,H., Ninomiya,N., Akalin,A., Sessa,L., Lavorgna,G., Brozzi,A., Luzi,L., Tan,S.L., Yang,L. et al. (2006) Complex loci in human and mouse genomes. PLoS Genet., 2, e47.
7. Shah,Z.H., O'Dell,K.M., Miller,S.C., An,X. and Jacobs,H.T. (1997) Metazoan nuclear genes for mitoribosomal protein S12. Gene, 204, 55-62.
8. Mariottini,P., Shah,Z.H., Toivonen,J.M., Bagni,C., Spelbrink,J.N., Amaldi,F. and Jacobs,H.T. (1999) Expression of the gene for mitoribosomal protein S12 is controlled in human cells at the levels of transcription, RNA splicing, and translation. J. Biol. Chem., 274, 31853-31862.
9. Johnson,D.F., Hamon,M. and Fischel-Ghodsian,N. (1998) Characterization of the human mitochondrial ribosomal S12 gene. Genomics, 52, 363-368.
10. Florentz,C., Sohm,B., Tryoen-Toth,P., Putz,J. and Sissler,M. (2003) Human mitochondrial tRNAs in health and disease. Cell Mol. Life Sci., 60, 1356-1375.
11. Miller,C., Saada,A., Shaul,N., Shabtai,N., Ben-Shalom,E., Shaag,A., Hershvovitz,E. and Elpeleg,O. (2004) Defective mitochondrial translation caused by a ribosomal protein (MRPS16) mutation. Ann. Neurol., 56, 734-738.
12. Toivonen,J.M., O'Dell,K.M., Petit,N., Irvine,S.C., Knight,G.K., Lehtonen,M., Longmuir,M., Luoto,K., Touraille,S., Wang,Z. et al. (2001) Technical knockout, a Drosophila model of mitochondrial deafness. Genetics, 159, 241-254.
13. Scarpulla,R.C. (2006) Nuclear control of respiratory gene expression in mammalian cells. J. Cell. Biochem., 97, 673-683.
14. Pinkham,J.L. and Guarente,L. (1985) Cloning and molecular analysis of the HAP2 locus: A global regulator of respiratory genes in Saccharomyces cerevisiae. Mol. Cell. Biol., 5, 3410-3416.
15. Dang,V.D., Valens,M., Bolotin-Fukuhara,M. and Daignan-Fornier,B. (1994) A genetic screen to isolate genes regulated by the yeast CCAAT-box binding protein Hap2p. Yeast, 10, 1273-1283.
16. Schuller,H.J. (2003) Transcriptional control of non-fermentative metabolism in the yeast Saccharomyces cerevisiae. Curr. Genet., 43, 139-160.
17. Manninen,A., Renkema,G.H. and Saksela,K. (2000) Synergistic activation of NFAT by HIV-1 nef and the Ras/MAPK pathway. J. Biol. Chem., 275, 16513-16517.
18. Wadman,I.A., Osada,H., Grutz,G.G., Agulnick,A.D., Westphal,H., Forster,A. and Rabbitts,T.H. (1997) The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. EMBO J., 16, 3145-3157.
19. Sun,J., Li,F., Chen,J. and Xu,J. (2004) Effect of ketamine on NF-kappa B activity and TNF-alpha production in endotoxin-treated rats. Ann. Clin. Lab. Sci., 34, 181-186.
20. Drouin,R., Angers,M., Dallaire,N., Rose,T.M., Khandjian,E.W. and Rousseau,F. (1997) Structural and functional characterization of the human FMR1 promoter reveals similarities with the hnRNP-A2 promoter region. Hum. Mol. Genet., 6, 2051-2060.
21. Pfeifer,G.P. and Tornaletti,S. (1997) Footprinting with UV irradiation and LMPCR. Methods., 11, 189-196.
22. Lacronique,V., Boquet,D., Lopez,S., Kahn,A. and Raymondjean,M. (1992) In vitro and in vivo protein-DNA interactions on the rat erythroid-specific L′ pyruvate kinase gene promoter. Nucleic Acids Res., 20, 5669-5976.
23. Maxam,A.M. and Gilbert,W. (1980) Sequencing end-labeled DNA with base-specific chemical cleavages. Meth. Enzymol., 65, 499-560.
24. Drouin,R., Gao,S. and Holmquist,G.P. (1996) Agarose gel electrophoresis for DNA damage analysis. In Pfeifer,G.P. (ed.), Technologies for Detection of DNA Damage and Mutations. Plenum, NY, pp. 37-43.
25. Angers,M., Cloutier,J.F., Castonguay,A. and Drouin,R. (2001) Optimal conditions to use Pfu exo(-) DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols. Nucleic Acids Res., 29, E83.
26. Spencer,V.A., Sun,J.M., Li,L. and Davie,J.R. (2003) Chromatin immunoprecipitation: A tool for studying histone acetylation and transcription factor binding. Methods, 31, 67-75.
27. Xing,Y., Fikes,J.D. and Guarente,L. (1993) Mutations in yeast HAP2/HAP3 define a hybrid CCAAT box binding domain. EMBO J., 12, 4647-4655.
28. McNabb,D.S., Xing,Y. and Guarente,L. (1995) Cloning of yeast HAP5: A novel subunit of a heterotrimeric complex required for CCAAT binding. Genes Dev., 9, 47-58.
29. Forsburg,S.L. and Guarente,L. (1989) Identification and characterization of HAP4: A third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev., 3, 1166-1178.
30. Raghevendran,V., Patil,K.R., Olsson,L. and Nielsen,J. (2006) Hap4 is not essential for activation of respiration at low specific growth rates in Saccharomyces cerevisiae. J. Biol. Chem., 281, 12308-12314.
31. Hooft van Huijsduijnen,R., Li,X.Y., Black,D., Matthes,H., Benoist,C. and Mathis,D. (1990) Co-evolution from yeast to mouse: CDNA cloning of the two NF-Y (CP-1/CBF) subunits. EMBO J., 9, 3119-3127.
32. Mantovani,R. (1998) A survey of 178 NF-Y binding CCAAT boxes. Nucleic Acids Res., 26, 1135-1143.
33. Wasner,M., Haugwitz,U., Reinhard,W., Tschop,K., Spiesbach,K., Lorenz,J., Mossner,J. and Engeland,K. (2003) Three CCAAT-boxes and a single cell cycle genes homology region (CHR) are the major regulating sites for transcription from the human cyclin B2 promoter. Gene, 312, 225-223.
34. Zwicker,J., Gross,C., Lucibello,F.C., Truss,M., Ehlert,F., Engeland,K. and Mu?ller,R. (1995) Cell cycle regulation of cdc25C transcription is mediated by the periodic repression of the glutamine-rich activators NF-Y and Sp1. Nucleic Acids Res., 23, 3822-3830.
35. Arcot,S.S., Flemington,E.K. and Deininger,P.L. (1989) The human thymidine kinase gene promoter. Deletion analysis and specific protein binding. J. Biol. Chem., 264, 2343-2349.
36. Ikeda,S., Ayabe,H., Mori,K., Seki,Y. and Seki,S. (2002) Identification of the functional elements in the bidirectional promoter of the mouse O-sialoglycoprotein endopeptidase and APEX nuclease genes. Biochem. Biophys. Res. Commun., 296, 785-791.
37. Ronchi,A., Bellorini,M., Mongelli,N. and Mantovani,R. (1995) CAAT-box binding protein NF-Y (CBF, CP1) recognizes the minor groove and distorts DNA. Nucleic Acids Res., 23, 4565-4572.
38. Mantovani,R., Pessara,U., Tronche,F., Li,X.Y., Knapp,A.M., Pasquali,J.L., Benoist,C. and Mathis,D. (1992) Monoclonal antibodies to NF-Y define its function in MHC class II and albumin gene transcription. EMBO J., 11, 3315-3322.
39. Milos,P.M. and Zaret,K.S. (1992) A ubiquitous factor is required for C/ EBP-related proteins to form stable transcription complexes on an albumin promoter segment in vitro. Genes Dev., 6, 991-1004.
40. Jackson,S.M., Ericsson,J., Mantovani,R. and Edwards,P.A. (1998) Synergistic activation of transcription by nuclear factor Y and sterol regulatory element binding protein. J. Lipid Res., 39, 767-776.
41. Park,S.K., Oh,S.Y., Lee,M.Y., Yoon,S., Kim,K.S. and Kim,J.W. (2004) CCAAT/enhancer binding protein and nuclear factor-Y regulate adiponectin gene expression in adipose tissue. Diabetes, 53, 2757-2766.
42. Zhu,Q.S., Qian,B. and Levy,D. (2004) CCAAT/enhancer-binding protein alpha (C/EBPalpha) activates transcription of the human microsomal epoxide hydrolase gene (EPHX1) through the interaction with DNA-bound NF-Y. J. Biol. Chem., 279, 29902-29910.
43. Xu,Y., Zhou,Y.L., Luo,W., Zhu,Q.S., Levy,D., MacDougald,O.A. and Snead,M.L. (2006) NF-Y and CCAAT/enhancer-binding protein alpha synergistically activate the mouse amelogenin gene. J. Biol. Chem., 281, 16090-16098.
44. Virbasius,J.V. and Scarpulla,R.C. (1991) Transcriptional activation through ETS domain binding sites in the cytochrome c oxidase subunit IV gene. Mol. Cell. Biol., 11, 5631-5638.
45. Martin,E., Chinenov,Y., Yu,M., Schmidt,T.K. and Yang,X.-Y. (1996) Redox regulation of GA-binding protein-α DNA binding activity. J. Biol. Chem., 271, 25617-25623.
46. Ammendola,R., Fiore,F., Esposito,F., Caserta,G., Mesuraca,M., Russo,T. and Cimino,F. (1995) Differentially expressed mRNAs as a consequence of oxidative stress in intact cells. FEBS Lett., 371, 209-213.
47. Zhang,C. and Wong-Riley,M.T. (2000) Depolarizing stimulation upregulates GA-binding protein in neurons: A transcription factor involved in the bigenomic expression of cytochrome oxidase subunits. Eur. J. Neurosci., 12, 1013-1023.
48. Brons,J.F., De Jong,M., Valens,M., Grivell,L.A., Bolotin-Fukuhara,M. and Blom,J. (2002) Dissection of the promoter of the HAP4 gene in S. cerevisiae unveils a complex regulatory framework of transcriptional regulation. Yeast, 19, 923-932.
49. Hansen,J.J., Bross,P., Westergaard,M., Nielsen,M.N., Eiberg,H., Borglum,A.D., Mogensen,J., Kristiansen,K., Bolund,L. and Gregersen,N. (2003) Genomic structure of the human mitochondrial chaperonin genes: HSP60 and HSP10 are localised head to head on chromosome 2 separated by a bidirectional promoter. Hum. Genet., 112, 71-77.