Identification of the 'NORE' (N-Oct-3 responsive element), a novel structural motif and composite element

Nucleic Acids Research

Volumn 33, Issue 5, 2005, Pages 1513-1523

  Alazard, Robert ^a   Blaud, Magali ^a   Elbaz, Shmouel ^a   Vossen, Christine ^a   Icre, Guillaume ^a   Joseph, Gérard ^a   Nieto, Laurence ^a   Erard, Monique ^a  

^a INSTITUT DE PHARMACOLOGIE ET DE BIOLOGIE STRUCTURALE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC LEVO AMINO ACID DECARBOXYLASE; CORTICOTROPIN RELEASING FACTOR; DNA; HEPATOCYTE NUCLEAR FACTOR 3; HEPATOCYTE NUCLEAR FACTOR 3BETA; OCTAMER TRANSCRIPTION FACTOR; PROTEIN DERIVATIVE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR N OCT 3; TRANSCRIPTION FACTOR PIT 1; TRANSCRIPTION FACTOR UNC; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; FOXA2 PROTEIN, HUMAN; FOXA2 PROTEIN, RAT; NUCLEAR PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; POU5F1 PROTEIN, HUMAN;

ARTICLE; BINDING SITE; CENTRAL NERVOUS SYSTEM; CONTROLLED STUDY; DIMERIZATION; DNA FOOTPRINTING; DNA RESPONSIVE ELEMENT; GEL MOBILITY SHIFT ASSAY; HUMAN; LUNG CARCINOGENESIS; LUNG SMALL CELL CANCER; LUNG TUMOR; MAMMAL; MOLECULAR DYNAMICS; MOLECULAR MODEL; NERVE CELL DIFFERENTIATION; NERVOUS SYSTEM DEVELOPMENT; NEUROENDOCRINE TUMOR; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; TISSUE SPECIFICITY; TRANSCRIPTION REGULATION; ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; NERVE CELL; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE; RAT; SMALL CELL CARCINOMA;

MAMMALIA;

AMINO ACID MOTIFS; ANIMALS; AROMATIC-L-AMINO-ACID DECARBOXYLASES; BASE SEQUENCE; BINDING SITES; CARCINOMA, SMALL CELL; CORTICOTROPIN-RELEASING HORMONE; DIMERIZATION; DNA FOOTPRINTING; DNA-BINDING PROTEINS; HEPATOCYTE NUCLEAR FACTOR 3-BETA; HUMANS; LUNG NEOPLASMS; MODELS, MOLECULAR; NEURONS; NUCLEAR PROTEINS; OCTAMER TRANSCRIPTION FACTOR-3; PROMOTER REGIONS (GENETICS); PROTEIN STRUCTURE, TERTIARY; RATS; RESPONSE ELEMENTS; TRANSCRIPTION FACTORS;

EID: 15044349256     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki284     Document Type: Article

References (64)

1. Veeramachaneni,V., Makalowski,W., Galdzicki,M., Sood,R. and Makalowska,I. (2004) Mammalian overlapping genes: The comparative perspective. [i#Genome Res.#1i], [b#14#1b], 280-286.
2. Warren,A.J. (2002) Eukaryotic transcription factors. [i#Curr. Opin. Struct. Biol.#1i], [b#12#1b], 107-114.
3. Hahn,S. (2004) Structure and mechanism of the RNA polymerase II transcription machinery. [i#Nature Struct. Mol. Biol.#1i], [b#11#1b], 394-403.
4. Johnson,W. and Jameson,J.L. (1998) Transcriptional control of gene expression. In Jameson,J.L. (ed.), [i#Principles of Molecular Medicine#1i] Humana Press Inc., Towota, NJ.
5. Latchman,D.S. (2000) Transcription factors as potential targets for therapeutic drugs. [i#Curr. Pharm. Biotechnol.#1i], [b#1#1b], 57-61.
6. Darnell,J.E.,Jr (2002) Transcription factors as targets for cancer therapy. [i#Nature Rev. Cancer#1i], [b#2#1b], 740-749.
7. Fujii,H. and Hamada,H. (1993) A CNS-specific POU transcription factor, Brn-2, is required for establishing mammalian neural cell lineages. [i#Neuron#1i], [b#11#1b], 1197-1206.
8. Nakai,S., Kawano,H., Yudate,T., Nishi,M., Kuno,J., Nagata,A., Jishage,K., Hamada,H., Fujii,H., Kawamura,K. [i#et al.#1i] (1995) The POU domain transcription factor Brn-2 is required for the determination of specific neuronal lineages in the hypothalamus of the mouse. [i#Genes Dev.#1i], [b#9#1b], 3109-3121.
9. Schonemann,M.D., Ryan,A.K., McEvilly,R.J., O'Connell,S.M., Arias,C.A., Kalla,K.A., Li,P., Sawchenko,P.E. and Rosenfeld,M.G. (1995) Development and survival of the endocrine hypothalamus and posterior pituitary gland requires the neuronal POU domain factor Brn-2. [i#Genes Dev.#1i], [b#9#1b] 3122-3135.
10. Andersen,B. and Rosenfeld,M.G. (2001) POU domain factors in the neuroendocrine system: Lessons from developmental biology provide insights into human disease. [i#Endocr. Rev.#1i], [b#22#1b], 2-35.
11. Eisen,T., Easty,D.J., Bennett,D.C. and Goding,C.R (1995) The POU domain transcription factor Brn-2: Elevated expression in malignant melanoma and regulation of melanocyte-specific gene expression. [i#Oncogene#1i], [b#11#1b], 2157-2164.
12. Eisen,T.G. (1996) The control of gene expression in melanocytes and melanomas. [i#Melanoma Res.#1i], [b#6#1b], 277-284.
13. Thomson,J.A., Murphy,K., Baker,E., Sutherland,G.R., Parsons,P.G., Sturm,R.A. and Thomson,F. (1995) The brn-2 gene regulates the melanocytic phenotype and tumorigenic potential of human melanoma cells. [i#Oncogene#1i], [b#11#1b], 691-700.
14. Goodall,J., Wellbrock,C., Dexter,T.J., Roberts,K., Marais,R. and Goding,C.R. (2004) The Brn-2 transcription factor links activated BRAF to melanoma proliferation. [i#Mol. Cell. Biol.#1i], [b#24#1b], 2923-2931.
15. Latchman,D.S. (1999) POU family transcription factors in the nervous system. [i#J. Cell. Physiol.#1i], [b#179#1b], 126-133.
16. Klemm,J.D., Rould,M.A., Aurora,R, Herr,W. and Pabo,C.O. (1994) Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules. [i#Cell#1i], [b#77#1b], 21-32.
17. Herr,W. and Cleary,M.A. (1995) The POU domain: Versatility in transcriptional regulation by a flexible two-in-one DNA-binding domain. [i#Genes Dev.#1i], [b#9#1b], 1679-1693.
18. Jacobson,E.M., Li,P., Leon-del-Rio,A., Rosenfeld,M.G. and Aggarwal,A.K. (1997) Structure of Pit-1 POU domain bound to DNA as a dimer: Unexpected arrangement and flexibility. [i#Genes Dev.#1i], [b#11#1b], 198-212.
19. van Leeuwen,H.C., Strating,M.J., Rensen,M., de Laat,W. and van der Vliet,P.C. (1997) Linker length and composition influence the flexibility of Oct-1 DNA binding. [i#EMBO J.#1i], [b#16#1b], 2043-2053.
20. Remenyi,A., Tomilin,A., Pohl,E., Lins,K., Philippsen,A., Reinbold,R., Scholer,H.R. and Wilmanns,M. (2001) Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. [i#Mol. Cell#1i], [b#8#1b], 569-580.
21. Millevoi,S., Thion,L., Joseph,G., Vossen,C., Ghisolfi-Nieto,L. and Erard,M. (2001) Atypical binding of the neuronal POU protein N-Oct3 to noncanonical DNA targets. Implications for heterodimerization with HNF-3 beta. [i#Eur. J. Biochem.#1i], [b#268#1b], 781-791.
22. Blaud,M., Vossen,C., Joseph,G., Alazard,R., Erard,M. and Nieto,L. (2004) Characteristic patterns of N Oct-3 binding to a set of neuronal promoters. [i#J. Mol. Biol.#1i], [b#339#1b], 1049-1058.
23. Le Van Thai,A., Coste,E., Allen,J.M., Palmiter,R.D. and Weber,M.J. (1993) Identification of a neuron-specific promoter of human aromatic L-amino acid decarboxylase gene. [i#Brain Res. Mol. Brain Res.#1i], [b#17#1b] 227-238.
24. Thompson,R.C., Seasholtz,A.F. and Herbert,E. (1987) Rat corticotropin-releasing hormone gene: Sequence and tissue-specific expression. [i#Mol. Endocrinol.#1i], [b#1#1b], 363-370.
25. Ausubel,F., Brent,R., Kingston,R., Moore,D., Seidman,J. and Struhl,K. (1993) [i#Current Protocols in Molecular Biology#1i]., John Wiley and Sons, Canada.
26. Kuwabara,M.D. and Sigman,D.S. (1987) Footprinting DNA-protein complexes [i#in situ#1i] following gel retardation assays using 1,10-phenanthroline-copper ion: [i#Escherichia coli#1i] RNA polymerase-lac promoter complexes. [i#Biochemistry#1i], [b#26#1b], 7234-7238.
27. Maxam,A.M. and Gilbert,W. (1977) A new method for sequencing DNA. [i#Proc. Natl Acad. Sci. USA#1i], [b#74#1b], 560-564.
28. Clark,K.L., Halay,E.D., Lai,E. and Burley,S.K. (1993) Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. [i#Nature#1i], [b#364#1b], 412-420.
29. Lavery,R. and Sklenar,H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. [i#J. Biomol. Struct. Dyn.#1i], [b#6#1b], 63-91.
30. Botquin,V., Hess,H., Fuhrmann,G., Anastassiadis,C., Gross,M.K., Vriend,G. and Scholer,H.R. (1998) New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2. [i#Genes Dev.#1i], [b#12#1b], 2073-2090.
31. Tomilin,A., Remenyi,A., Lins,K., Bak,H., Leidel,S., Vriend,G., Wilmanns,M. and Scholer,H.R. (2000) Synergism with the coactivator OBF-1 (OCA-B, BOB-1) is mediated by a specific POU dimer configuration. [i#Cell#1i], [b#103#1b], 853-864.
32. Scully,K.M., Jacobson,E.M., Jepsen,K., Lunyak,V., Viadiu,H., Carriere,C., Rose,D.W., Hooshmand,F., Aggarwal,A.K. and Rosenfeld,M.G. (2000) Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. [i#Science#1i], [b#290#1b], 1127-1131.
33. Spassky,A. and Sigman,D.S. (1985) Nuclease activity of 1,10-phenanthroline-copper ion. Conformational analysis and footprinting of the lac operon. [i#Biochemistry#1i], [b#24#1b], 8050-8056.
34. Schaeffer,F., Rimsky,S. and Spassky,A. (1996) DNA-stacking interactions determine the sequence specificity of the deoxyribonuclease activity of 1,10-phenanthroline-copper ion. [i#J. Mol. Biol.#1i], [b#260#1b], 523-539.
35. Diamond,M.I., Miner,J.N., Yoshinaga,S.K. and Yamamoto,K.R. (1990) Transcription factor interactions: Selectors of positive or negative regulation from a single DNA element. [i#Science#1i], [b#249#1b], 1266-1272.
36. Kel-Margoulis,O.V., Kel,A.E., Reuter,I., Deineko,I.V. and Wingender,E. (2002) TRANSCompel: A database on composite regulatory elements in eukaryotic genes. [i#Nucleic Acids Res.#1i], [b#30#1b], 332-334.
37. Makeev,V.J., Lifanov,A.P., Nazina,A.G. and Papatsenko,D.A. (2003) Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. [i#Nucleic Acids Res.#1i], [b#31#1b], 6016-6026.
38. Ambrosetti,D.C., Basilico,C. and Dailey,L. (1997) Synergistic activation of the fibroblast growth factor 4 enhancer by Sox2 and Oct-3 depends on protein-protein interactions facilitated by a specific spatial arrangement of factor binding sites. [i#Mol. Cell. Biol.#1i], [b#17#1b], 6321-6329.
39. Nishimoto,M., Fukushima,A., Okuda,A. and Muramatsu,M. (1999) The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. [i#Mol. Cell. Biol.#1i], [b#19#1b], 5453-5465.
40. Tomioka,M., Nishimoto,M., Miyagi,S., Katayanagi,T., Fukui,N., Niwa,H., Muramatsu,M. and Okuda,A. (2002) Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex. [i#Nucleic Acids Res.#1i], [b#30#1b], 3202-3213.
41. Katoh,M. (2004) Human FOX gene family (Review). [i#Int. J. Oncol.#1i], [b#25#1b], 1495-1500.
42. Costa,R.H., Kalinichenko,V.V. and Lim,L. (2001) Transcription factors in mouse lung development and function. [i#Am. J. Physiol. Lung Cell. Mol. Physiol.#1i], [b#280#1b], L823-L838.
43. Lantz,K.A., Vatamaniuk,M.Z., Brestelli,J.E., Friedman,J.R., Matschinsky,F.M. and Kaestner,K.H. (2004) Foxa2 regulates multiple pathways of insulin secretion. [i#J. Clin. Invest.#1i], [b#114#1b], 512-520.
44. Wan,H., Xu,Y., Ikegami,M., Stahlman,M.T., Kaestner,K.H., Ang,S.L. and Whitsett,J.A. (2004) Foxa2 is required for transition to air breathing at birth. [i#Proc. Natl Acad. Sci. USA#1i], [b#101#1b], 14449-14454.
45. Khoor,A., Stahlman,M.T., Johnson,J.M., Olson,S.J. and Whitsett,J.A. (2004) Forkhead box A2 transcription factor is expressed in all types of neuroendocrine lung tumors. [i#Hum. Pathol.#1i], [b#35#1b], 560-564.
46. Stupp,R., Monnerat,C., Turrisi,A.T.,III, Perry,M.C. and Leyvraz,S. (2004) Small cell lung cancer: State of the art and future perspectives. [i#Lung Cancer#1i], [b#45#1b], 105-117.
47. Rossi,A., Maione,P., Colantuoni,G., Guerriero,C. and Gridelli,C. (2004) The role of new targeted therapies in small-cell lung cancer. [i#Crit. Rev. Oncol. Hematol.#1i], [b#51#1b], 45-53.
48. Muller-Hagen,G., Beinert,T. and Sommer,A. (2004) Aspects of lung cancer gene expression profiling. [i#Curr. Opin. Drug Discov. Devel.#1i], [b#7#1b] 290-303.
49. Vachtenheim,J. and Novotna,H. (1997) Expression of the aromatic L-amino acid decarboxylase mRNA in human tumour cell lines of neuroendocrine and neuroectodermal origin. [i#Eur. J. Cancer#1i], [b#33#1b], 2411-2417.
50. Schreiber,E., Himmelmann,A., Malipiero,U., Tobler,A., Stahel,R. and Fontana,A. (1992) Human small cell lung cancer expresses the octamer DNA-binding and nervous system-specific transcription factor N-Oct 3 (brain-2). [i#Cancer Res.#1i], [b#52#1b], 6121-6124.
51. Auchus,R.J., Mastorakos,G., Friedman,T.C. and Chrousos,G.P. (1994) Corticotropin-releasing hormone production by a small cell carcinoma in a patient with ACTH-dependent Cushing's syndrome. [i#J. Endocrinol. Invest.#1i], [b#17#1b], 447-452.
52. Moody,T.W., Zia,F., Venugopal,R., Korman,L.Y., Goldstein,A.L. and Fagarasan,M. (1994) Corticotropin-releasing factor stimulates cyclic AMP, arachidonic acid release, and growth of lung cancer cells. [i#Peptides#1i], [b#15#1b], 281-285.
53. Inagaki,H., Eimoto,T., Haimoto,H., Hosoda,S. and Kato,K. (1993) Aldolase C in neuroendocrine tumors: An immunohistochemical study. [i#Virchows Arch. B Cell Pathol. Incl. Mol. Pathol.#1i], [b#64#1b], 297-302.
54. Rhee,J.M., Gruber,C.A., Brodie,T.B., Trieu,M. and Turner,E.E. (1998) Highly cooperative homodimerization is a conserved property of neural POU proteins. [i#J. Biol. Chem.#1i], [b#273#1b], 34196-34205.
55. Hannenhalli,S. and Levy,S. (2002) Predicting transcription factor synergism. [i#Nucleic Acids Res.#1i], [b#30#1b], 4278-4284.
56. Wasserman,W.W. and Krivan,W. (2003) [i#In silico#1i] identification of metazoan transcriptional regulatory regions. [i#Naturwissenschaften#1i], [b#90#1b], 156-166.
57. Khorasanizadeh,S. and Rastinejad,F. (2001) Nuclear-receptor interactions on DNA-response elements. [i#Trends Biochem. Sci.#1i], [b#26#1b], 384-390.
58. Newman,J.R. and Keating,A.E. (2003) Comprehensive identification of human bZIP interactions with coiled-coil arrays. [i#Science#1i], [b#300#1b] 2097-2101.
59. Garvie,C.W. and Wolberger,C. (2001) Recognition of specific DNA sequences. [i#Mol. Cell#1i], [b#8#1b], 937-946.
60. Selvaraj,S., Kono,H. and Sarai,A. (2002) Specificity of protein-DNA recognition revealed by structure-based potentials: Symmetric/asymmetric and cognate/non-cognate binding. [i#J. Mol. Biol.#1i], [b#322#1b], 907-915.
61. Hoglund,A. and Kohlbacher,O. (2004) From sequence to structure and back again: Approaches for predicting protein-DNA binding. [i#Proteome Sci.#1i] [b#2#1b], 3.
62. Steffen,N.R., Murphy,S.D., Tolleri,L., Hatfield,G.W. and Lathrop,R.H. (2002) DNA sequence and structure: Direct and indirect recognition in protein-DNA binding. [i#Bioinformatics#1i], [b#18#1b] (Suppl. 1), S22-S30.
63. Paillard,G. and Lavery,R. (2004) Analyzing protein-DNA recognition mechanisms. [i#Structure (Camb.)#1i], [b#12#1b], 113-122.
64. Dragan,A.I., Read,C.M., Makeyeva,E.N., Milgotina,E.I., Churchill,M.E., Crane-Robinson,C. and Privalov,P.L. (2004) DNA Binding and Bending by HMG Boxes: Energetic Determinants of Specificity. [i#J. Mol. Biol.#1i], [b#343#1b], 371-393.