Genomic structure and functional characterisation of the promoters of human and mouse nogo/rtn4

Journal of Molecular Biology

Volumn 325, Issue 2, 2003, Pages 299-323

  Oertle, Thomas ^a   Huber, Chantal ^a   Van der Putten, Herman ^b   Schwab, Martin E ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

Comparative gene analysis; Gene structure; Nogo; Promoter; Reticulon

Indexed keywords

ISOPROTEIN; PROTEIN NOGO A; PROTEIN NOGO B; PROTEIN NOGO C; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ANIMAL CELL; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; FEMALE; GENE CONTROL; GENE SILENCING; GENE STRUCTURE; GENOME ANALYSIS; HUMAN; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN VARIANT; RNA SPLICING; TRANSCRIPTION INITIATION SITE;

VERTEBRATA;

EID: 0037225041     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01179-8     Document Type: Article

References (74)

1. Caroni, P. & Schwab, M. E. (1988). Two membrane protein fractions from rat central myelin with inhibitory properties for neurite growth and fibroblast spreading. J. Cell Biol. 106, 1281-1288.
2. Bandtlow, C. E., Zachleder, T. & Schwab, M. E. (1990). Oligodendrocytes arrest neurite growth by contact inhibition. J. Neurosci. 10, 3837-3848.
3. Bandtlow, C. E. & Löschinger, J. (1997). Developmental changes in neuronal responsiveness to the CNS myelin-associated neurite growth inhibitor NI-35/250. Eur. J. Neurosci. 9, 2743-2752.
4. Spillmann, A. A., Bandtlow, C. E., Lottspeich, F., Keller, F. & Schwab, M. E. (1998). Identification and characterization of a bovine neurite growth inhibitor (bNI-220). J. Biol. Chem. 273, 19283-19293.
5. Chen, M. S., Huber, A. B., van der Haar, M. E., Frank, M., Schnell, L., Spillmann, A. A., Christ, F. & Schwab, M. E. (2000). Nogo-A is a myelin-associated neurite outgrowth inhibitor and an antigen form monoclonal antibody IN-1. Nature, 403, 434-439.
6. GrandPré, T., Nakamura, F., Vartanian, T. & Strittmatter, S. M. (2000). Identification of the Nogo inhibitor of axon regeneration as a reticulon protein. Nature, 403, 439-444.
7. Prinjha, R., Moore, S. E., Vinson, M., Blake, S., Morrow, R., Christie, G., Michalovich, D., Simmons, D. L. & Walsh, F. S. (2000). Inhibitor of neurite outgrowth in humans. Nature, 403, 383-384.
8. Roebroek, A. J., Ayoubi, T. A., van de Velde, H. J., Schoenmakers, E. F., Pauli, I. G. & Van de Ven, W. J. (1996). Genomic organization of the human NSP gene, prototype of a novel gene family encoding reticulons. Genomics, 32, 191-199.
9. van de Velde, H. J. K., Roebroek, A. J., Senden, N. H. & Ramaekers, F. C. (1994). NSP-encoded reticulons, neuroendocrine proteins of a novel gene family associated with membranes of the endoplasmic reticulum. J. Cell Sci. 107, 2403-2416.
10. Geisler, J. G., Palmer, R. J., Stubbs, L. J. & Mucenski, M. L. (1999). Nspl1, a new Z-band-associated protein. J. Muscle Res. Cell. Motil. 20, 661-668.
11. Huber, A. B., Weinmann, O., Brosamle, C., Oertle, T. & Schwab, M. E. (2002). Patterns of nogo mRNA and protein expression in the developing and adult rat and after CNS lesions. J. Neurosci. 22, 3553-3567.
12. Geisler, J. G., Stubbs, L. J., Wasserman, W. W. & Mucenski, M. L. (1998). Molecular cloning of a novel mouse gene with predominant muscle and neural expression. Mamm. Genome, 9, 274-282.
13. Schafer, G. L., Crabbe, J. C. & Wiren, K. M. (1998). Identification of neuroendocrine-specific protein as an ethanol-regulated gene with mRNA differential display. Mamm. Genome, 9, 979-982.
14. Bai, Y. & Hart, R. P. (1998). Cultured sympathetic neurons express functional interleukin-1 receptors. J. Neuroimmunol. 91, 43-54.
15. Dowling, A. L., Martz, G. U., Leonard, J. L. & Zoeller, R. T. (2000). Acute changes in maternal thyroid hormone induce rapid and transient changes in gene expression in fetal rat brain. J. Neurosci. 20, 2255-2265.
16. Zingrillo, M., Torlontano, M., Ghiggi, M. R., Frusciante, V., Varraso, A., Liuzzi, A. & Trischitta, V. (2000). Radioiodine and percutaneous ethanol injection in the treatment of large toxic thyroid nodule: A long-term study. Thyroid, 10, 985-989.
17. Kools, P. F., Roebroek, A. J., van de Velde, H. J. K., Marynen, P., Bullerdiek, J. & Van de Ven, W. J. (1994). Regional mapping of the human NSP gene to chromosome region 14q21 → q22 by fluorescence in situ hybridization analysis. Cytogenet. Cell. Genet. 66, 48-50.
18. Roebroek, A. J. M., Contreras, B., Pauli, I. G. & Van de Ven, W. J. (1998). cDNA cloning, genomic organization, and expression of the human RTN2 gene, a member of a gene family encoding reticulons. Genomics, 51, 98-106.
19. Moreira, E. F., Jaworski, C. J. & Rodriguez, I. R. (1999). Cloning of a novel member of the reticulon gene family (RTN3): Gene structure and chromosomal localization to 11q13. Genomics, 58, 73-81.
20. Nagase, T., Ishikawa, K., Suyama, M., Kikuno, R., Hirosawa, M., Miyajima, N., Tanaka, A., Kotani, H., Nomura, N. & Ohara, O. (1998). Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 5, 355-364.
21. Yang, J., Yu, L., Bi, A. D. & Zhao, S. Y. (2000). Assignment of the human reticulon 4 gene (RTN4). To chromosome 2p14 → 2p13 by radiation hybrid mapping. Cytogenet. Cell. Genet. 88, 101-102.
22. Burset, M., Seledtsov, I. A. & Solovyev, V. V. (2000). Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucl. Acids Res. 28, 4364-4375.
23. Schwartz, S., Zhang, Z., Frazer, K. A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R. & Miller, W. (2000). PipMaker - A web server for aligning two genomic DNA sequences. Genome Res. 10, 577-586.
24. Basile, V., Vicente, A., Martignetti, J. A., Skryabin, B. V., Brosius, J. & Kennedy, J. L. (1998). Assignment of the human BC200 RNA gene (BCYRN1). to chromosome 2p16 by radiation hybrid mapping. Cytogenet. Cell. Genet. 82, 271-272.
25. Kuryshev, V. Y., Skryabin, B. V., Kremerskothen, J., Jurka, J. & Brosius, J. (2001). Birth of a gene: Locus of neuronal BC200 snmRNA in three prosimians and human BC200 pseudogenes as archives of change in the Anthropoidea lineage. J. Mol. Biol. 309, 1049-1066.
26. Suzuki, Y., Yoshitomo-Nakagawa, K., Maruyama, K., Suyama, A. & Sugano, S. (1997). Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library. Gene, 200, 149-156.
27. Meyuhas, O. (2000). Synthesis of the translational apparatus is regulated at the translational level. Eur. J. Biochem. 267, 6321-6330.
28. Kozak, M. (1997). Recognition of AUG and alternative initiator codons is augmented by G in position +4 but is not generally affected by the nucleotides in positions +5 and +6. EMBO J. 16, 2482-2492.
29. Boeck, R. & Kolakofsky, D. (1994). Positions +5 and +6 can be major determinants of the efficiency of non-AUG initiation codons for protein synthesis. EMBO J. 13, 3608-3617.
30. Kozak, M. (2000). Do the 5′ untranslated domains of human cDNAs challenge the rules for initiation of translation (or is it vice versa)? Genomics, 70, 396-406.
31. Ioshikhes, I. P. & Zhang, M. Q. (2000). Large-scale human promoter mapping using CpG islands. Nature Genet. 26, 61-63.
32. Olek, A., Oswald, J. & Walter, J. (1996). A modified and improved method for bisulphite based cytosine methylation analysis. Nucl. Acids Res. 24, 5064-5066.
33. Schmid, C. W. (1996). Alu: Structure, origin, evolution, significance and function of one-tenth of human DNA. Prog. Nucl. Acid Res. Mol. Biol. 53, 283-319.
34. Tagami, S., Eguchi, Y., Kinoshita, M., Takeda, M. & Tsujimoto, Y. (2000). A novel protein RTN-XS, interacts with both Bcl-XL and Bcl-2 on endoplasmic reticulum and reduces their anti-apoptotic activity. Oncogene, 19, 5736-5746.
35. Zhou, Z. M., Sha, J. H., Li, J. M., Lin, M., Zhu, H., Zhou, Y. D., Wang, L. R., Wang, Y. Q. & Zhou, K. Y. (2002). Expression of a novel reticulon-like gene in human testis. Reproduction, 123, 227-234.
36. Oertle, T., Bandtlow, C. E. & Schwab, M. E. (2000). Characterization of the gene structure and the inhibitory regions of Nogo-RTN4. Soc. Neurosci. Abstr. 26, 573.
37. Li, Q., Qi, B., Oka, K., Shimakage, M., Yoshioka, N., Inoue, H., Hakura, A., Kodama, K., Stanbridge, E. J. & Yutsudo, M. (2001). Link of a new type of apoptosis-inducing gene ASY/Nogo-B to human cancer. Oncogene, 20, 3929-3936.
38. Davuluri, R. V., Suzuki, Y., Sugano, S. & Zhang, M. Q. (2000). CART classification of human 5′ UTR sequences. Genome Res. 10, 1807-1816.
39. Beaudoing, E., Freier, S., Wyatt, J. R., Claverie, J. M. & Gautheret, D. (2000). Patterns of variant poly-adenylation signal usage in human genes. Genome Res. 10, 1001-1010.
40. Cok, S. J. & Morrison, A. R. (2001). The 3′-untranslated region of murine cyclooxygenase-2 contains multiple regulatory elements that alter message stability and translational efficiency. J. Biol. Chem. 276, 23179-23185.
41. Schlicker, M., Reim, K., Schluter, G. & Engel, W. (1997). Specific binding of a 47-kilodalton protein to the 3′ untranslated region of rat transition protein 2 messenger ribonucleic acid. Biol. Reprod. 56, 697-706.
42. Le Cam, A. & Legraverend, C. (1995). Transcriptional repression, a novel function for 3′ untranslated regions. Eur. J. Biochem. 231, 620-627.
43. Gautreau, D., Cote, C. A. & Mowry, K. L. (1997). Two copies of a subelement from the Vg1 RNA localization sequence are sufficient to direct vegetal localization in Xenopus oocytes. Development, 124, 5013-5020.
44. Wegner, M. (2000). Transcriptional control in myelinating glia: Flavors and spices. Glia, 31, 1-14.
45. Werner, T. (1999). Models for prediction and recognition of eukaryotic promoters. Mamm. Genome, 10, 168-175.
46. Schaffner, G., Schirm, S., Muller-Baden, B., Weber, F. & Schaffner, W. (1988). Redundancy of information in enhancers as a principle of mammalian transcription control. J. Mol. Biol. 201, 81-90.
47. Henson, J., Saffer, J. & Furneaux, H. (1992). The transcription factor Sp1 binds to the JC virus promoter and is selectively expressed in glial cells in human brain. Ann. Neurol. 32, 72-77.
48. Imataka, H., Sogawa, K., Yasumoto, K., Kikuchi, Y., Sasano, K., Kobayashi, A., Hayami, M. & Fujii-Kuriyama, Y. (1992). Two regulatory proteins that bind to the basic transcription element (BTE), a GC box sequence in the promoter region of the rat P-4501A1 gene. EMBO J. 11, 3663-3671.
49. Subramaniam, M., Harris, S. A., Oursler, M. J., Rasmussen, K., Riggs, B. L. & Spelsberg, T. C. (1995). Identification of a novel TGF-beta-regulated gene encoding a putative zinc finger protein in human osteoblasts. Nucl. Acids Res. 23, 4907-4912.
50. Tretiakova, A., Steplewski, A., Johnson, E. M., Khalili, K. & Amini, S. (1999). Regulation of myelin basic protein gene transcription by Sp1 and Puralpha: Evidence for association of Sp1 and Puralpha in brain. J. Cell. Physiol. 181, 160-168.
51. Birnbaum, M. J., van Wijnen, A. J., Odgren, P. R., Last, T. J., Suske, G., Stein, G. S. & Stein, J. L. (1995). Sp1 trans-activation of cell cycle regulated promoters is selectively repressed by Sp3. Biochemistry, 34, 16503-16508.
52. Brown, A. M. & Lemke, G. (1997). Multiple regulatory elements control transcription of the peripheral myelin protein zero gene. J. Biol. Chem. 272, 28939-28947.
53. Mantovani, R. (1998). A survey of 178 NF-Y binding CCAAT boxes. Nucl. Acids Res. 26, 1135-1143.
54. Mantovani, R. (1999). The molecular biology of the CCAAT-binding factor NF-Y. Gene, 239, 15-27.
55. McKnight, S. L. (2001). McBindall - A better name for CCAAT/enhancer binding proteins? Cell, 107, 259-261.
56. Wright, K. L., Moore, T. L., Vilen, B. J., Brown, A. M. & Ting, J. P. (1995). Major histocompatibility complex class II-associated invariant chain gene expression is up-regulated by cooperative interactions of Sp1 and NF-Y. J. Biol. Chem. 270, 20978-20986.
57. Bellorini, M., Lee, D. K., Dantonel, J. C., Zemzoumi, K., Roeder, R. G., Tora, L. & Mantovani, R. (1997). CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues. Nucl. Acids Res. 25, 2174-2181.
58. Magnusson, C., Johansson, R. S. & Tagerud, S. (2001). Differential expression of Nogo (Reticulon 4) transcripts in innervated and denervated mouse skeletal muscle. Soc. Neurosci. Abstr. 27, 1367.
59. Shomer, M. H. & Chesselet, M-F. (2001). Lesion-specific upregulation of Nogo-A mRNA in adult brain. Soc. Neurosci. Abstr. 27, 671.
60. Josephson, A., Widenfalk, J., Widmer, H. W., Olson, L. & Spenger, C. (2001). NOGO mRNA expression in adult and fetal human and rat nervous tissue and in weight drop injury. Expt. Neurol. 169, 319-328.
61. Esteller, M. & Herman, J. G. (2002). Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours. J. Pathol. 196, 1-7.
62. Werner, H., Dimou, L., Klugmann, M., Pfeiffer, S. & Nave, K. A. (2001). Multiple splice isoforms of proteolipid M6B in neurons and oligodendrocytes. Mol. Cell. Neurosci. 18, 593-605.
63. Thanaraj, T. A. & Clark, F. (2001). Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions. Nucl. Acids Res. 29, 2581-2593.
64. Weil, D., Bernard, M., Combates, N., Wirtz, M. K., Hollister, D. W., Steinmann, B. & Ramirez, F. (1988). Identification of a mutation that causes exon skipping during collagen pre-mRNA splicing in an Ehlers-Danlos syndrome variant. J. Biol. Chem. 263, 8561-8564.
65. Morris, N. J., Ross, S. A., Neveu, J. M., Lane, W. S. & Lienhard, G. E. (1999). Cloning and characterization of a 22 kDa protein from rat adipocytes: A new member of the reticulon family. Biochim. Biophys. Acta, 1450, 68-76.
66. Suzuki, Y., Taira, H., Tsunoda, T., Mizushima-Sugano, J., Sese, J., Hata, H., Ota, T., Isogai, T., Tanaka, T., Morishita, S. et al. (2001). Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep. 2, 388-393.
67. Tanaka, M., Ito, S. & Kiuchi, K. (2001). The 5′-untranslated region of the mouse glial cell line-derived neurotrophic factor gene regulates expression at both the transcriptional and translational levels. Brain Res. Mol. Brain Res. 91, 81-95.
68. Harigai, M., Miyashita, T., Hanada, M. & Reed, J. C. (1996). A cis-acting element in the BCL-2 gene controls expression through translational mechanisms. Oncogene, 12, 1369-1374.
69. Linz, B., Koloteva, N., Vasilescu, S. & McCarthy, J. E. (1997). Disruption of ribosomal scanning on the 5′-untranslated region, and not restriction of translational initiation per se, modulates the stability of nonaberrant mRNAs in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 272, 9131-9140.
70. Opstelten, D. J., Vogels, R., Robert, B., Kalkhoven, E., Zwartkruis, F., de Laaf, L., Destree, O. H., Deschamps, J., Lawson, K. A. & Meijlink, F. (1991). The mouse homeobox gene, S8, is expressed during embryogenesis predominantly in mesenchyme. Mech. Dev. 34, 29-41.
71. Chin, E. R., Olson, E. N., Richardson, J. A., Yang, Q., Humphries, C., Shelton, J. M., Wu, H., Zhu, W., Bassel-Duby, R. & Williams, R. S. (1998). A calcineurin-dependent transcriptional pathway controls skeletal muscle fiber type. Genes Dev. 12, 2499-2509.
72. Crabtree, G. R. (1999). Generic signals and specific outcomes: Signaling through Ca2+, calcineurin, and NF-AT. Cell, 96, 611-614.
73. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl. Acids Res. 25, 3389-3402.
74. Rubin, B. P., Spillmann, A. A., Bandtlow, C. E., Keller, F. & Schwab, M. E. (1995). Inhibition of PC12 cell attachment and neurite outgrowth by detergent solubilized CNS myelin proteins. Eur. J. Neurosci. 7, 2524-2529.