Identification of regulatory regions which confer muscle-specific gene expression

Journal of Molecular Biology

Volumn 278, Issue 1, 1998, Pages 167-181

  Wasserman, Wyeth W ^a   Fickett, James W ^a  

^a Bioinfo Res Grp SmithKline B   (United States)

Author keywords

Logistic regression analysis; Muscle specific expression; Phylogenetic footprinting; Position weight matrix; Regulatory region prediction

Indexed keywords

PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENOME; MUSCLE; PHYLOGENY; PRIORITY JOURNAL; REGRESSION ANALYSIS; SEQUENCE ANALYSIS;

EID: 0032562789     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1700     Document Type: Article

References (71)

1. Amacher S.L., Buskin J.N., Hauschka S.D. Multiple regulatory elements contribute differentially to muscle creatine kinase enhancer activity in skeletal and cardiac muscle. Mol. Cell. Biol. 13:1993;2753-2764
2. Andres V., Cervera M., Mahdavi V. Determination of the consensus binding site for MEF-2 expressed in muscle and brain reveals tissue-specific sequence constraints. J. Biol. Chem. 270:1995;23246-23249
3. Aparicio S., Morrison A., Gould A., Gilthorpe J., Chaudhuri C., Rigby P., Krumlauf R., Brenner S. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl Acad. Sci. USA. 92:1995;1684-1688
4. Arnone M.I., Davidson E.H. The hardwiring of development organization and function of genomic regulatory systems. Development. 124:1997;1851-1864
5. Berg O.G., von Hippel P.H. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193:1987;723-750
6. Berg O.G., von Hippel P.H. Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol. 200:1988;709-723
7. Bione S., Maestrini E., Rivella S., Mancini M., Regis S., Romeo G., Toniolo D. Identification of a novel X-linked gene responsible for Emery-Dreifuss muscular dystrophy. Nature Genet. 8:1994;323-327
8. Bisaha J.G., Simon T.C., Gordon J.I., Breslow J.L. Characterization of an enhancer element in the human apolipoprotein C-III gene that regulates human apolipoprotein A-I gene expression in the intestinal epithelium. J. Biol. Chem. 270:1995;19979-19988
9. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212:1990;563-578
10. Bucher P., Trifonov E.N. Compilation and analysis of eukaryotic pol II promoter sequences. Nucl. Acids Res. 14:1986;10009-10026
11. Buckingham M. Making muscle in mammals. Trends Genet. 8:1992;144-148
12. Buckingham M. Muscle the regulation of myogenesis. Curr. Opin. Genet. Dev. 4:1994;745-751
13. Chen Q.K., Hertz G.Z., Stormo G.D. PromFD 1.0 A computer program that predicts eukaryotic polII promoters using strings and IMD matrices. Comput. Appl. Biosci. 13:1997;29-35
14. Claverie J.M., Audic S. The statistical significance of nucleotide position-weight matrix matches. Comput. Appl. Biosci. 12:1996;431-439
15. Claverie J.M., Sauvaget I. Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters. Comput. Appl. Biosci. 1:1985;95-104
16. Crowley E.M., Roeder K., Bina M. A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol. 269:1997;8-14
17. Davis R.L., Weintraub H., Lassar A.B. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell. 51:1987;987-1000
18. Duret L., Bucher P. Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol. 7:1997;399-406
19. Eddy S.R. Hidden Markov models. Curr. Opin. Struct. Biol. 6:1996;361-365
20. Fabre-Suver C., Hauschka S.D. A novel site in the muscle creatine kinase enhancer is required for expression in skeletal but not cardiac muscle. J. Biol. Chem. 271:1996;4646-4652
21. Farrance I.K., Ordahl C.P. The role of transcription enhancer factor-1 (TEF-1) related proteins in the formation of M-CAT binding complexes in muscle and non-muscle tissues. J. Biol. Chem. 271:1996;8266-8274
22. Fickett J.W. Coordinate positioning of MEF-2 and myogenin binding sites. Gene. 172:1996;GC19-GC32
23. Fickett J.W. Quantitative discrimination of MEF-2 sites. Mol. Cell. Biol. 16:1996;437-441
24. Fickett J.W., Hatzigeorgiou A.G. Eukaryotic promoter recognition. Genome Res. 7:1997;861-878
25. Firulli A.B., Olson E.N. Modular regulation of muscle gene transcription a mechanism for muscle cell diversity. Trends Genet. 13:1997;364-369
26. Fondrat C., Kalogeropoulos A. Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae application to chromosome III. Comput. Appl. Biosci. 12:1996;363-374
27. Frech K., Danescu-Mayer J., Werner T. A novel method to develop highly specific models for regulatory units detects a new LTR in GenBank which contains a functional promoter. J. Mol. Biol. 270:1997;674-687
28. Funk W.D., Wright W.E. Cyclic amplification and selection of targets for multicomponent complexes myogenin interacts with factors recognizing binding sites for basic helix-loop-helix, nuclear factor 1, myocyte-specific enhancer-binding factor 2, and COMP1 factor. Proc. Natl Acad. Sci. USA. 89:1992;9484-9488
29. Geisler J.G., Stubbs L.J., Wasserman W.W., Mucenski M.L. Molecular cloning of a novel murine gene with predominant muscle and neural expression. Mammalian Genome. 9:1998;274-282
30. Gopal-Srivastava R., Haynes J.I., Piatigorsky J. Regulation of the murine alpha B-crystallin/small heat shock protein gene in cardiac muscle. Mol. Cell. Biol. 15:1995;7081-7090
31. Gossett L.A., Kelvin D.J., Sternberg E.A., Olson E.N. A new myocyte-specific enhancer-binding factor that recognizes a conserved element associated with multiple muscle-specific genes. Mol. Cell. Biol. 9:1989;5022-5033
32. Hauschka S.D. The embryonic origin of muscle. Engel A.G., Franzini-Armstrong C. Myology, Basic and Clinical. 1994;3-73 McGraw-Hill, New York
33. Hirst J.D., Sternberg M.J. Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks. Biochemistry. 31:1992;7211-7218
34. Hosmer D.W., Lemeshow S. Applied Logistic Regression. 1989;John Wiley & Sons, New York. pp. 1-36
35. Houlgatte R., Mariage SamsonR., Duprat S., Tessier A., Bentolila S., Lamy B., Auffray C. The Genexpress Index a resource for gene discovery and the genic map of the human genome. Genome Res. 5:1995;272-304
36. Jacquemin P., Hwang J.J., Martial J.A., Dolle P., Davidson I. A novel family of developmentally regulated mammalian transcription factors containing the TEA/ATTS DNA binding domain. J. Biol. Chem. 271:1996;21775-21785
37. Knotts S., Rindt H., Neumann J., Robbins J. In vivo regulation of the mouse beta myosin heavy chain gene. J. Biol. Chem. 269:1994;31275-31282
38. Kondrakhin Y.V., Kel A.E., Kolchanov N.A., Romaschenko A.G., Milanesi L. Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11:1995;477-488
39. Lanfranchi G., Muraro T., Caldara F., Pacchioni B., Pallavicini A., Pandolfo D., Toppo S., Trevisan S., Scarso S., Valle G. Identification of 4370 expressed sequence tags from a 3′-end-specific cDNA library of human skeletal muscle by DNA sequencing and filter hybridization. Genome Res. 6:1996;35-42
40. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F., Wootton J.C. Detecting subtle sequence signals a Gibbs sampling strategy for multiple alignment. Science. 262:1993;208-214
41. Lee T.C., Shi Y., Schwartz R.J. Displacement of BrdUrd-induced YY1 by serum response factor activates skeletal alpha-actin transcription in embryonic myoblasts. Proc. Natl Acad. Sci. USA. 89:1992;9814-9818
42. Leifer D., Golden J., Kowall N.W. Myocyte-specific enhancer binding factor 2C expression in human brain development. Neuroscience. 63:1994;1067-1079
43. Mietus-Snyder M., Sladek F.M., Ginsburg G.S., Kuo C.F., Ladias J.A., Darnell J.E. Jr, Karathanasis S.K. Antagonism between apolipoprotein AI regulatory protein 1, Ear3/COUP-TF, and hepatocyte nuclear factor 4 modulates apolipoprotein CIII gene expression in liver and intestinal cells. Mol. Cell. Biol. 12:1992;1708-1718
44. Olson E.N. Interplay between proliferation and differentiation within the myogenic lineage. Dev. Biol. 154:1992;261-272
45. Pallavicini A., Zimbello R., Tiso N., Muraro T., Rampoldi L., Bortoluzzi S., Valle G., Lanfranchi G., Danieli G.A. The preliminary transcript map of a human skeletal muscle. Hum. Mol. Genet. 9:1997;1445-1450
46. Parmacek M.S., Ip H.S., Jung F., Shen T., Martin J.F., Vora A.J., Olson E.N., Leiden J.M. A novel myogenic regulatory circuit controls slow/cardiac troponin C gene transcription in skeletal muscle. Mol. Cell. Biol. 14:1994;1870-1885
47. Parrish J.E., Ciccodicola A., Wehhert M., Cox G.F., Chen E., Nelson D.L. A muscle-specific DNase I-like gene in human Xq28. Hum. Mol. Genet. 4:1995;1557-1564
48. Pergolizzi R., Appierto V., Bosetti A., DeBellis G.L., Rovida E., Biunno I. Cloning of a gene encoding a DNase I-like endonuclease in the human Xq28 region. Gene. 168:1996;267-270
49. Pietu G., Alibert O., Guichard V., Lamy B., Bois F., Leroy E., Mariage SampsonR., Houlgatte R., Soularue P., Auffray C. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array. Genome Res. 6:1996;492-503
50. Pollock R., Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucl. Acids Res. 18:1990;6197-6204
51. Pollock R., Treisman R. Human SRF-related proteins DNA-binding properties and potential regulatory targets. Genes Dev. 5:1991;2327-2341
52. Prestridge D.S. Predicting pol II promoter sequences using transcription factor binding sites. J. Mol. Biol. 249:1995;923-932
53. Sartorelli V., Webster K.A., Kedes L. Muscle-specific expression of the cardiac alpha-actin gene requires MyoD1, CArG-box binding factor, and Sp-1. Genes Dev. 4:1990;1811-1822
54. Shimizu N., Prior G., Umeda P.K., Zak R. cis-acting elements responsible for muscle-specific expression of the myosin heavy chain beta gene. Nucl. Acids Res. 20:1992;1793-1799
55. Shimizu N., Smith G., Izumo S. Both a ubiquitous factor mTEF-1 and a distinct muscle-specific factor bind to the M-CAT motif of the myosin heavy chain beta gene. Nucl. Acids Res. 21:1993;4103-4110
56. Solovyev V., Salamov A. The Gene-Finder computer tools for analysis of human and model organism genome sequences. Gaasterland T., Karp P., Karplus K., Ouzounis C., Sander C., Valencia A. Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology. 1997;294-302 AAAI Press, Menlo Park
57. Spicer D.B., Rhee J., Cheung W.L., Lassar A.B. Inhibition of myogenic bHLH and Mef-2 transcription factors by the bHLH protein Twist. Science. 272:1996;1476-1480
58. Spitz F., Salminen M., Demignon J., Kahn A., Daegelen D., Maire P. A combination of MEF3 and NFI proteins activates transcription in a subset of fast-twitch muscles. Mol. Cell. Biol. 17:1997;656-666
59. Staden R. Computer methods to locate signals in nucleic acid sequences. Nucl. Acids Res. 12:1984;505-519
60. Stockdale F.E. Myogenic cell lineages. Dev. Biol. 156:1992;281-298
61. Stormo G.D. Consensus patterns in DNA. Methods Enzymol. 183:1990;211-221
62. Supp D.M., Witte D.P., Branford W.W., Smith E.P., Potter S.S. Sp4, a member of the Sp-1-family of zinc finger transcription factors, is required for normal murine growth, viability, and male fertility. Dev. Biol. 176:1996;284-299
63. Taylor S.M., Jones P.A. Multiple new phenotypes induced in 10T1/2 and 3T3 cells treated with 5-azacytidine. Cell. 17:1979;771-779
64. Thiesen H.J., Bach C. Target Detection Assay (TDA) a versatile procedure to determine DNA binding sites as demonstrated on SP-1 protein. Nucl. Acids Res. 18:1990;3203-3209
65. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680
66. Toyoda A., Sakai T., Sugiyama Y., Kusuda J., Hashimoto K., Maeda H. Isolation and analysis of a novel gene, HXC-26, adjacent to the rab GDP dissociation inhibitor gene located at human chromosome Xq28 region. DNA Res. 3:1996;337-340
67. Tronche F., Ringeisen F., Blumenfeld M., Yaniv M., Pontoglio M. Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 266:1997;231-245
68. Vandromme M., Gauthier RouviereC., Carnac G., Lamb N., Fernandez A. Serum response factor p67SRF is expressed and required during myogenic differentiation of both mouse C2 and rat L6 muscle cell lines. J. Cell. Biol. 118:1992;1489-1500
69. Vollmer R.T. Multivariate statistical analysis for pathologists. Am. J. Clin. Pathol. 105:1996;115-126
70. Wagner A. A computational genomics approach to the identification of gene networks. Nucl. Acids Res. 25:1997;3594-3604
71. Weintraub H.L., Davis R., Lockshon D., Lassar A. MyoD binds cooperatively to two sites in a target enhancer sequence occupancy of two sites is required for activation. Proc. Natl Acad. Sci. USA. 87:1990;5623-5627