A general approach for identifying distant regulatory elements applied to the Gdf6 gene

Genome Research

Volumn 13, Issue 9, 2003, Pages 2069-2081

  Mortlock, Douglas P ^a,b   Guenther, Catherine ^b   Kingsley, David M ^b  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA GALACTOSIDASE; BONE MORPHOGENETIC PROTEIN; PROTEIN GDF6; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CONTROLLED STUDY; DNA SEQUENCE; EMBRYO; GENE CONSTRUCT; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENOME; GESTATION PERIOD; HUMAN; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION;

ANIMALS; BETA-GALACTOSIDASE; BONE MORPHOGENETIC PROTEINS; CHROMOSOME DELETION; CHROMOSOMES, ARTIFICIAL, BACTERIAL; EMBRYO; GENETIC ENGINEERING; GENETIC MARKERS; HUMANS; MICE; MICE, INBRED C57BL; MICE, INBRED CBA; MICE, TRANSGENIC; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; TRANSFORMING GROWTH FACTOR BETA; TRANSGENES;

BACTERIA (MICROORGANISMS);

EID: 0141519291     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1306003     Document Type: Article

References (51)

1. Carvajal, J.J., Cox, D., Summerbell, D., and Rigby, P.W. 2001. A BAC transgenic analysis of the Mrf4/Myf5 locus reveals interdigitated elements that control activation and maintenance of gene expression during muscle development. Dev. Suppl. 128: 1857-1868.
2. Chang, C. and Hemmati-Brivanlou, A. 1999. Xenopus GDF6, a new antagonist of noggin and a partner of BMPs. Dev. Suppl. 126: 3347-3357.
3. Chang, S.C., Hoang, B., Thomas, J.T., Vukicevic, S., Luyten, F.P., Ryba, NJ., Kozak, C.A., Reddi, A.H., and Moos, M. 1994. Cartilage-derived morphogenetic proteins. New members of the transforming growth factor-β superfamily predominantly expressed in long bones during human embryonic development. J. Biol. Chem. 269: 28227-28234.
4. Copeland, N.G., Jenkins, N.A., and Court, D.L. 2001. Recombineering: A powerful new tool for mouse functional genomics. Nat. Rev. Genet. 2: 769-779.
5. Delot, E., Kataoka, H., Goutel, C., Yan, Y.L., Postlethwait, J., Wittbrodt, J., and Rosa, F.M. 1999. The BMP-related protein radar: A maintenance factor for dorsal neuroectoderm cells? Mech. Dev. 85: 15-25.
6. DiLeone, R.J., Russell, L.B., and Kingsley, D.M. 1998. An extensive 3′ regulatory region controls expression of Bmp5 in specific anatomical structures of the mouse embryo. Genetics 148: 401-408.
7. DiLeone, R.J., Marcus, G.A., Johnson, M.D., and Kingsley, D.M. 2000. Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes. Proc. Nat. Acad. Sci. 97: 1612-1617.
8. Ducy, P. and Karsenty, G. 2000. The family of bone morphogenetic proteins. Kidney Int. 57: 2207-2214.
9. Erlacher, L., Ng, C.K., Ullrich, R., Krieger, S., and Luyten, F.P. 1998. Presence of cartilage-derived morphogenetic proteins in articular cartilage and enhancement of matrix replacement in vitro. Arthritis Rheum. 41: 263-273.
10. Friedrich, G. and Soriano, P. 1991. Promoter traps in embryonic stem cells: A genetic screen to identify and mutate developmental genes in mice. Genes & Dev. 5: 1513-1523.
11. Giraldo, P. and Montoliu, L. 2001. Size matters: Use of YACs, BACs, and PACs in transgene animals. Transgenic Res. 10: 83-103.
12. Goutel, C., Kishimoto, Y., Schulte-Marker, S., and Rosa, F. 2000. The ventralizing activity of Radar, a maternally expressed bone morphogenetic protein, reveals complex bone morphogenetic protein interactions controlling dorso-ventral patterning in zebrafish. Mech. Dev. 99: 15-27.
13. Hadchouel, J., Tajbakhsh, S., Primig, M., Chang, T.H., Daubas, P., Rocancourt, D., and Buckingham, M. 2000. Modular long-range regulation of Myf5 reveals unexpected heterogeneity between skeletal muscles in the mouse embryo. Development 127: 4455-4467.
14. Harafuji, N., Keys, D.N., and Levine, M. 2002. Genome-wide identification of tissue-specific enhancers in the Ciona tadpole. Proc. Natl. Acad. Sci. 99: 6802-6805.
15. Higgs, D.R., Wood, W.G., Jarman, A.P., Sharpe, J., Lida, J., Pretorius, I.M., and Ayyub, H. 1990. A major positive regulatory region located far upstream of the human α-globin gene locus. Genes & Dev. 4: 1588-1601.
16. Jessen, J.R., Meng, A., McFarlane, R.J., Paw, B.H., Zon, L.I., Smith, G.R., and Lin, S. 1998. Modification of bacterial artificial chromosomes through chi-stimulated homologous recombination and its application in zebrafish transgenesis. Proc. Natl. Acad. Sci. 95: 5121-5126.
17. Kent, W.J. 2002. BLAT-The BLAST-like alignment tool. Genome Res. 12: 656-664.
18. Kim, D.G., Kang, H.M., Jang, S.K., and Shin, H.S. 1992. Construction of a bifunctional mRNA in the mouse by using the internal ribosomal entry site of the encephalomyocarditis virus. Mol. Cell Biol. 12: 3636-3643.
19. Kleinjan, D.A., Seawright, A., Schedl, A., Quinlan, R.A., Danes, S., and van Heyningen, V. 2001. Aniridia-associated translocations, DNase hypersensitivity, sequence comparison and transgenic analysis redefine the functional domain of PAX6. Hum. Mol. Genet. 10: 2049-2059.
20. Kroll, K.L. and Amaya, E. 1996. Transgenic Xenopus embryos from sperm nuclear transplantations reveal FGF signaling requirements during gastrulation. Development 122: 3173-3183.
21. Lee, E.C., Yu, D., Martinez de Velasco, J., Tessarollo, L., Swing, D.A., Court, D.L., Jenkins, N.A., and Copeland, N.G. 2001. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73: 56-65.
22. Lee, K.J., Mendelsohn, M., and Jessell, T.M. 1998. Neuronal patterning by BMPs: A requirement for GDF7 in the generation of a discrete class of commissural interneurons in the mouse spinal cord. Genes & Dev. 12: 3394-3407.
23. Lynch, M., O' Hely, M., Walsh, B., and Force, A. 2001. The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804.
24. Malaney, S., Heng, H.H., Tsui, L.C., Shi, X.M., and Robinson, B.H. 1996. Localization of the human gene encoding the 13.3-kDa subunit of mitochondrial complex III (UQCRB) to 8q22 by in situ hybridization. Cytogenet. Cell Genet. 73: 297-299.
25. Mayor, C., Brudno, M., Schwartz, J.R., Poliakov, A., Rubin, E.M., Frazer, K.A., Pachter, L.S., and Dubchak, I. 2000. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16: 1046-1047.
26. Morotome, Y., Goseki-Sone, M., Ishikawa, I., and Oida, S. 1998. Gene expression of growth and differentiation factors-5, -6, and -7 in developing bovine tooth at the root forming stage. [erratum appears in Biochem. Biophys. Res. Commun. 1998 May 29; 246(3):925.]. Biochem. Biophys. Res. Commun. 244: 85-90.
27. Mountford, P., Zevnik, B., Duwel, A., Nichols, J., Li, M., Dani, C., Robertson, M., Chambers, I., and Smith, A. 1994. Dicistronic targeting constructs: Reporters and modifiers of mammalian gene expression. Proc. Nat. Acad. Sci. 91: 4303-4307.
28. The Mouse Genome Sequencing Consortium, 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
29. Muyrers, J.P., Zhang, Y., Testa, G., and Stewart, A.F. 1999. Rapid modification of bacterial artificial chromosomes by ET-recombination. Nucleic Acids Res. 27: 1555-1557.
30. Nielsen, L.B., Kahn, D., Duell, T., Weier, H.U., Taylor, S., and Young, S.G. 1998. Apolipoprotein B gene expression in a series of human apolipoprotein B transgenic mice generated with recA-assisted restriction endonuclease cleavage-modified bacterial artificial chromosomes. An intestine-specific enhancer element is located between 54 and 62 kilobases 5′ to the structural gene. J. Biol. Chem. 273: 21800-21807.
31. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, New York.
32. Osoegawa, K., Tateno, M., Woon, P.Y., Frengen, E., Mammoser, A.G., Catanese, J.J., Hayashizaki, Y., and de Jong, P.J. 2000. Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res. 10: 116-128.
33. Peterson, K.R., Clegg, C.H., Li, Q., and Stamatoyannopoulos, G. 1997. Production of transgenic mice with yeast artificial chromosomes. Trends Genet. 13: 61-66.
34. Polinkovsky, A., Robin, N.H., Thomas, J.T., Irons, M., Lynn, A., Goodman, F.R., Reardon, W., Kant, S.G., Brunner, H.G., van der Burgt, I., et al. 1997. Mutations in CDMP1 cause autosomal dominant brachydactyly type C. Nat. Genet. 17: 18-19.
35. Riley, J., Butler, R., Ogilvie, D., Finniear, R., Jenner, D., Powell, S., Anand, R., Smith, J.C., and Markham, A.F. 1990. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18: 2887-2890.
36. Rissi, M., Wittbrodt, J., Delot, E., Naegeli, M., and Rosa, F.M. 1995. Zebrafish Radar: A new member of the TGF-β superfamily defines dorsal regions of the neural plate and the embryonic retina. Mech. Dev. 49: 223-234.
37. Roessler, E., Ward, D.E., Gaudenz, K., Belloni, E., Scherer, S.W., Donnai, D., Siegel-Bartelt, J., Tsui, L.C., and Muenke, M. 1997. Cytogenetic rearrangements involving the loss of the Sonic Hedgehog gene at 7q36 cause holoprosencephaly. Hum. Genet. 100: 172-181.
38. Schwartz, S., Zhang, Z., Frazer, K.A., Smit, A., Riemer, C., Bouck, J., Gibbs, R., Hardison, R., and Miller, W. 2000. PipMaker-A web server for aligning two genomic DNA sequences. Genome Res. 10: 577-586.
39. Settle, S., Marker, P., Gurley, K., Sinha, A., Thacker, A., Wang, Y., Higgins, K., Cunha, G., and Kingsley, D.M. 2001. The BMP family member Gdf7 is required for seminal vesicle growth, branching morphogenesis, and cytodifferentiation. Dev. Biol. 234: 138-150.
40. Settle Jr., S.H., Rountree, R.B., Sinha, A., Thacker, A., Higgins, K., and Kingsley, D.M. 2003. Multiple joint and skeletal patterning defects caused by single and double mutations in the mouse Gdf6 and Gdf5 genes. Dev. Biol. 254: 116-130.
41. Storm, E.E., Huynh, T.V., Copeland, N.G., Jenkins, N.A., Kingsley, D.M., and Lee, S.J. 1994. Limb alterations in brachypodism mice due to mutations in a new member of the TGF β-superfamily. [see comments]. Nature 368: 639-643.
42. Summerbell, D., Ashby, P.R., Coutelle, O., Cox, D., Yee, S., and Rigby, P.W. 2000. The expression of Myf5 in the developing mouse embryo is controlled by discrete and dispersed enhancers specific for particular populations of skeletal muscle precursors. Development 127: 3745-3757.
43. Swaminathan, S., Ellis, H.M., Waters, L.S., Yu, D., Lee, E.C., Court, D.L., and Sharan, S.K. 2001. Rapid engineering of bacterial artificial chromosomes using oligonucleotides. Genesis 29: 14-21.
44. Thomas, J.T., Lin, K., Nandedkar, M., Camargo, M., Cervenka, J., and Luyten, F.P. 1996. A human chondrodysplasia due to a mutation in a TGF-β superfamily member. Nat. Genet. 12: 315-317.
45. Thomas, J.T., Kilpatrick, M.W., Lin, K., Erlacher, L., Lembessis, P., Costa, T., Tsipouras, P., and Luyten, F.P. 1997. Disruption of human limb morphogenesis by a dominant negative mutation in CDMP1. Nat. Genet. 17: 58-64.
46. Tomaski, S.M. and Zalzal, G.H. 1999. In vitro regulation of expression of cartilage-derived morphogenetic proteins by growth hormone and insulin-like growth factor 1 in the bovine cricoid chondrocyte. Arch. Otolaryngol. Head Neck Surg. 125: 901-906.
47. Townes, T.M. and Behringer, R.R. 1990. Human globin locus activation region (LAR): Role in temporal control. Trends Genet. 6: 219-223.
48. Wolfman, N.M., Hattersley, G., Cox, K., Celeste, A.J., Nelson, R., Yamaji, N., Dube, J.L., DiBlasio-Smith, E., Nove, J., Song, J.J., et al. 1997. Ectopic induction of tendon and ligament in rats by growth and differentiation factors 5, 6, and 7, members of the TGF-β gene family. J. Clin. Invest. 100: 321-330.
49. Wunderle, V.M., Critcher, R., Hastie, N., Goodfellow, P.N., and Schedl, A. 1998. Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia. Proc. Nat. Acad. Sci. 95: 10649-10654.
50. Yan, Y.L., Talbot, W.S., Egan, E.S., and Postlethwait, J.H. 1998. Mutant rescue by BAC clone injection in zebrafish. Genomics 50: 287-289.
51. Yang, X.W., Model, P., and Heintz, N. 1997. Homologous recombination based modification in Escherichia coli and germline transmission in transgenic mice of a bacterial artificial chromosome. Nat. Biotech. 15: 859-865.