Nucleic Acids Research, 1989, Vol. 17, No. 10 3645-3653
© 1989
MOLECULAR BIOLOGY |
Whole genome PCR: application to the identification of sequences bound by gene regulatory protein
The Oncology Center, The Johns Hopkins University School of Medicine 424- N. Bond Street, Baltimors MD 21231. USA
Received March 15, 1989. Revised April 3, 1989. Accepted April 3, 1989.
A strategy is described that allows the isolation of DNA sequences that can bind to gene regulatory proteins. Total genomic DNA is first converted to a form that is suitable for amplification by the polymerase chain reaction (Whole Genome PCR), and the DNA sequences of interest are selected by binding to the regulatory protein and immune precipitation. Because sequences recovered from the selection step can be amplified by PCR, the selection process can be designed for maximum enrichment with little concern about recovery. Furthermore, the selection process can be repeated as often as necessary. Sequences recovered after amplification can be cloned and/or used as hybridization probes. As a test of this strategy, we selected human sequences that bound to Xenopus transcription factor IIIA (TFIIIA). Seven clones were isolated that were on the average 94% identical to the previously described 61 bp binding site of TFIIIA. This strategy could be adapted to isolate sequences that can be selected by any physical or biological method.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L. Guo, S. Chen, K. Liu, Y. Liu, L. Ni, K. Zhang, and L. Zhang Isolation of Heat Shock Factor HsfA1a-binding Sites in vivo Revealed Variations of Heat Shock Elements in Arabidopsis Thaliana Plant Cell Physiol., September 1, 2008; 49(9): 1306 - 1315. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Shostak, M. R. Van Gilst, A. Antebi, and K. R. Yamamoto Identification of C. elegans DAF-12-binding sites, response elements, and target genes Genes & Dev., October 15, 2004; 18(20): 2529 - 2544. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Sanyal, M. Baum, and J. Carbon Centromeric DNA sequences in the pathogenic yeast Candida albicans are all different and unique PNAS, August 3, 2004; 101(31): 11374 - 11379. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Dressman, H. Yan, G. Traverso, K. W. Kinzler, and B. Vogelstein Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations PNAS, July 22, 2003; 100(15): 8817 - 8822. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Shtatland, S. C. Gill, B. E. Javornik, H. E. Johansson, B. S. Singer, O. C. Uhlenbeck, D. A. Zichi, and L. Gold Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX Nucleic Acids Res., November 1, 2000; 28(21): e93 - e93. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Yamazaki, Y. Ohnishi, and S. Horinouchi An A-Factor-Dependent Extracytoplasmic Function Sigma Factor (sigma AdsA) That Is Essential for Morphological Development in Streptomyces griseus J. Bacteriol., August 15, 2000; 182(16): 4596 - 4605. [Abstract] [Full Text]
|
|
|
|
|
|
S. E. Harris, C. L. Winchester, and K. J. Johnson Functional analysis of the homeodomain protein SIX5 Nucleic Acids Res., May 1, 2000; 28(9): 1871 - 1878. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. V. Ponomarenko, G. V. Orlova, M. P. Ponomarenko, S. V. Lavryushev, A. S. Frolov, S. V. Zybova, and N. A. Kolchanov SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation Nucleic Acids Res., January 1, 2000; 28(1): 205 - 208. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Lucito, M. Nakimura, J. A. West, Y. Han, K. Chin, K. Jensen, R. McCombie, J. W. Gray, and M. Wigler Genetic analysis using genomic representations PNAS, April 14, 1998; 95(8): 4487 - 4492. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S C Farmer, C W Sun, G E Winnier, B L Hogan, and T M Townes The bZIP transcription factor LCR-F1 is essential for mesoderm formation in mouse development. Genes & Dev., March 15, 1997; 11(6): 786 - 798. [Abstract] [PDF]
|
|
|
|
 |
|
 D P Mortlock, M R Nelson, and J W Innis An efficient method for isolating putative promoters and 5'-transcribed sequences from large genomic clones. Genome Res., April 1, 1996; 6(4): 327 - 335. [Abstract] [PDF]
|
|
|
|
 |
|
 X. Tang, H.-O. Li, O. Sakatsume, T. Ohta, H. Tsutsui, A. F. A. Smit, M. Horikoshi, P. Kourilsky, A. Israël, G. Gachelin, et al. Cooperativity between an Upstream TATA-like Sequence and a CAA Repeated Element Mediates E1A-dependent Negative Repression of the H-2K^b Class I Gene J. Biol. Chem., February 3, 1995; 270(5): 2327 - 2336. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L Su, R J Hershberger, and I L Weissman LYAR, a novel nucleolar protein with zinc finger DNA-binding motifs, is involved in cell growth regulation. Genes & Dev., May 1, 1993; 7(5): 735 - 748. [Abstract] [PDF]
|
|
|
|
 |
|
 R. Myers The pluses of subtraction Science, February 12, 1993; 259(5097): 942 - 943.
|
|
|
|
|
|
W. Bickmore, K Oghene, M. Little, A Seawright, V van Heyningen, and N. Hastie Modulation of DNA binding specificity by alternative splicing of the Wilms tumor wt1 gene transcript Science, July 10, 1992; 257(5067): 235 - 237. [Abstract] [PDF]
|
|
|
|
|
|
H. Erlich, D Gelfand, and J. Sninsky Recent advances in the polymerase chain reaction Science, June 21, 1991; 252(5013): 1643 - 1651. [Abstract] [PDF]
|
|
|
|
|
|
U. Stelzl, C. M. T. Spahn, and K. H. Nierhaus Selecting rRNA binding sites for the ribosomal proteins L4 and L6 from randomly fragmented rRNA: Application of a method called SERF PNAS, April 25, 2000; 97(9): 4597 - 4602. [Abstract] [Full Text] [PDF]
|
|