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. 1997 Feb 15;25(4):781–786. doi: 10.1093/nar/25.4.781

Libraries for genomic SELEX.

B S Singer 1, T Shtatland 1, D Brown 1, L Gold 1
PMCID: PMC146522  PMID: 9016629

Abstract

An increasing number of proteins are being identified that regulate gene expression by binding specific nucleic acidsin vivo. A method termed genomic SELEX facilitates the rapid identification of networks of protein-nucleic acid interactions by identifying within the genomic sequences of an organism the highest affinity sites for any protein of the organism. As with its progenitor, SELEX of random-sequence nucleic acids, genomic SELEX involves iterative binding, partitioning, and amplification of nucleic acids. The two methods differ in that the variable region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coli, Saccharomyces cerevisiae, and human genomic DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts starting at most of the positions within the genome, making these libraries suitable for genomic SELEX.

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Selected References

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  1. Chu E., Voeller D. M., Jones K. L., Takechi T., Maley G. F., Maley F., Segal S., Allegra C. J. Identification of a thymidylate synthase ribonucleoprotein complex in human colon cancer cells. Mol Cell Biol. 1994 Jan;14(1):207–213. doi: 10.1128/mcb.14.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ellington A. D., Szostak J. W. In vitro selection of RNA molecules that bind specific ligands. Nature. 1990 Aug 30;346(6287):818–822. doi: 10.1038/346818a0. [DOI] [PubMed] [Google Scholar]
  3. Evangelista C., Lockshon D., Fields S. The yeast two-hybrid system: prospects for protein linkage maps. Trends Cell Biol. 1996 May;6(5):196–199. doi: 10.1016/0962-8924(96)40002-2. [DOI] [PubMed] [Google Scholar]
  4. Fester T., Schuster W. Potato mitochondrial manganese superoxide dismutase is an RNA-binding protein. Biochem Mol Biol Int. 1995 May;36(1):67–75. [PubMed] [Google Scholar]
  5. Gold L., Brown D., He Y., Shtatland T., Singer B. S., Wu Y. From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops. Proc Natl Acad Sci U S A. 1997 Jan 7;94(1):59–64. doi: 10.1073/pnas.94.1.59. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gold L., Polisky B., Uhlenbeck O., Yarus M. Diversity of oligonucleotide functions. Annu Rev Biochem. 1995;64:763–797. doi: 10.1146/annurev.bi.64.070195.003555. [DOI] [PubMed] [Google Scholar]
  7. Grothues D., Cantor C. R., Smith C. L. PCR amplification of megabase DNA with tagged random primers (T-PCR). Nucleic Acids Res. 1993 Mar 11;21(5):1321–1322. doi: 10.1093/nar/21.5.1321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hentze M. W. Enzymes as RNA-binding proteins: a role for (di)nucleotide-binding domains? Trends Biochem Sci. 1994 Mar;19(3):101–103. doi: 10.1016/0968-0004(94)90198-8. [DOI] [PubMed] [Google Scholar]
  9. Irvine D., Tuerk C., Gold L. SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis. J Mol Biol. 1991 Dec 5;222(3):739–761. doi: 10.1016/0022-2836(91)90509-5. [DOI] [PubMed] [Google Scholar]
  10. Kinzler K. W., Vogelstein B. Whole genome PCR: application to the identification of sequences bound by gene regulatory proteins. Nucleic Acids Res. 1989 May 25;17(10):3645–3653. doi: 10.1093/nar/17.10.3645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kyrpides N. C., Ouzounis C. A. Nucleic acid-binding metabolic enzymes: living fossils of stereochemical interactions? J Mol Evol. 1995 Jun;40(6):564–569. doi: 10.1007/BF00160502. [DOI] [PubMed] [Google Scholar]
  12. Manley J. L., Tacke R. SR proteins and splicing control. Genes Dev. 1996 Jul 1;10(13):1569–1579. doi: 10.1101/gad.10.13.1569. [DOI] [PubMed] [Google Scholar]
  13. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Philippsen P., Stotz A., Scherf C. DNA of Saccharomyces cerevisiae. Methods Enzymol. 1991;194:169–182. doi: 10.1016/0076-6879(91)94014-4. [DOI] [PubMed] [Google Scholar]
  15. Singh N. K., Atreya C. D., Nakhasi H. L. Identification of calreticulin as a rubella virus RNA binding protein. Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12770–12774. doi: 10.1073/pnas.91.26.12770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sompayrac L., Danna K. J. Method to identify genomic targets of DNA binding proteins. Proc Natl Acad Sci U S A. 1990 May;87(9):3274–3278. doi: 10.1073/pnas.87.9.3274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Tasheva E. S., Roufa D. J. Regulation of human RPS14 transcription by intronic antisense RNAs and ribosomal protein S14. Genes Dev. 1995 Feb 1;9(3):304–316. doi: 10.1101/gad.9.3.304. [DOI] [PubMed] [Google Scholar]
  18. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 1990 Aug 3;249(4968):505–510. doi: 10.1126/science.2200121. [DOI] [PubMed] [Google Scholar]
  19. Wu D. Y., Ugozzoli L., Pal B. K., Qian J., Wallace R. B. The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA Cell Biol. 1991 Apr;10(3):233–238. doi: 10.1089/dna.1991.10.233. [DOI] [PubMed] [Google Scholar]
  20. van Gelder C. W., Gunderson S. I., Jansen E. J., Boelens W. C., Polycarpou-Schwarz M., Mattaj I. W., van Venrooij W. J. A complex secondary structure in U1A pre-mRNA that binds two molecules of U1A protein is required for regulation of polyadenylation. EMBO J. 1993 Dec 15;12(13):5191–5200. doi: 10.1002/j.1460-2075.1993.tb06214.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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