Crossref journal-article
American Association for the Advancement of Science (AAAS)
Science (221)
Abstract

The TATA-binding protein (TBP)–related factor 1 (TRF1) is expressed in a tissue-restricted fashion during Drosophila embryogenesis and may serve as a promoter-specific recognition factor that can replace TBP in regulating transcription. However, bona fide target promoters that would preferentially respond to TRF1 have remained elusive. Polytene chromosome staining, chromatin immunoprecipitation, direct messenger RNA analysis, and transient cotransfection assays identified the Drosophila gene tudor as containing a TRF1-responsive promoter. Reconstituted in vitro transcription reactions and deoxyribonuclease I footprinting assays confirmed the ability of TRF1 to bind preferentially and direct transcription of the tudor gene from an alternate promoter. Thus, metazoans appear to have evolved gene-selective and tissue-specific components of the core transcription machinery to regulate gene expression.

Bibliography

Holmes, M. C., & Tjian, R. (2000). Promoter-Selective Properties of the TBP-Related Factor TRF1. Science, 288(5467), 867–870.

Authors 2
  1. Michael C. Holmes (first)
  2. Robert Tjian (additional)
References 32 Referenced 89
  1. Hill C. S., Treisman R., Cell 80, 199 (1995); (10.1016/0092-8674(95)90403-4) / Cell by Hill C. S. (1995)
  2. 10.1126/science.284.5414.606
  3. 10.1016/S0092-8674(00)80599-1
  4. Crowley T. E., et al., Nature 361, 557 (1993). (10.1038/361557a0) / Nature by Crowley T. E. (1993)
  5. 10.1016/S0092-8674(01)80010-6
  6. Orlando V., Paro R., Cell 75, 1187 (1993); (10.1016/0092-8674(93)90328-N) / Cell by Orlando V. (1993)
  7. . Cells were treated for 15 min at 25°C with 1% formaldehyde (final concentration). After lysis with a buffer containing 50 mM Hepes (pH 7.6) 140 mM NaCl 1 mM EDTA 1% Triton X-100 0.1% Na-deoxycholate and 0.5 mM phenylmethylsulfonyl fluoride (PMSF) the resuspended nuclear pellets were sonicated four times for 30 s to shear the chromatin into fragments averaging 500 bp. The fragmented chromatin extract was dialyzed into a 3 M urea solution to dissociate TRF1-associated factors and non-crosslinked DNA-bound proteins. The extracts were spun for 15 min at 15 000 g the urea was dialyzed out and the extracts were respun. Each precipitation was performed with extracts from 1.5 × 10 8 cells. The extracts were precleared for 1 hour with protein A–Sepharose beads (Amersham Pharmacia). The beads were removed and the immunoprecipitations were carried out overnight with 2 μg of antibody and 15 μl of protein A–Sepharose beads. The beads were washed six times with lysis buffer and six times with a buffer containing 0.1 M tris-HCl (pH 7.9) 0.5 M LiCl 1% NP-40 1% Na-deoxycholate and 0.5 mM PMSF. The antibody-antigen complexes were eluted and the crosslinks were reversed. The proteins were treated with proteinase K and the DNA isolated by phenol-chloroform extraction and ethanol precipitation. The DNA was radiolabeled by random priming using the Klenow fragment and random hexameric primers in the presence of cold deoxynucleotide triphosphates and [α- 32 P]deoxycytidine triphosphate and then used to probe DNA hybridization blots containing restriction fragments of the tudor and AntP1 promoters.
  8. England B. P., Heberlein U., Tjian R., J. Biol. Chem. 265, 5086 (1990). (10.1016/S0021-9258(19)34088-8) / J. Biol. Chem. by England B. P. (1990)
  9. Bunch T. A., Grinblat Y., Goldstein L. S., Nucleic Acids Res. 16, 1043 (1988). (10.1093/nar/16.3.1043) / Nucleic Acids Res. by Bunch T. A. (1988)
  10. M. C. Holmes and R. Tjian unpublished data.
  11. Sadovsky Y., et al., Mol. Cell. Biol. 15, 1554 (1995); (10.1128/MCB.15.3.1554) / Mol. Cell. Biol. by Sadovsky Y. (1995)
  12. Colgan J., Manley J. L., Genes Dev. 6, 304 (1992). (10.1101/gad.6.2.304) / Genes Dev. by Colgan J. (1992)
  13. S. Takada and R. Tjian unpublished data.
  14. M. C. Holmes P. Hurban K. P. White R. Tjian unpublished data.
  15. 10.1073/pnas.96.9.4791
  16. Maldonado E., J. Biol. Chem. 274, 12963 (1999); (10.1074/jbc.274.19.12963) / J. Biol. Chem. by Maldonado E. (1999)
  17. 10.1093/nar/27.3.750
  18. Wieczorek E., et al., Nature 393, 187 (1998). (10.1038/30283) / Nature by Wieczorek E. (1998)
  19. 10.1016/S0092-8674(00)81330-6
  20. ; M. Hiller T.-Y. Lin M. Fuller unpublished data.
  21. Margolis P., Driks A., Losick R., Curr. Opin. Genet. Dev. 1, 330 (1991). (10.1016/S0959-437X(05)80296-5) / Curr. Opin. Genet. Dev. by Margolis P. (1991)
  22. Courey A. J., Tjian R., Cell 55, 887 (1988); (10.1016/0092-8674(88)90144-4) / Cell by Courey A. J. (1988)
  23. . The tudor and HSV TK promoters were fused to the luciferase reporter gene in the pGL3-Basic vector (Promega). Cells were transiently transfected by the calcium phosphate coprecipitation method. The luciferase reporter constructs were cotransfected with increasing amounts of a pPAC vector expressing either TRF1 or TBP under the actin 5C promoter. The ø lanes are control transfections with only the luciferase reporter constructs transfected. These values were set to 1 to represent the basal level for each promoter. Cells (3 × 10 6 ) were transfected with 300 ng of the luciferase reporter construct 50 ng of a CMV-renilla construct as an internal standard and 100 ng 500 ng or 1 μg of the pPAC vector expressing either TRF1 or TBP. An empty pPAC vector was added to each transfection experiment to bring the total amount of pPAC in each experiment up to 1 μg and salmon sperm was added to bring the total amount of DNA in each transfection to 5 μg.
  24. Recombinant TBP TFIIA and TFIIB were purified as described [
  25. 10.1016/0092-8674(95)90029-2
  26. Pugh B. F., Tjian R., Genes Dev. 5, 1935 (1991); (10.1101/gad.5.11.1935) / Genes Dev. by Pugh B. F. (1991)
  27. ]. TRF1 was expressed recombinantly in Escherichia coli and purified as described (5). TFIID TFIIE TFIIF TFIIH and RNA Pol II were purified from nuclear extracts derived from 0- to 12-hour Drosophila embryos. Nuclear extracts were prepared as described [
  28. Heberlein U., Tjian R., Nature 331, 410 (1988); (10.1038/331410a0) / Nature by Heberlein U. (1988)
  29. ] dialyzed into 0.1 M KCl HEMG buffer [25 mM Hepes (pH 7.6) 12.5 mM MgCl 2 0.1 mM EDTA 10% glycerol 1 mM dithiothreitol 1 mM PMSF and 1 mM sodium metabisulfite] and loaded onto a 40-ml Poros 20 HE1 column. The basal factors were stepped off with 0.4 M NaCl HEMG buffer and loaded onto a 520-ml Sephacryl-300 column (S300 Pharmacia) equilibrated in 0.1 M NaCl HEMG buffer. The proteins were resolved isocratically and the fractions assayed for transcriptional activity. TFIID activity was isolated from fractions corresponding to the void volume of the S300 column. Several fractions eluting after the void volume and TFIID were tested and found to contain the TFIIE TFIIF TFIIH and RNA Pol II activities used in the experiments for this study. TFIID was further purified by directly loading the S300 fractions containing TFIID activity onto an 8-ml Mono-Q HR 10/10 column (Pharmacia). TFIID was eluted from the column with a 25-column volume gradient from 0.1 to 0.5 M NaCl in HEMG buffer. TFIID activity eluted between 0.25 and 0.3 M NaCl.
  30. Yokomori K., et al., Genes Dev. 8, 2313 (1994). (10.1101/gad.8.19.2313) / Genes Dev. by Yokomori K. (1994)
  31. Maxam A. M., Gilbert W., Proc. Natl. Acad. Sci. U.S.A. 74, 560 (1977). (10.1073/pnas.74.2.560) / Proc. Natl. Acad. Sci. U.S.A. by Maxam A. M. (1977)
  32. We thank R. Freiman C. Inouye A. Ladurner A. Hochheimer J. Ziegelbauer and D. Rio for critical reading and comments on the manuscript; J. Zwicker for collaborating in setting up a reconstituted in vitro transcription system; S. Takada for stably transformed SL2 cell lines and affinity-purified antibodies to TRF1; R. Jacobson and S. Ryu for reagents; and T. O'Brien for helpful scientific discussions and advice. Supported in part by NIH grant CA25417 (R.T.).
Dates
Type When
Created 23 years ago (July 27, 2002, 5:35 a.m.)
Deposited 1 year, 7 months ago (Jan. 13, 2024, 5:05 a.m.)
Indexed 2 weeks, 4 days ago (Aug. 5, 2025, 8:52 a.m.)
Issued 25 years, 3 months ago (May 5, 2000)
Published 25 years, 3 months ago (May 5, 2000)
Published Print 25 years, 3 months ago (May 5, 2000)
Funders 0

None

@article{Holmes_2000, title={Promoter-Selective Properties of the TBP-Related Factor TRF1}, volume={288}, ISSN={1095-9203}, url={http://dx.doi.org/10.1126/science.288.5467.867}, DOI={10.1126/science.288.5467.867}, number={5467}, journal={Science}, publisher={American Association for the Advancement of Science (AAAS)}, author={Holmes, Michael C. and Tjian, Robert}, year={2000}, month=may, pages={867–870} }