Transcription Factor Binding Sites and Other Features in Human and Drosophila Proximal Promoters

  • Charles Vinson
  • Raghunath Chatterjee
  • Peter Fitzgerald
Chapter
Part of the Subcellular Biochemistry book series (SCBI, volume 52)

Abstract

Eukaryotic promoters determine transcription start sites (TSSs), and are often enriched for transcription factor binding sites (TFBSs), which presumably play a major role in determining the location and activity of the TSS. In mammalian systems, proximal promoters are enriched for the CpG dinucleotide. The TFBSs that are enriched in proximal promoters (–200 bps to the TSS) are CCAAT, ETS, NRF1, SP1, E-Box, CRE, BoxA, and TATA. Only TATA occurs in a DNA strand dependent manner. In Drosophila, proximal promoters are AT rich and many putative TFBSs are enriched in proximal promoters. These sequences are different from those that occur in human promoters, except for TATA and E-Box, and many occur on a single strand of DNA giving directionality to the promoter. Thus, fundamental differences have arisen as promoters evolved in metazoans.

Keywords

Transcriptional Start Site Proximal Promoter Palindromic Sequence Human Promoter cAMP Responsive Element 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Ohler U, Liao GC, Niemann H, Rubin GM (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol 3:RESEARCH0087PubMedCrossRefGoogle Scholar
  2. 2.
    FitzGerald PC, Shlyakhtenko A, Mir AA, Vinson C (2004) Clustering of DNA sequences in human promoters. Genome Res 14:1562–1574PubMedCrossRefGoogle Scholar
  3. 3.
    Fitzgerald PC, Sturgill D, Shyakhtenko A, Oliver B, Vinson C (2006) Comparative genomics of Drosophila and human core promoters. Genome Biol 7:R53PubMedCrossRefGoogle Scholar
  4. 4.
    Marino-Ramirez L, Spouge JL, Kanga GC, Landsman D (2004) Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res 32:949–958PubMedCrossRefGoogle Scholar
  5. 5.
    Bina M, et al. (2004) Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics 84:929–940PubMedCrossRefGoogle Scholar
  6. 6.
    Bina M, et al. (2009) Discovering sequences with potential regulatory characteristics. Genomics 93:314–322PubMedCrossRefGoogle Scholar
  7. 7.
    Suzuki Y, Yamashita R, Sugano S, Nakai K (2004) DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res 32:D78–81PubMedCrossRefGoogle Scholar
  8. 8.
    Zhang MQ (1998) A discrimination study of human core-promoters. Pac Symp Biocomput 3:240–251Google Scholar
  9. 9.
    Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321:209–213PubMedCrossRefGoogle Scholar
  10. 10.
    Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282PubMedCrossRefGoogle Scholar
  11. 11.
    Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21PubMedCrossRefGoogle Scholar
  12. 12.
    Rozenberg JM, et al. (2008) All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues. BMC Genomics 9:67PubMedCrossRefGoogle Scholar
  13. 13.
    Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683–692PubMedCrossRefGoogle Scholar
  14. 14.
    Eckhardt F, et al. (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385PubMedCrossRefGoogle Scholar
  15. 15.
    Weber M, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466PubMedCrossRefGoogle Scholar
  16. 16.
    Mito Y, Henikoff JG, Henikoff S (2005) Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet 37:1090–1097PubMedCrossRefGoogle Scholar
  17. 17.
    Yuan GC, et al. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626–630PubMedCrossRefGoogle Scholar
  18. 18.
    Tillo D, Hughes TR (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10:442PubMedCrossRefGoogle Scholar
  19. 19.
    Tillo D, et al. (2010) High nucleosome occupancy is encoded at human regulatory sequences. PLoS One 5:9129CrossRefGoogle Scholar
  20. 20.
    Polavarapu N, Marino-Ramirez L, Landsman D, McDonald JF, Jordan IK (2008) Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics 9:226PubMedCrossRefGoogle Scholar
  21. 21.
    Weirauch MT, Hughes TR (2010) Dramatic changes in transcription factor binding over evolutionary time. Genome Biol 11:122PubMedCrossRefGoogle Scholar
  22. 22.
    Pavletich NP, Pabo CO (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252:809–817PubMedCrossRefGoogle Scholar
  23. 23.
    Dynan WS, Tjian R (1985) Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. Nature 316:774–778PubMedCrossRefGoogle Scholar
  24. 24.
    Sinha S, Maity SN, Lu J, de Crombrugghe B (1995) Recombinant rat CBF-C, the third subunit of CBF/NFY, allows formation of a protein-DNA complex with CBF-A and CBF-B and with yeast HAP2 and HAP3. Proc Natl Acad Sci U S A 92:1624–1628PubMedCrossRefGoogle Scholar
  25. 25.
    Sharrocks AD (2001) The ETS-domain transcription factor family. Nat Rev Mol Cell Biol 2:827–837PubMedCrossRefGoogle Scholar
  26. 26.
    Graves BJ, Petersen JM (1998) Specificity within the ets family of transcription factors. Adv Cancer Res 75:1–55PubMedCrossRefGoogle Scholar
  27. 27.
    Brown TA, McKnight SL (1992) Specificities of protein–protein and protein–DNA interaction of GABP alpha and two newly defined ets-related proteins. Genes Dev 6:2502–2512PubMedCrossRefGoogle Scholar
  28. 28.
    Wei GH, et al. (2010) Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo. Embo J 29:2147–2160PubMedCrossRefGoogle Scholar
  29. 29.
    Jolma A, et al. Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 20:861–873Google Scholar
  30. 30.
    Kim Y, Geiger JH, Hahn S, Sigler PB (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature 365:512–520PubMedCrossRefGoogle Scholar
  31. 31.
    Geiger JH, Hahn S, Lee S, Sigler PB (1996) Crystal structure of the yeast TFIIA/TBP/DNA complex. Science 272:830–836PubMedCrossRefGoogle Scholar
  32. 32.
    Kim TH, et al. (2005) A high-resolution map of active promoters in the human genome. Nature 436:876–880PubMedCrossRefGoogle Scholar
  33. 33.
    Perry RP (2005) The architecture of mammalian ribosomal protein promoters. BMC Evol Biol 5:15PubMedCrossRefGoogle Scholar
  34. 34.
    Kim J, Kim J (2009) YY1’s longer DNA-binding motifs. Genomics 93:152–158PubMedCrossRefGoogle Scholar
  35. 35.
    Scarpulla RC (2006) Nuclear control of respiratory gene expression in mammalian cells. J Cell Biochem 97:673–683PubMedCrossRefGoogle Scholar
  36. 36.
    Bendall AJ, Molloy PL (1994) Base preferences for DNA binding by the bHLH-Zip protein USF: effects of MgCl2 on specificity and comparison with binding of Myc family members. Nucleic Acids Res 22:2801–2810PubMedCrossRefGoogle Scholar
  37. 37.
    Boyd KE, Farnham PJ (1999) Coexamination of site-specific transcription factor binding and promoter activity in living cells. Mol Cell Biol 19:8393–8399PubMedGoogle Scholar
  38. 38.
    Ferre-D’Amare AR, Prendergast GC, Ziff EB, Burley SK (1993) Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363:38–45PubMedCrossRefGoogle Scholar
  39. 39.
    Montminy M (1997) Transcriptional regulation by cyclic AMP. Annu Rev Biochem 66:807–822PubMedCrossRefGoogle Scholar
  40. 40.
    Shaywitz AJ, Greenberg ME (1999) CREB: a stimulus-induced transcription factor activated by a diverse array of extracellular signals. Annu Rev Biochem 68:821–861PubMedCrossRefGoogle Scholar
  41. 41.
    Mayr B, Montminy M (2001) Transcriptional regulation by the phosphorylation-dependent factor CREB. Nat Rev Mol Cell Biol 2:599–609PubMedCrossRefGoogle Scholar
  42. 42.
    Vinson C, et al. (2002) Classification of human B-ZIP proteins based on dimerization properties. Mol Cell Biol 22:6321–6335PubMedCrossRefGoogle Scholar
  43. 43.
    Iguchi-Ariga SM, Schaffner W (1989) CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev 3:612–619PubMedCrossRefGoogle Scholar
  44. 44.
    Vinson CR, Hai T, Boyd SM (1993) Dimerization specificity of the leucine zipper-containing bZIP motif on DNA binding: prediction and rational design. Genes Dev 7:1047–1058PubMedCrossRefGoogle Scholar
  45. 45.
    Shuman JD, Cheong J, Coligan JE (1997) ATF-2 and C/EBPalpha can form a heterodimeric DNA binding complex in vitro. Functional implications for transcriptional regulation. J Biol Chem 272:12793–12800PubMedCrossRefGoogle Scholar
  46. 46.
    Schumacher MA, Goodman RH, Brennan RG (2000) The structure of a CREB bZIP.somatostatin CRE complex reveals the basis for selective dimerization and divalent cation-enhanced DNA binding. J Biol Chem 275:35242–35247PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Charles Vinson
    • 1
  • Raghunath Chatterjee
    • 1
  • Peter Fitzgerald
    • 2
  1. 1.Laboratory of MetabolismNCI, NIHBethesdaUSA
  2. 2.Genome Analysis UnitNCI, NIHBethesdaUSA

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