Skip to main content
SpringerLink
Log in

Protein Binding Microarrays for the Characterization of DNA–Protein Interactions

  • Chapter
  • First Online:
Analytics of Protein–DNA Interactions

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 104))

Abstract

A number of important cellular processes, such as transcriptional regulation, recombination, replication, repair, and DNA modification, are performed by DNA binding proteins. Of particular interest are transcription factors (TFs) which, through their sequence-specific interactions with DNA binding sites, modulate gene expression in a manner required for normal cellular growth and differentiation, and also for response to environmental stimuli. Despite their importance, the DNA binding specificities of most DNA binding proteins still remain unknown, since prior technologies aimed at identifying DNA–protein interactions have been laborious, not highly scalable, or have required limiting biological reagents. Recently a new DNA microarray-based technology, termed protein binding microarrays (PBMs), has been developed that allows rapid, high-throughput characterization of the in vitro DNA binding site sequence specificities of TFs, other DNA binding proteins, or synthetic compounds. DNA binding site data from PBMs combined with gene annotation data, comparative sequence analysis, and gene expression profiling, can be used to predict what genes are regulated by a given TF, what the functions are of a given TF and its predicted target genes, and how that TF may fit into the cell's transcriptional regulatory network.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Abbreviations

ChIP:

Chromatin immunoprecipitation

Dam:

DNA adenine methyltransferase

dsDNA:

Double-stranded DNA

GST:

glutathione S-transferase

PBM:

Protein binding microarray

TF:

Transcription factor

References

  1. Wyrick J, Young R (2002) Curr Opin Genet Dev 12:130

    Article  CAS  Google Scholar 

  2. Lockhart DJ, Winzeler EA (2000) Nature 405:827

    Article  CAS  Google Scholar 

  3. Choo Y, Klug A (1994) Proc Natl Acad Sci USA 91:11168

    Article  CAS  Google Scholar 

  4. Hallikas O, Palin K, Sinjushina N et al (2006) Cell 124:47

    Article  CAS  Google Scholar 

  5. Benos P, Bulyk M, Stormo G (2002) Nucleic Acids Res 30:4442

    Article  CAS  Google Scholar 

  6. Bulyk M, Johnson P, Church G (2002) Nucleic Acids Res 30:1255

    Article  CAS  Google Scholar 

  7. Lee M-L, Bulyk M, Whitmore G, Church G (2002) Biometrics 58:981

    Article  Google Scholar 

  8. Man TK, Stormo GD (2001) Nucleic Acids Res 29:2471

    Article  CAS  Google Scholar 

  9. Pease AC, Solas D, Sullivan EJ et al (1994) Proc Natl Acad Sci USA 91:5022

    Article  CAS  Google Scholar 

  10. Schena M, Shalon D, Davis RW, Brown PO (1995) Science 270:467

    Article  CAS  Google Scholar 

  11. MacBeath G, Schreiber SL (2000) Science 289:1760

    CAS  Google Scholar 

  12. MacBeath G, Koehler AN, Schreiber SL (1999) J Am Chem Soc 121:7967

    Article  CAS  Google Scholar 

  13. Lieb JD, Liu X, Botstein D, Brown PO (2001) Nat Genet 28:327

    Article  CAS  Google Scholar 

  14. Iyer VR, Horak CE, Scafe CS et al (2001) Nature 409:533

    Article  CAS  Google Scholar 

  15. Ren B, Robert F, Wyrick JJ et al (2000) Science 290:2306

    Article  CAS  Google Scholar 

  16. Reid JL, Iyer VR, Brown PO, Struhl K (2000) Mol Cell 6:1297

    Article  CAS  Google Scholar 

  17. Lee T, Rinaldi N, Robert R et al (2002) Science 298:799

    Article  CAS  Google Scholar 

  18. Harbison CT, Gordon DB, Lee TI et al (2004) Nature 431:99

    Article  CAS  Google Scholar 

  19. van Steensel B, Henikoff S (2000) Nat Biotechnol 18:424

    Article  CAS  Google Scholar 

  20. van Steensel B, Delrow J, Henikoff S (2001) Nat Genet 27:304

    Article  CAS  Google Scholar 

  21. Tompa R, McCallum C, Delrow J et al (2002) Curr Biol 12:65

    Article  CAS  Google Scholar 

  22. Oliphant A, Brandl C, Struhl K (1989) Mol Cell Biol 9:2944

    CAS  Google Scholar 

  23. Amendt B, Sutherland L, Russo A (1999) J Biol Chem 274:11635

    Article  CAS  Google Scholar 

  24. Walter J, Dever C, Biggin M (1994) Genes Dev 8:1678

    Article  CAS  Google Scholar 

  25. Udalova I, Mott R, Field D, Kwiatkowski D (2002) Proc Natl Acad Sci USA 99:8167

    Article  CAS  Google Scholar 

  26. Mukherjee S, Berger MF, Jona G et al (2004) Nat Genet 36:1331

    Article  CAS  Google Scholar 

  27. Roulet E, Busso S, Camargo AA et al (2002) Nat Biotechnol 20:831

    CAS  Google Scholar 

  28. Vargo MA, Nguyen L, Colman RF (2004) Biochemistry 43:3327

    Article  CAS  Google Scholar 

  29. Warren CL, Kratochvil NC, Hauschild KE et al. (2006) Proc Natl Acad Sci USA 103:867–872

    Article  CAS  Google Scholar 

  30. Doi N, Takashima H, Kinjo M et al (2002) Genome Res 12:487

    Article  CAS  Google Scholar 

  31. Braun P, Hu Y, Shen B et al (2002) Proc Natl Acad Sci USA 99:2654

    Article  CAS  Google Scholar 

  32. Hughes TR, Mao M, Jones AR et al (2001) Nat Biotechnol 19:342

    Article  CAS  Google Scholar 

  33. Singh-Gasson S, Green RD, Yue Y et al (1999) Nat Biotechnol 17:974

    Article  CAS  Google Scholar 

  34. Nuwaysir EF, Huang W, Albert TJ et al (2002) Genome Res 12:1749

    Article  CAS  Google Scholar 

  35. Albert TJ, Norton J, Ott M et al (2003) Nucleic Acids Res 31:e35

    Article  CAS  Google Scholar 

  36. Bulyk ML, Huang X, Choo Y, Church GM (2001) Proc Natl Acad Sci USA 98:7158

    Article  CAS  Google Scholar 

  37. Bulyk ML, Gentalen E, Lockhart DJ, Church GM (1999) Nat Biotechnol 17:573

    Article  CAS  Google Scholar 

  38. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW 3rd, Bulyk ML (2006) Nature Biotechnol (in press)

    Google Scholar 

  39. Odom DT, Zizlsperger N, Gordon DB et al (2004) Science 303:1378

    Article  CAS  Google Scholar 

  40. Weinmann AS, Yan PS, Oberley MJ et al (2002) Genes Dev 16:235

    Article  CAS  Google Scholar 

  41. Berger MF, Bulyk ML (2006) In: Bina M (ed) Gene mapping, discovery, and expression (Methods Mol Biol). Humana, Totowa, New Jersey

    Google Scholar 

  42. DeRisi J, Penland L, Brown PO et al (1996) Nat Genet 14:457

    Article  CAS  Google Scholar 

  43. Dudley A, Aach J, Steffen M, Church G (2002) Proc Natl Acad Sci USA 99:7554

    Article  CAS  Google Scholar 

  44. Berg OG, Winter RB, von Hippel PH (1981) Biochemistry 20:6929

    Article  CAS  Google Scholar 

  45. Taylor J (1997) An introduction to error analysis. University Science Books, Sausalito, CA

    Google Scholar 

  46. Sokal R, Rohlf R (1995) Biometry: the principles and practice of statistics in biological research. Freeman, New York

    Google Scholar 

  47. Liu X, Brutlag D, Liu J (2001) Pac Symp Biocomput 127

    Google Scholar 

  48. Hughes JD, Estep PW, Tavazoie S, Church GM (2000) J Mol Biol 296:1205

    Article  CAS  Google Scholar 

  49. Roth FP, Hughes JD, Estep PW, Church GM (1998) Nat Biotechnol 16:939

    Article  CAS  Google Scholar 

  50. Bailey T, Elkan C (1995) Proc Int Conf Intell Syst Mol Biol 3:21

    CAS  Google Scholar 

  51. Liu X, Brutlag D, Liu J (2002) Nat Biotechnol 20:835

    CAS  Google Scholar 

  52. Schneider TD, Stephens RM (1990) Nucleic Acids Res 18:6097

    Article  CAS  Google Scholar 

  53. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) Genome Res 14:1188

    Article  CAS  Google Scholar 

  54. Kellis M, Patterson N, Endrizzi M et al (2003) Nature 423:241

    Article  CAS  Google Scholar 

  55. Cliften P, Sudarsanam P, Desikan A et al (2003) Science 301:71

    Article  CAS  Google Scholar 

  56. Tavazoie S, Hughes J, Campbell M et al (1999) Nat Genet 22:281

    Article  CAS  Google Scholar 

  57. Robinson M, Grigull J, Mohammad N, Hughes T (2002) BMC Bioinformatics 3:35

    Article  Google Scholar 

  58. Planta RJ (1997) Yeast 13:1505

    Article  CAS  Google Scholar 

  59. Mewes H, Frishman D, Guldener U et al (2002) Nucleic Acids Res 30:31

    Article  CAS  Google Scholar 

  60. Michelson AM, Bulyk ML (2006) Mol Syst Biol 2:2006.0018

    Article  Google Scholar 

  61. Venter JC, Adams MD, Myers EW et al (2001) Science 291:1304

    Article  CAS  Google Scholar 

  62. Jones RB, Gordus A, Krall JA, MacBeath G (2006) Nature 439:168

    Article  CAS  Google Scholar 

  63. Pierce M, Benjamin KR, Montano SP et al (2003) Mol Cell Biol 23:4814

    Article  CAS  Google Scholar 

  64. Desjarlais JR, Berg JM (1992) Proc Natl Acad Sci USA 89:7345

    Article  CAS  Google Scholar 

  65. Desjarlais JR, Berg JM (1992) Proteins 12:101

    Article  CAS  Google Scholar 

  66. Jacobs G (1992) EMBO J 11:4507

    CAS  Google Scholar 

  67. Suzuki M, Yagi N (1994) Proc Natl Acad Sci USA 91:12357

    Article  CAS  Google Scholar 

  68. Mandel-Gutfreund Y, Baron A, Margalit H (2001) Pac Symp Biocomput 139

    Google Scholar 

  69. Pomerantz JL, Sharp PA, Pabo CO (1995) Science 267:93

    Article  CAS  Google Scholar 

  70. Pomerantz JL, Pabo CO, Sharp PA (1995) Proc Natl Acad Sci USA 92:9752

    Article  CAS  Google Scholar 

  71. Choo Y, Klug A (1994) Proc Natl Acad Sci USA 91:11163

    Article  CAS  Google Scholar 

  72. Rebar EJ, Pabo CO (1994) Science 263:671

    Article  CAS  Google Scholar 

  73. Pabo CO, Nekludova L (2000) J Mol Biol 301:597

    Article  CAS  Google Scholar 

Download references

Acknowledgments

I thank Michael F. Berger and Tom Volkert for technical assistance. This work was supported in part by National Institutes of Health grants from the National Human Genome Research Institute to M.L.B. (R01 HG002966, R01 HG003420, and R01 HG003985).

Author information

Authors and Affiliations

  1. Division of Genetics, Department of Medicine, Department of Pathology, Division of Health Sciences & Technology (HST), Brigham & Women's Hospital and Harvard Medical School, Harvard Medical School New Research Bldg., Room 466D, 77 Avenue Louis Pasteur, 02115, Boston, MA, USA

    Martha L. Bulyk

Authors
  1. Martha L. Bulyk
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Martha L. Bulyk .

Editor information

Harald Seitz

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bulyk, M.L. (2006). Protein Binding Microarrays for the Characterization of DNA–Protein Interactions. In: Seitz, H. (eds) Analytics of Protein–DNA Interactions. Advances in Biochemical Engineering/Biotechnology, vol 104. Springer, Berlin, Heidelberg . https://doi.org/10.1007/10_025

Download citation

Publish with us

Policies and ethics

Search

Navigation