Skip to main content
SpringerLink
Log in

Identification of Transcription Factor–DNA Interactions In Vivo

  • Chapter
  • First Online:
A Handbook of Transcription Factors

Part of the book series: Subcellular Biochemistry ((SCBI,volume 52))

Abstract

Recent technological developments have revolutionized our understanding of transcriptional regulation by providing an unprecedented ability to interrogate in vivo transcription factor binding. The combination of high-throughput sequencing with chromatin precipitation of transcription factors and specifically labeled histones has allowed direct protein-DNA contacts to be visualized across genomes as large and complex as mammals at base-pair resolution. This chapter reviews the developments that led to these insights, with particular focus on examples of early protein-DNA localization experiments using genomic microarrays in mammals and yeast. Four state-of-the-art research directions are highlighted as examples of previously unimaginable frontiers now under active investigation.

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 EPUB and 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

References

  1. Gilbert W (1986) Evolution of antibodies. The road not taken. Nature 320(6062):485–486

    Article  PubMed  CAS  Google Scholar 

  2. Wing R, et al. (1980) Crystal structure analysis of a complete turn of B-DNA. Nature 287(5784):755–758

    Article  PubMed  CAS  Google Scholar 

  3. Watson JD, Crick FH (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature 171(4361):964–967

    Article  PubMed  CAS  Google Scholar 

  4. Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171(4356):737–738

    Article  PubMed  CAS  Google Scholar 

  5. Vaquerizas JM, et al. (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10(4):252–263

    Article  PubMed  CAS  Google Scholar 

  6. Riechmann JL, et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290(5499):2105–2110

    Article  PubMed  CAS  Google Scholar 

  7. Riano-Pachon DM, et al. (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8:42

    Article  PubMed  Google Scholar 

  8. Jordan SR, Pabo CO (1988) Structure of the lambda complex at 2.5 A resolution: details of the repressor–operator interactions. Science 242(4880):893–899

    Article  PubMed  CAS  Google Scholar 

  9. Chenoweth DM, Dervan PB (2009) Allosteric modulation of DNA by small molecules. Proc Natl Acad Sci U S A 106(32):13175–13179

    Article  PubMed  CAS  Google Scholar 

  10. Galas DJ, Schmitz A (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 5(9):3157–3170

    Article  PubMed  CAS  Google Scholar 

  11. Hardison RC, et al. (1979) The structure and transcription of four linked rabbit beta-like globin genes. Cell 18(4):1285–1297

    Article  PubMed  CAS  Google Scholar 

  12. Stranick KS, et al. (1997) Identification of transcription factor binding sites important in the regulation of the human interleukin-5 gene. J Biol Chem 272(26):16453–16465

    Article  PubMed  CAS  Google Scholar 

  13. Kardassis D, et al. (1990) Characterization of the promoter elements required for hepatic and intestinal transcription of the human apoB gene: definition of the DNA-binding site of a tissue-specific transcriptional factor. Mol Cell Biol 10(6):2653–2659

    PubMed  CAS  Google Scholar 

  14. Kardassis D, Zannis VI, Cladaras C (1992) Organization of the regulatory elements and nuclear activities participating in the transcription of the human apolipoprotein B gene. J Biol Chem 267(11):7956

    PubMed  CAS  Google Scholar 

  15. Shibata Y, Crawford GE (2009) Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip). Methods Mol Biol 556:177–190

    Article  PubMed  CAS  Google Scholar 

  16. Quitschke WW, et al. (2000) Differential effect of zinc finger deletions on the binding of CTCF to the promoter of the amyloid precursor protein gene. Nucleic Acids Res 28(17):3370–3378

    Article  PubMed  CAS  Google Scholar 

  17. Perry RP, Kelley DE (1966) Evidence for specific association of protein with newly formed ribosomal subunits. Biochem Biophys Res Commun 24(3):459–465

    Article  PubMed  CAS  Google Scholar 

  18. Economidis IV, Rousseau GG (1985) Association of the glucocorticoid hormone receptor with ribonucleic acid. FEBS Lett 181(1):47–52

    Article  PubMed  CAS  Google Scholar 

  19. Licatalosi DD, et al. (2008) HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature 456(7221):464–469

    Article  PubMed  CAS  Google Scholar 

  20. Wang Z, et al. (2009) CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods 48(3):287–293

    Article  PubMed  Google Scholar 

  21. Solomon MJ, Varshavsky A (1985) Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc Natl Acad Sci U S A 82(19):6470–6474

    Article  PubMed  CAS  Google Scholar 

  22. Varshavsky AJ, Sundin O, Bohn M (1979) A stretch of “late” SV40 viral DNA about 400 bp long which includes the origin of replication is specifically exposed in SV40 minichromosomes. Cell 16(2):453–466

    Article  PubMed  CAS  Google Scholar 

  23. Gasch AP, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241–4257

    PubMed  CAS  Google Scholar 

  24. Causton HC, et al. (2001) Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12(2):323–337

    PubMed  CAS  Google Scholar 

  25. Ross DT, et al. (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24(3):227–235

    Article  PubMed  CAS  Google Scholar 

  26. Alizadeh AA, et al. (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769):503–511

    Article  PubMed  CAS  Google Scholar 

  27. Boldrick JC, et al. (2002) Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A 99(2):972–977

    Article  PubMed  CAS  Google Scholar 

  28. Iyer VR, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409(6819):533–538

    Article  PubMed  CAS  Google Scholar 

  29. Ren B, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290(5500):2306–2309

    Article  PubMed  CAS  Google Scholar 

  30. Lieb JD, et al. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28(4):327–334

    Article  PubMed  CAS  Google Scholar 

  31. Horak CE, et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev 16(23):3017–3033

    Article  PubMed  CAS  Google Scholar 

  32. Lee TI, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594):799–804

    Article  PubMed  CAS  Google Scholar 

  33. Gilad Y, Wiebe V, Przeworski M, Lancet D, Pääbo S (2004) Finishing the euchromatic sequence of the human genome. Nature 431(7011):931–945

    Article  Google Scholar 

  34. Waterston RH, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520–562

    Article  PubMed  CAS  Google Scholar 

  35. Weinmann AS, et al. (2002) Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16(2):235–244

    Article  PubMed  CAS  Google Scholar 

  36. Ren B, et al. (2002) E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev 16(2):245–256

    Article  PubMed  CAS  Google Scholar 

  37. Odom DT, et al. (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303(5662):1378–1381

    Article  PubMed  CAS  Google Scholar 

  38. Horak CE, et al. (2002) GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A 99(5):2924–2929

    Article  PubMed  CAS  Google Scholar 

  39. Martone R, et al. (2003) Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A 100(21):12247–12252

    Article  PubMed  CAS  Google Scholar 

  40. Carroll JS, et al. (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122(1):33–43

    Article  PubMed  CAS  Google Scholar 

  41. Massie CE, et al. (2007) New androgen receptor genomic targets show an interaction with the ETS1 transcription factor. EMBO Rep 8(9):871–878

    Article  PubMed  CAS  Google Scholar 

  42. Bernstein BE, et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120(2):169–181

    Article  PubMed  CAS  Google Scholar 

  43. Vera JC, et al. (2008) Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol 17(7):1636–1647

    Article  PubMed  CAS  Google Scholar 

  44. Schuster SC (2008) Next-generation sequencing transforms today’s biology. Nat Methods 5(1):16–18

    Article  PubMed  CAS  Google Scholar 

  45. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74(12):5463–5467

    Article  PubMed  CAS  Google Scholar 

  46. Gibbs RA, et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428(6982):493–521

    Article  PubMed  CAS  Google Scholar 

  47. Gibbs RA, et al. (2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science 316(5822):222–234

    Article  PubMed  CAS  Google Scholar 

  48. Mikkelsen TS, et al. (2007) Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447(7141):167–177

    Article  PubMed  CAS  Google Scholar 

  49. Shendure J, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741):1728–1732

    Article  PubMed  CAS  Google Scholar 

  50. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26(10):1135–1145

    Article  PubMed  CAS  Google Scholar 

  51. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  PubMed  CAS  Google Scholar 

  52. Schadt EE, et al. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6(5):e107

    Article  PubMed  Google Scholar 

  53. Yang X, et al. (2006) Tissue-specific expression and regulation of sexually dimorphic genes in mice. Genome Res 16(8):995–1004

    Article  PubMed  CAS  Google Scholar 

  54. Kasowski M, et al. (2010) Variation in transcription factor binding among humans. Science 328(5975):232–235

    Article  PubMed  CAS  Google Scholar 

  55. McDaniell R, et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328(5975):235–239

    Article  PubMed  CAS  Google Scholar 

  56. Odom DT, et al. (2007) Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39(6):730–732

    Article  PubMed  CAS  Google Scholar 

  57. Schmidt D, et al. (2010) Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328(5981):1036–1040

    Article  PubMed  CAS  Google Scholar 

  58. Bourque G (2009) Transposable elements in gene regulation and in the evolution of vertebrate genomes. Curr Opin Genet Dev 19(6):607–612

    Article  PubMed  CAS  Google Scholar 

  59. Kunarso G, et al. (2010) Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet 42(7):631–634

    Article  PubMed  CAS  Google Scholar 

  60. Birney E, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816

    Article  PubMed  CAS  Google Scholar 

  61. Wilson MD, et al. (2008) Species-specific transcription in mice carrying human chromosome 21. Science 322(5900):434–438

    Article  PubMed  CAS  Google Scholar 

  62. Brockes JP, Kumar A (2005) Appendage regeneration in adult vertebrates and implications for regenerative medicine. Science 310(5756):1919–1923

    Article  PubMed  CAS  Google Scholar 

  63. MacArthur S, et al. (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10(7):R80

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Cancer Research UK, Li Ka Shing Centre, University of Cambridge, Cambridge, UK

    Duncan T. Odom

Authors
  1. Duncan T. Odom
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Duncan T. Odom .

Editor information

Editors and Affiliations

  1. , Centre for Cellular and Biomolecular Res, University of Toronto, College St. 160, Toronto, M5S 3E1, Canada

    Timothy R. Hughes

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Odom, D.T. (2011). Identification of Transcription Factor–DNA Interactions In Vivo. In: Hughes, T. (eds) A Handbook of Transcription Factors. Subcellular Biochemistry, vol 52. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9069-0_8

Download citation

Publish with us

Policies and ethics

Search

Navigation