dna footprinting


Summary: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)

Top Publications

  1. Bell O, Tiwari V, Thoma N, Schübeler D. Determinants and dynamics of genome accessibility. Nat Rev Genet. 2011;12:554-64 pubmed publisher
    ..Here we discuss the interplay of these processes by reviewing our current understanding of how chromatin access contributes to the regulation of transcription, replication and repair. ..
  2. Bowers S, Mirabella F, Calero Nieto F, Valeaux S, Hadjur S, Baxter E, et al. A conserved insulator that recruits CTCF and cohesin exists between the closely related but divergently regulated interleukin-3 and granulocyte-macrophage colony-stimulating factor genes. Mol Cell Biol. 2009;29:1682-93 pubmed publisher
    ..We suggest that one important role of these sites is to enable the independent regulation of the IL-3 and GM-CSF genes. ..
  3. Gao H, Zhou D, Li Y, Guo Z, Han Y, Song Y, et al. The iron-responsive Fur regulon in Yersinia pestis. J Bacteriol. 2008;190:3063-75 pubmed publisher
    ..The data presented here give us an overview of the iron-responsive Fur regulon in Y. pestis. ..
  4. Rusling D, Peng G, Srinivasan N, Fox K, Brown T. DNA triplex formation with 5-dimethylaminopropargyl deoxyuridine. Nucleic Acids Res. 2009;37:1288-96 pubmed publisher
  5. Teramoto J, Yoshimura S, Takeyasu K, Ishihama A. A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions. Nucleic Acids Res. 2010;38:3605-18 pubmed publisher
    ..We then propose that YgiP is a novel nucleoid protein of E. coli under anaerobiosis and propose to rename it Dan (DNA-binding protein under anaerobic conditions). ..
  6. Sun D. In vitro footprinting of promoter regions within supercoiled plasmid DNA. Methods Mol Biol. 2010;613:223-33 pubmed publisher
    ..This is demonstrated with the proximal promoter region of the human vascular endothelial growth factor (VEGF) gene, which also contains multiple binding sites for Sp1 and Egr-1 transcription factors. ..
  7. Sun D, Hurley L. Biochemical techniques for the characterization of G-quadruplex structures: EMSA, DMS footprinting, and DNA polymerase stop assay. Methods Mol Biol. 2010;608:65-79 pubmed publisher
  8. Ishida Y, Kori A, Ishihama A. Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon. J Bacteriol. 2009;191:6136-44 pubmed publisher
    ..Taken together, these data suggest a metabolic link through interplay between the asc and prp operons. ..
  9. Chen Z, Lewis K, Shultzaberger R, Lyakhov I, Zheng M, Doan B, et al. Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res. 2007;35:6762-77 pubmed
    ..The Pseudomonas aeruginosa and Bacillus subtilis Fur models are highly similar to the E. coli Fur model, suggesting that the Fur-DNA recognition mechanism may be conserved for even distantly related bacteria. ..

More Information


  1. Doyle M, Feuerbaum E, Fox K, Hinds J, Thurston D, Taylor P. Response of Staphylococcus aureus to subinhibitory concentrations of a sequence-selective, DNA minor groove cross-linking pyrrolobenzodiazepine dimer. J Antimicrob Chemother. 2009;64:949-59 pubmed publisher
    ..aureus by forming multiple interstrand and intrastrand DNA cross-links, resulting in induction of the DNA damage response, derepression of resident prophages and modulation of a limited number of genes involved with cell wall synthesis. ..
  2. Murray E, Strauch M, Stanley Wall N. SigmaX is involved in controlling Bacillus subtilis biofilm architecture through the AbrB homologue Abh. J Bacteriol. 2009;191:6822-32 pubmed publisher
    ..Furthermore, Abh is shown to activate transcription from the promoter of the eps operon through its control of SlrR. These findings add to the increasingly complex transcriptional network that controls biofilm formation by B. subtilis. ..
  3. Ingram R, Gao C, LeBon J, Liu Q, Mayoral R, Sommer S, et al. PAP-LMPCR for improved, allele-specific footprinting and automated chromatin fine structure analysis. Nucleic Acids Res. 2008;36:e19 pubmed publisher
    ..In addition, we have adapted this technique for automation, thus enabling the simultaneous and rapid analysis of chromatin structure at many different genes. ..
  4. Guo K, Gokhale V, Hurley L, Sun D. Intramolecularly folded G-quadruplex and i-motif structures in the proximal promoter of the vascular endothelial growth factor gene. Nucleic Acids Res. 2008;36:4598-608 pubmed publisher
  5. Peeters E, Albers S, Vassart A, Driessen A, Charlier D. Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes. Mol Microbiol. 2009;71:972-88 pubmed publisher
    ..Based on these results, it appears that not all regulators belonging to the archaeal Lrp family perform a function related to the amino acid metabolism, unlike the bacterial Lrp-like regulators. ..
  6. Nesbit A, Fleischhacker A, Teter S, Kiley P. ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli. J Bacteriol. 2012;194:6892-9 pubmed publisher
    ..In sum, a combination of ArcA and AppY antirepression of IscR function, lower levels of IscR, and weak repression by [2Fe-2S]-IscR leads to increased P(hyaA) expression under anaerobic conditions. ..
  7. Husnain S, Thomas M. Downregulation of the Escherichia coli guaB promoter by FIS. Microbiology. 2008;154:1729-38 pubmed publisher
    ..Binding of FIS to these sites results in repression of P(guaB) in vitro but not in vivo. Deletion of the fis gene results in increased P(guaB) activity in vivo, but GRDC of P(guaB) is maintained. ..
  8. Li Y, Gao H, Qin L, Li B, Han Y, Guo Z, et al. Identification and characterization of PhoP regulon members in Yersinia pestis biovar Microtus. BMC Genomics. 2008;9:143 pubmed publisher
    ..These results help us gain insights into the PhoP-dependent mechanisms by which Y. pestis survives the antibacterial strategies employed by host macrophages. ..
  9. Umezawa Y, Shimada T, Kori A, Yamada K, Ishihama A. The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. J Bacteriol. 2008;190:5890-7 pubmed publisher
    ..This is an addition to the mode of controlling activity of transcription factors by alkylation with chemical agents. ..
  10. Smith L, Stapleton M, Fullstone G, Crack J, Thomson A, Le Brun N, et al. Mycobacterium tuberculosis WhiB1 is an essential DNA-binding protein with a nitric oxide-sensitive iron-sulfur cluster. Biochem J. 2010;432:417-27 pubmed publisher
    ..A model incorporating regulation of whiB1 expression in response to nitric oxide and cAMP is discussed with implications for sensing two important signals in establishing M. tuberculosis infections. ..
  11. Michlewski G, Guil S, Semple C, Caceres J. Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol Cell. 2008;32:383-93 pubmed publisher
    ..Altogether, these data suggest the existence of auxiliary factors for the processing of specific miRNAs, revealing an additional level of complexity for the regulation of miRNA biogenesis. ..
  12. Shimada T, Hirao K, Kori A, Yamamoto K, Ishihama A. RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Mol Microbiol. 2007;66:744-57 pubmed
    ..Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines. ..
  13. Patterson Fortin L, Owttrim G. A Synechocystis LexA-orthologue binds direct repeats in target genes. FEBS Lett. 2008;582:2424-30 pubmed publisher
    ..Characterization of this site provides the basis for identification of additional LexA targets and further evidence for LexA's divergence during evolution. ..
  14. Hesselberth J, Chen X, Zhang Z, Sabo P, Sandstrom R, Reynolds A, et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009;6:283-9 pubmed publisher
    ..Digital genomic footprinting should be a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence. ..
  15. Gilmour D, Fan R. Detecting transcriptionally engaged RNA polymerase in eukaryotic cells with permanganate genomic footprinting. Methods. 2009;48:368-74 pubmed publisher
    ..The method should prove useful in assessing if promoter bound Pol II has engaged in transcription and for investigating the establishment and regulation of transcriptionally engaged Pol II. ..
  16. Tiberghien A, Evans D, Kiakos K, Martin C, Hartley J, Thurston D, et al. An asymmetric C8/C8'-tripyrrole-linked sequence-selective pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimer DNA interstrand cross-linking agent spanning 11 DNA base pairs. Bioorg Med Chem Lett. 2008;18:2073-7 pubmed publisher
  17. Gonzalo Asensio J, Soto C, Arbués A, Sancho J, del Carmen Menéndez M, Garcia M, et al. The Mycobacterium tuberculosis phoPR operon is positively autoregulated in the virulent strain H37Rv. J Bacteriol. 2008;190:7068-78 pubmed publisher
    ..Finally, we discuss the possible role in virulence of a single point mutation found in the phoP gene from the attenuated H37Ra strain but not in virulent members of the M. tuberculosis complex. ..
  18. Hampshire A, Fox K. Preferred binding sites for the bifunctional intercalator TANDEM determined using DNA fragments that contain every symmetrical hexanucleotide sequence. Anal Biochem. 2008;374:298-303 pubmed
    We have prepared novel DNA footprinting substrates that contain all 64 symmetrical hexanucleotide sequences...
  19. Ogasawara H, Yamamoto K, Ishihama A. Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis. J Bacteriol. 2011;193:2587-97 pubmed publisher
    ..Taking these findings together, we propose that the cell motility for planktonic growth is repressed by CsgD, thereby promoting the switch to biofilm formation. ..
  20. Li L, Alvey R, Bezy R, Kehoe D. Inverse transcriptional activities during complementary chromatic adaptation are controlled by the response regulator RcaC binding to red and green light-responsive promoters. Mol Microbiol. 2008;68:286-97 pubmed publisher
    ..These results provide important insights into the long-standing enigma of CCA regulation and complete the first description of an entire two-component system controlled by a phytochrome-class photoreceptor. ..
  21. Sun D, Liu W, Guo K, Rusche J, Ebbinghaus S, Gokhale V, et al. The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex-interactive agents. Mol Cancer Ther. 2008;7:880-9 pubmed publisher
    ..Our results also provide further support for the idea that G-quadruplex structures may play structural roles in vivo and therefore might provide insight into novel methodologies for rational drug design. ..
  22. Furukawa T, Shida Y, Kitagami N, Mori K, Kato M, Kobayashi T, et al. Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei. Fungal Genet Biol. 2009;46:564-74 pubmed publisher
    ..Our results suggest that, together with the inverted repeat motifs, the single 5'-GGC(A/T)(4)-3' motifs play important roles as functional XYR1-binding sites in the regulation of cellulase and xylanase gene expression in T. reesei. ..
  23. Sabogal A, Rio D. A green fluorescent protein solubility screen in E. coli reveals domain boundaries of the GTP-binding domain in the P element transposase. Protein Sci. 2010;19:2210-8 pubmed publisher
    ..This study highlights the use of a GFP-based solubility screen on a large multidomain protein to identify highly expressed, soluble truncated domain subregions. ..
  24. Neph S, Vierstra J, Stergachis A, Reynolds A, Haugen E, Vernot B, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012;489:83-90 pubmed publisher
  25. Vora T, Hottes A, Tavazoie S. Protein occupancy landscape of a bacterial genome. Mol Cell. 2009;35:247-53 pubmed publisher
    ..Our observations implicate these transcriptionally silent EPODs as the elusive organizing centers, long proposed to topologically isolate chromosomal domains...
  26. He X, Li R, Pan Y, Liu G, Tan H. SanG, a transcriptional activator, controls nikkomycin biosynthesis through binding to the sanN-sanO intergenic region in Streptomyces ansochromogenes. Microbiology. 2010;156:828-37 pubmed publisher
    ..These results indicated that the ATPase/GTPase activity of SanG modulated the transcriptional activation of SanG target genes during nikkomycin biosynthesis. ..
  27. Nadai M, Sattin G, Palu G, Palumbo M, Richter S. Clerocidin-mediated DNA footprinting discriminates among different G-quadruplex conformations and detects tetraplex folding in a duplex environment. Biochim Biophys Acta. 2013;1830:4660-8 pubmed publisher
    ..The use of clerocidin as footprinting agent to identify G-quadruplex structures under genomically relevant conditions may allow detection of new G-quadruplex-based regulatory regions. ..
  28. Cogoi S, Paramasivam M, Spolaore B, Xodo L. Structural polymorphism within a regulatory element of the human KRAS promoter: formation of G4-DNA recognized by nuclear proteins. Nucleic Acids Res. 2008;36:3765-80 pubmed publisher
    ..Our study suggests a role of quadruplex DNA in KRAS transcription and provides the basis for the rationale design of molecular strategies to inhibit the expression of KRAS. ..
  29. Qin Y, Rezler E, Gokhale V, Sun D, Hurley L. Characterization of the G-quadruplexes in the duplex nuclease hypersensitive element of the PDGF-A promoter and modulation of PDGF-A promoter activity by TMPyP4. Nucleic Acids Res. 2007;35:7698-713 pubmed
    ..On the basis of these results, we have established that ligand-mediated stabilization of G-quadruplex structures within the PDGF-A NHE can silence PDGF-A expression. ..
  30. Liu G, Yin Y, Kunchakarra S, Mukherjee B, Gerion D, Jett S, et al. A nanoplasmonic molecular ruler for measuring nuclease activity and DNA footprinting. Nat Nanotechnol. 2006;1:47-52 pubmed publisher
  31. Lou C, Xiao Q, Brennan L, Light M, Vergara Irigaray N, Atkinson E, et al. Synthesis and properties of triplex-forming oligonucleotides containing 2'-O-(2-methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine. Bioorg Med Chem. 2010;18:6389-97 pubmed publisher
    ..The TFOs gave very high triplex stability with their target duplexes as measured by ultraviolet/fluorescence melting and DNase I footprinting. The incorporation of MEPU into TFOs renders them resistant to degradation by serum nucleases. ..
  32. Hatoum A, Roberts J. Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Mol Microbiol. 2008;68:17-28 pubmed publisher
    ..In addition to promoter-proximal RNAP trapping, we observed transcription-dependent DNA modifications spanning the tnaA and cspA leader regions up to 100 bp downstream of the transcription start site. ..
  33. Neusser T, Gildehaus N, Wurm R, Wagner R. Studies on the expression of 6S RNA from E. coli: involvement of regulators important for stress and growth adaptation. Biol Chem. 2008;389:285-97 pubmed publisher
    ..Our results underline that regulation of 6S RNA transcription depends on a complex network, involving a set of bacterial regulators with general importance in the adaptation to changing growth conditions. ..
  34. Tramonti A, De Canio M, De Biase D. GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites. Mol Microbiol. 2008;70:965-82 pubmed publisher
    ..The presence of five GadX/GadW-specific binding sites in the AFI suggests that GadX and GadW may act as H-NS counter-silencers. ..
  35. Munde M, Ismail M, Arafa R, Peixoto P, Collar C, Liu Y, et al. Design of DNA minor groove binding diamidines that recognize GC base pair sequences: a dimeric-hinge interaction motif. J Am Chem Soc. 2007;129:13732-43 pubmed
    ..This compound represents a new direction in the development of DNA sequence-specific agents, and it is the first non-polyamide, synthetic compound to specifically recognize a DNA sequence with a majority of GC base pairs. ..
  36. Teytelman L, Ozaydin B, Zill O, Lefrançois P, Snyder M, Rine J, et al. Impact of chromatin structures on DNA processing for genomic analyses. PLoS ONE. 2009;4:e6700 pubmed publisher
    ..These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome. ..
  37. Peeters E, Nguyen Le Minh P, Foulquié Moreno M, Charlier D. Competitive activation of the Escherichia coli argO gene coding for an arginine exporter by the transcriptional regulators Lrp and ArgP. Mol Microbiol. 2009;74:1513-26 pubmed publisher
    ..The repertoire of bacterial transcription regulation mechanisms is vast, but the competitive activation of a single promoter by two activator proteins as described here appears to be rare. ..
  38. Carter J, Friedrich N, Kleinstiver B, Edgell D. Strand-specific contacts and divalent metal ion regulate double-strand break formation by the GIY-YIG homing endonuclease I-BmoI. J Mol Biol. 2007;374:306-21 pubmed
  39. Hampshire A, Rusling D, Bryan S, Paumier D, Dawson S, Malkinson J, et al. DNA binding by analogues of the bifunctional intercalator TANDEM. Biochemistry. 2008;47:7900-6 pubmed publisher
    ..By using fragments with different lengths of [(AT) n ], we demonstrate that these ligands bind best to the center of the longer (AT) n tracts. ..
  40. Pilonieta M, Bodero M, Munson G. CfaD-dependent expression of a novel extracytoplasmic protein from enterotoxigenic Escherichia coli. J Bacteriol. 2007;189:5060-7 pubmed
    ..These studies suggest that CexE may be a novel ETEC virulence factor because its expression is controlled by the virulence regulator CfaD, and its distribution is restricted to ETEC...
  41. Mohd Sarip A, van der Knaap J, Wyman C, Kanaar R, Schedl P, Verrijzer C. Architecture of a polycomb nucleoprotein complex. Mol Cell. 2006;24:91-100 pubmed
    ..Indeed, chromatin immunoprecipitations (ChIPs) and nuclease mapping demonstrated that PREs are nucleosome depleted in vivo. We discuss the implications of these findings for models explaining PRE function. ..
  42. Yamamoto K, Ishihama A. Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli. Biosci Biotechnol Biochem. 2006;70:1688-95 pubmed
    ..The difference in the orientation and location of the CpxR box is discussed with respect to the regulation mechanism among CpxR-regulon genes. ..
  43. Caryl J, Thomas C. Investigating the basis of substrate recognition in the pC221 relaxosome. Mol Microbiol. 2006;60:1302-18 pubmed
    ..Based on these observations we propose a model of layered specificity in the assembly of pC221-family relaxosomes, whereby a common MobC:mcb complex presents the oriT substrate, which is then nicked only by the cognate MobA. ..
  44. Ogasawara H, Ishida Y, Yamada K, Yamamoto K, Ishihama A. PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli. J Bacteriol. 2007;189:5534-41 pubmed
    ..Taken together, we propose that PdhR is a master regulator for controlling the formation of not only the PDH complex but also the respiratory electron transport system. ..
  45. Turner E, Dorman C. H-NS antagonism in Shigella flexneri by VirB, a virulence gene transcription regulator that is closely related to plasmid partition factors. J Bacteriol. 2007;189:3403-13 pubmed
    ..Alterations to one heptameric motif within this DNA sequence attenuated VirB binding and derepression of icsB transcription. ..
  46. Pul U, Wurm R, Wagner R. The role of LRP and H-NS in transcription regulation: involvement of synergism, allostery and macromolecular crowding. J Mol Biol. 2007;366:900-15 pubmed
    ..The formation of this regulatory structure appears to be directly affected by environmental changes. ..
  47. Tagoh H, Cockerill P, Bonifer C. In vivo genomic footprinting using LM-PCR methods. Methods Mol Biol. 2006;325:285-314 pubmed
    ..In this chapter, we describe detailed procedures for the examination of chromatin fine-structure and nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation. ..
  48. Gupta S, Cheng H, Mollah A, Jamison E, Morris S, Chance M, et al. DNA and protein footprinting analysis of the modulation of DNA binding by the N-terminal domain of the Saccharomyces cerevisiae TATA binding protein. Biochemistry. 2007;46:9886-98 pubmed
    ..Taken together, these results are consistent with the N-terminal domain actively modulating TATA box binding by TBP and nonionic detergent modulating the interdomain interaction...
  49. Ward C, Wardle S, Singh R, Haniford D. The global regulator H-NS binds to two distinct classes of sites within the Tn10 transpososome to promote transposition. Mol Microbiol. 2007;64:1000-13 pubmed
    ..The binding of H-NS to a transposase protein is a novel function for this important regulatory molecule. ..
  50. Ogasawara H, Hasegawa A, Kanda E, Miki T, Yamamoto K, Ishihama A. Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade. J Bacteriol. 2007;189:4791-9 pubmed
    ..With these data taken together, we conclude that the expression of both asr and csgD is under the direct control of the PhoQP-RstBA signal relay cascade. ..
  51. Castella S, Bingham G, Sanders C. Common determinants in DNA melting and helicase-catalysed DNA unwinding by papillomavirus replication protein E1. Nucleic Acids Res. 2006;34:3008-19 pubmed
    ..One possible mechanism is that with the DNA locked in the loop/PS1betaH DNA binding site, ATP-dependent conformational changes draw the DNA inwards in a twisting motion to promote unwinding. ..
  52. Cogoi S, Xodo L. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res. 2006;34:2536-49 pubmed
    ..Such a mechanism, which is probably adopted by other growth-related genes, provides useful hints for the rational design of anticancer drugs against the KRAS oncogene. ..
  53. Shcherbakova I, Mitra S, Beer R, Brenowitz M. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res. 2006;34:e48 pubmed