Journal articles: 'DNase I Footprinting'

1

Carey, M. F., C. L. Peterson, and S. T. Smale. "DNase I Footprinting." Cold Spring Harbor Protocols 2013, no. 5 (May 1, 2013): pdb.prot074328. http://dx.doi.org/10.1101/pdb.prot074328.

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Ward, Brian, and James C. Dabrowiak. "Stability of DNase I in footprinting experiments." Nucleic Acids Research 16, no. 17 (1988): 8724. http://dx.doi.org/10.1093/nar/16.17.8724.

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3

Wilson, Douglas O., Peter Johnson, and Bruce R. McCord. "Nonradiochemical DNase I footprinting by capillary electrophoresis." ELECTROPHORESIS 22, no. 10 (June 2001): 1979–86. http://dx.doi.org/10.1002/1522-2683(200106)22:10<1979::aid-elps1979>3.0.co;2-a.

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Smith, Susan E., and Athanasios G. Papavassiliou. "A coupled Southwestern - DNase I footprinting assay." Nucleic Acids Research 20, no. 19 (1992): 5239–40. http://dx.doi.org/10.1093/nar/20.19.5239.

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Nagawa, Fumikiyo, Kei-ichiro Ishiguro, Akio Tsuboi, Tomoyuki Yoshida, Akiko Ishikawa, Toshitada Takemori, Anthony J. Otsuka, and Hitoshi Sakano. "Footprint Analysis of the RAG Protein Recombination Signal Sequence Complex for V(D)J Type Recombination." Molecular and Cellular Biology 18, no. 1 (January 1, 1998): 655–63. http://dx.doi.org/10.1128/mcb.18.1.655.

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ABSTRACT We have studied the interaction between recombination signal sequences (RSSs) and protein products of the truncated forms of recombination-activating genes (RAG) by gel mobility shift, DNase I footprinting, and methylation interference assays. Methylation interference with dimethyl sulfate demonstrated that binding was blocked by methylation in the nonamer at the second-position G residue in the bottom strand and at the sixth- and seventh-position A residues in the top strand. DNase I footprinting experiments demonstrated that RAG1 alone, or even a RAG1 homeodomain peptide, gave footprint patterns very similar to those obtained with the RAG1-RAG2 complex. In the heptamer, partial methylation interference was observed at the sixth-position A residue in the bottom strand. In DNase I footprinting, the heptamer region was weakly protected in the bottom strand by RAG1. The effects of RSS mutations on RAG binding were evaluated by DNA footprinting. Comparison of the RAG-RSS footprint data with the published Hin model confirmed the notion that sequence-specific RSS-RAG interaction takes place primarily between the Hin domain of the RAG1 protein and adjacent major and minor grooves of the nonamer DNA.

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Wilson, D. O., P. Johnson, and B. R. McCord. "Non-radiochemical DNase I footprinting by capillary electrophoresis." Biochemical Society Transactions 28, no. 5 (October 1, 2000): A366. http://dx.doi.org/10.1042/bst028a366a.

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7

Sandaltzopoulos, Raphael, and Peter B. Becker. "Solid phase DNase I footprinting: quick and versatile." Nucleic Acids Research 22, no. 8 (1994): 1511–12. http://dx.doi.org/10.1093/nar/22.8.1511.

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8

Nightingale, K. P., and K. R. Fox. "Interaction of bleomycin with a bent DNA fragment." Biochemical Journal 284, no. 3 (June 15, 1992): 929–34. http://dx.doi.org/10.1042/bj2840929.

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The interaction of bleomycin with a kinetoplast DNA fragment has been examined using various footprinting techniques. This DNA adopts a bent structure and displays an unusually low gel mobility on account of its phased runs of adenines. The bleomycin-cobalt complex increases the mobility of this DNA fragment, in contrast with other DNAs which show a decreased rate of gel migration, suggesting that the antibiotic removes DNA bending, possibly via an unwinding mechanism. Removal of the bending is confirmed by hydroxy-radical footprinting which produces a more even ladder of bands in the presence of the ligand. Cleavage by bleomycin is at the sequence G-pyrimidine, though not all such sites are affected to the same extent and some cutting is found at GA and GG. DNase I footprinting confirms the antibiotic-binding sites but reveals that some strong cleavage sites do not yield footprints. Bleomycin renders adenines on the 3′ side of its cleavage sites (GT, GC and GA) hyper-reactive to diethyl pyrocarbonate.

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ANGERS, Martin, Régen DROUIN, Magdalena BACHVAROVA, Isabelle PARADIS, Brad BISSELL, Makoto HIROMURA, Anny USHEVA, and Dimcho BACHVAROV. "In vivo DNase I-mediated footprinting analysis along the human bradykinin B1 receptor (BDKRB1) gene promoter: evidence for cell-specific regulation." Biochemical Journal 389, no. 1 (June 21, 2005): 37–46. http://dx.doi.org/10.1042/bj20042104.

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By applying in vivo dimethyl sulphate and UV light type C-footprinting analysis, we previously showed that specific DNA sequences in the −1349/+42 core promoter region of the inducible human BDKRB1 (bradykinin B1 receptor) gene correlated with its transcriptional activity. In the present study we used the highly sensitive DNase I in vivo footprinting approach to delineate more precisely the functional domains of the BDKRB1 gene promoter in human SMCs (smooth muscle cells). Human lymphocytes that do not express a functional BDKRB1 were also studied as a reference using dimethyl sulphate, UV light type C and DNase I treatments. An obvious difference was found in the DNase I-footprinting patterns between cellular systems that express a functional BDKRB1 (SMCs) in comparison with human lymphocytes, where randomly distributed nucleosome-like footprinting patterns were found in the bulk of the core promoter region studied. Gel-shift assays and expression studies pointed to the implication of the YY1 and a TBP/TFIIB (TATA-box-binding protein/transcription factor IIB) transcription factor in the regulation of BDKRB1 gene expression in SMCs and possible YY1 involvement in the mechanisms of nuclear factor κB-mediated regulation of the receptor expression. No significant changes in the promoter foot-printing pattern were found after treatment with interleukin-1β or serum (known BDKRB1 gene inducers), indicating that definite regulatory motifs could exist outside the BDKRB1 gene core promoter region studied.

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Goodisman, Jerry, and James C. Dabrowiak. "Structural changes and enhancements in DNase I footprinting experiments." Biochemistry 31, no. 4 (February 1992): 1058–64. http://dx.doi.org/10.1021/bi00119a014.

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11

Gusmao, Eduardo G., Manuel Allhoff, Martin Zenke, and Ivan G. Costa. "Analysis of computational footprinting methods for DNase sequencing experiments." Nature Methods 13, no. 4 (February 22, 2016): 303–9. http://dx.doi.org/10.1038/nmeth.3772.

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12

Staynov, D. Z. "DNase I footprinting of the nucleosome in whole nuclei." Biochemical and Biophysical Research Communications 372, no. 1 (July 2008): 226–29. http://dx.doi.org/10.1016/j.bbrc.2008.05.024.

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13

Frost, Nadine R., Maureen McKeague, Darren Falcioni, and Maria C. DeRosa. "An in solution assay for interrogation of affinity and rational minimer design for small molecule-binding aptamers." Analyst 140, no. 19 (2015): 6643–51. http://dx.doi.org/10.1039/c5an01075f.

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An adaptation of the DNase I footprinting assay allows for the screening of aptamer binding affinity for small molecule targets, and provides structural information for the rational design of minimers.

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Liu, Yongjing, Liangyu Fu, Kerstin Kaufmann, Dijun Chen, and Ming Chen. "A practical guide for DNase-seq data analysis: from data management to common applications." Briefings in Bioinformatics 20, no. 5 (June 4, 2019): 1865–77. http://dx.doi.org/10.1093/bib/bby057.

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Abstract Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.

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Cousins, D. J., D. Richards, D. M. Kemeny, S. Romagnani, T. H. Lee, and D. Z. Staynov. "DNase I footprinting of the human interleukin-5 gene promoter." Immunology 99, no. 1 (January 2000): 101–8. http://dx.doi.org/10.1046/j.1365-2567.2000.00947.x.

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16

Sambrook, Joseph, and David W. Russell. "Mapping Protein-binding Sites on DNA by DNase I Footprinting." Cold Spring Harbor Protocols 2006, no. 1 (June 2006): pdb.prot3947. http://dx.doi.org/10.1101/pdb.prot3947.

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17

Zheng, Ming, Xunde Wang, Bernard Doan, Karen A. Lewis, Thomas D. Schneider, and Gisela Storz. "Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli." Journal of Bacteriology 183, no. 15 (August 1, 2001): 4571–79. http://dx.doi.org/10.1128/jb.183.15.4571-4579.2001.

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ABSTRACT A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted OxyR binding sites upstream ofdsbG, encoding a periplasmic disulfide bond chaperone-isomerase; upstream of fhuF, encoding a protein required for iron uptake; and within yfdI. DNase I footprinting assays confirmed that oxidized OxyR bound to the predicted site centered 54 bp upstream of the dsbG gene and 238 bp upstream of a known OxyR binding site in the promoter region of the divergently transcribed ahpC gene. Although the new binding site was near dsbG, Northern blotting and primer extension assays showed that OxyR binding to thedsbG-proximal site led to the induction of a secondahpCF transcript, while OxyR binding to theahpCF-proximal site leads to the induction of bothdsbG and ahpC transcripts. Oxidized OxyR binding to the predicted site centered 40 bp upstream of thefhuF gene was confirmed by DNase I footprinting, but these assays further revealed a second higher-affinity site in thefhuF promoter. Interestingly, the two OxyR sites in thefhuF promoter overlapped with two regions bound by the Fur repressor. Expression analysis revealed that fhuFwas repressed by hydrogen peroxide in an OxyR-dependent manner. Finally, DNase I footprinting experiments showed OxyR binding to the site predicted to be within the coding sequence of yfdI. These results demonstrate the versatile modes of regulation by OxyR and illustrate the need to learn more about the ensembles of binding sites and transcripts in the E. coli genome.

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18

Mirkovitch, J., T. Decker, and J. E. Darnell. "Interferon induction of gene transcription analyzed by in vivo footprinting." Molecular and Cellular Biology 12, no. 1 (January 1992): 1–9. http://dx.doi.org/10.1128/mcb.12.1.1.

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The promoters of two interferon-induced genes (the ISG54 and guanylate-binding protein [GBP] genes) have been analyzed in whole cells and in isolated nuclei by using a new genomic sequencing technique. The ISG54 gene contains an interferon-simulating response element (ISRE), earlier shown to be necessary and sufficient for alpha interferon (IFN-alpha) induction, that appeared complexed with proteins in both transcribing and nontranscribing cells. However, the extent of protection and hypersensitivity to DNase I or dimethyl sulfate within the ISRE region was changed upon transcriptional induction, suggesting the binding of different factors in different transcriptional states. In addition to the ISRE, the GBP gene needs a newly recognized DNA element, called the GAS, that partly overlaps the ISRE for full induction by either IFN-alpha or IFN-gamma. This GAS element was transiently protected against DNase I in the nuclei of interferon-treated cells but was not protected at later times when transcription reached maximal levels. Thus, the GAS-binding activity may be necessary only transiently for the initial assembly of a transcription initiation complex on the GBP promoter. Dimethyl sulfate methylation of genomic DNA performed on intact cells showed a characteristic sensitivity over the GAS that correlated with transcription levels and that persisted longer than did DNase I protection over the GAS. These results demonstrate the involvement of the GAS in IFN-alpha and -gamma induction of GBP and suggest the presence of an altered DNA conformation or a small protein in the major groove of the GAS associated with ongoing GBP transcription.

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19

Mirkovitch, J., T. Decker, and J. E. Darnell. "Interferon induction of gene transcription analyzed by in vivo footprinting." Molecular and Cellular Biology 12, no. 1 (January 1992): 1–9. http://dx.doi.org/10.1128/mcb.12.1.1-9.1992.

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The promoters of two interferon-induced genes (the ISG54 and guanylate-binding protein [GBP] genes) have been analyzed in whole cells and in isolated nuclei by using a new genomic sequencing technique. The ISG54 gene contains an interferon-simulating response element (ISRE), earlier shown to be necessary and sufficient for alpha interferon (IFN-alpha) induction, that appeared complexed with proteins in both transcribing and nontranscribing cells. However, the extent of protection and hypersensitivity to DNase I or dimethyl sulfate within the ISRE region was changed upon transcriptional induction, suggesting the binding of different factors in different transcriptional states. In addition to the ISRE, the GBP gene needs a newly recognized DNA element, called the GAS, that partly overlaps the ISRE for full induction by either IFN-alpha or IFN-gamma. This GAS element was transiently protected against DNase I in the nuclei of interferon-treated cells but was not protected at later times when transcription reached maximal levels. Thus, the GAS-binding activity may be necessary only transiently for the initial assembly of a transcription initiation complex on the GBP promoter. Dimethyl sulfate methylation of genomic DNA performed on intact cells showed a characteristic sensitivity over the GAS that correlated with transcription levels and that persisted longer than did DNase I protection over the GAS. These results demonstrate the involvement of the GAS in IFN-alpha and -gamma induction of GBP and suggest the presence of an altered DNA conformation or a small protein in the major groove of the GAS associated with ongoing GBP transcription.

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20

BROWN, Philip M., and Keith R. FOX. "DNA triple-helix formation on nucleosome-bound poly(dA)·poly(dT) tracts." Biochemical Journal 333, no. 2 (July 15, 1998): 259–67. http://dx.doi.org/10.1042/bj3330259.

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We have used DNase I and hydroxyl-radical footprinting to examine the formation of intermolecular DNA triple helices on nucleosome-bound DNA fragments containing An·Tn tracts. We found that it is possible to form triplexes on these nucleosome-bound DNAs, but the stability of the complexes depends on the orientation of the A tract with respect to the protein surface. Hydroxyl-radical cleavage of these complexes suggests that the DNA fragments are still associated with the nucleosome. However, the phased cleavage pattern is lost in the vicinity of the triplex, suggesting that the DNA has locally moved away from the protein surface.

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21

Coin, Frédéric, Philippe Frit, Benoit Viollet, Bernard Salles, and Jean-Marc Egly. "TATA Binding Protein Discriminates between Different Lesions on DNA, Resulting in a Transcription Decrease." Molecular and Cellular Biology 18, no. 7 (July 1, 1998): 3907–14. http://dx.doi.org/10.1128/mcb.18.7.3907.

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ABSTRACT DNA damage recognition by basal transcription factors follows different mechanisms. Using transcription-competition, nitrocellulose filter binding, and DNase I footprinting assays, we show that, although the general transcription factor TFIIH is able to target any kind of lesion which can be repaired by the nucleotide excision repair pathway, TATA binding protein (TBP)-TFIID is more selective in damage recognition. Only genotoxic agents which are able to induce kinked DNA structures similar to the one for the TATA box in its TBP complex are recognized. Indeed, DNase I footprinting patterns reveal that TBP protects equally 4 nucleotides upstream and 6 nucleotides downstream from the A-T (at position −29 of the noncoding strand) of the adenovirus major late promoter and from the G-G of a cisplatin-induced 1,2-d(GpG) cross-link. Together, our results may partially explain differences in transcription inhibition rates following DNA damage.

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22

Huibregtse, J. M., and D. R. Engelke. "Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region." Molecular and Cellular Biology 9, no. 8 (August 1989): 3244–52. http://dx.doi.org/10.1128/mcb.9.8.3244.

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We have shown by genomic footprinting that the 5'-flanking region of the Saccharomyces cerevisiae tRNASUP53 gene is protected from DNase I digestion. The protected region has a 5' boundary at -40 (relative to the transcription initiation site) and extends into the coding region of the gene, with a 3' boundary at approximately +15. Although the DNase I protection over this region was much greater than at the A- and B-box internal promoters, point mutations within the A or B box that reduced transcription in vitro eliminated the upstream DNase I protection. This implies that formation of a stable complex over the 5'-flanking region is dependent on interaction of the gene with transcription factor IIIC but that stability of the complex may not require continued interaction with this factor. The DNase I protection under varied growth conditions further suggested that the upstream complex is composed of two or more components. The region over the transcription initiation site (approximately +15 to -10) was less protected in stationary-phase cultures, whereas the more upstream region (approximately -10 to -40) was protected in both exponential- and stationary-phase cultures.

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Huibregtse, J. M., and D. R. Engelke. "Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region." Molecular and Cellular Biology 9, no. 8 (August 1989): 3244–52. http://dx.doi.org/10.1128/mcb.9.8.3244-3252.1989.

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We have shown by genomic footprinting that the 5'-flanking region of the Saccharomyces cerevisiae tRNASUP53 gene is protected from DNase I digestion. The protected region has a 5' boundary at -40 (relative to the transcription initiation site) and extends into the coding region of the gene, with a 3' boundary at approximately +15. Although the DNase I protection over this region was much greater than at the A- and B-box internal promoters, point mutations within the A or B box that reduced transcription in vitro eliminated the upstream DNase I protection. This implies that formation of a stable complex over the 5'-flanking region is dependent on interaction of the gene with transcription factor IIIC but that stability of the complex may not require continued interaction with this factor. The DNase I protection under varied growth conditions further suggested that the upstream complex is composed of two or more components. The region over the transcription initiation site (approximately +15 to -10) was less protected in stationary-phase cultures, whereas the more upstream region (approximately -10 to -40) was protected in both exponential- and stationary-phase cultures.

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24

Kemper, B., P. D. Jackson, and G. Felsenfeld. "Protein-binding sites within the 5' DNase I-hypersensitive region of the chicken alpha D-globin gene." Molecular and Cellular Biology 7, no. 6 (June 1987): 2059–69. http://dx.doi.org/10.1128/mcb.7.6.2059.

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We mapped at high resolution and as a function of development the hypersensitive domain in the 5'-flanking region of the chicken alpha D-globin gene and determined the specific protein-binding sites within the domain. The domain extends from -130 to +80 nucleotides (nt) relative to the cap site. DNase I footprinting within intact embryonic erythrocyte nuclei revealed a strongly protected area from -71 to -52 nt. The same area was weakly protected in adult nuclei. A factor was present in extracts of erythrocyte nuclei from both embryos and adults that protected the sequence AAGATAAGG (-63 to -55 nt) in DNase I footprinting experiments; at higher concentrations of extract, sequences immediately adjacent (-73 to -64 and -53 to -38) were also protected. The same pattern of binding was revealed by gel mobility shift assays. The identical AAGATAAGG sequence is found in the 5'-flanking region of the beta rho gene; it competed for binding of the alpha D-specific factor, suggesting that regulatory elements are shared.

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Kemper, B., P. D. Jackson, and G. Felsenfeld. "Protein-binding sites within the 5' DNase I-hypersensitive region of the chicken alpha D-globin gene." Molecular and Cellular Biology 7, no. 6 (June 1987): 2059–69. http://dx.doi.org/10.1128/mcb.7.6.2059-2069.1987.

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We mapped at high resolution and as a function of development the hypersensitive domain in the 5'-flanking region of the chicken alpha D-globin gene and determined the specific protein-binding sites within the domain. The domain extends from -130 to +80 nucleotides (nt) relative to the cap site. DNase I footprinting within intact embryonic erythrocyte nuclei revealed a strongly protected area from -71 to -52 nt. The same area was weakly protected in adult nuclei. A factor was present in extracts of erythrocyte nuclei from both embryos and adults that protected the sequence AAGATAAGG (-63 to -55 nt) in DNase I footprinting experiments; at higher concentrations of extract, sequences immediately adjacent (-73 to -64 and -53 to -38) were also protected. The same pattern of binding was revealed by gel mobility shift assays. The identical AAGATAAGG sequence is found in the 5'-flanking region of the beta rho gene; it competed for binding of the alpha D-specific factor, suggesting that regulatory elements are shared.

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26

Fox, Keith R., and Michael J. Waring. "Nucleotide sequence binding preferences of nogalamycin investigated by DNase I footprinting." Biochemistry 25, no. 15 (July 1986): 4349–56. http://dx.doi.org/10.1021/bi00363a026.

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27

Ellis, Tom, David A. Evans, Christopher R. H. Martin, and John A. Hartley. "A 96-well DNase I footprinting screen for drug–DNA interactions." Nucleic Acids Research 35, no. 12 (June 2007): e89. http://dx.doi.org/10.1093/nar/gkm467.

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Schwartz, A., and M. Leng. "DNase I footprinting of cis- or trans-Diamminedichloroplatinum(II)-modified DNA." Journal of Molecular Biology 236, no. 4 (March 1994): 969–74. http://dx.doi.org/10.1016/0022-2836(94)90002-7.

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29

Fletcher, M. C., R. K. Olsen, and K. R. Fox. "Dissociation of the AT-specific bifunctional intercalator [N-MeCys3,N-MeCys7]TANDEM from TpA sites in DNA." Biochemical Journal 306, no. 1 (February 15, 1995): 15–19. http://dx.doi.org/10.1042/bj3060015.

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We have examined the dissociation of [N-MeCys3,N-MeCys7]TANDEM, an AT-selective bifunctional intercalator, from TpA sites in mixed-sequence DNAs by a modification of the footprinting technique. Dissociation of complexes between the ligand and radiolabelled DNA fragments was initiated by adding a vast excess of unlabelled calf thymus DNA. Portions of this mixture were subjected to DNAse I footprinting at various times after adding the competitor DNA. Dissociation of the ligand from each site was seen by the time-dependent disappearance of the footprinting pattern. Within a natural DNA fragment (tyrT) the ligand dissociates from TTAT faster than from ATAT. We found that the stability of complexes with isolated TpA steps decreases in the order ATAT > TTAA > TATA. Dissociation from each of these sites is much faster than from longer regions of (AT)n. These results confirm the requirement for A and T base-pairs surrounding the TpA step and suggest that the interaction is strongest with regions of alternating AT, possibly as a result of its unusual structure. The ligand dissociates more slowly from the centre of (AT)n tracts than from the edges, suggesting that variations in dissociation rate arise from sequence-dependent variations in local DNA structure.

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Slieman, Tony A., Roberto Rebeil, and Wayne L. Nicholson. "Spore Photoproduct (SP) Lyase from Bacillus subtilisSpecifically Binds to and Cleaves SP (5-Thyminyl-5,6-Dihydrothymine) but Not Cyclobutane Pyrimidine Dimers in UV-Irradiated DNA." Journal of Bacteriology 182, no. 22 (2000): 6412–17. http://dx.doi.org/10.1128/jb.182.22.6412-6417.2000.

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The predominant photolesion in the DNA of UV-irradiated dormant bacterial spores is the thymine dimer 5-thyminyl-5,6-dihydrothymine, commonly referred to as spore photoproduct (SP). A major determinant of SP repair during spore germination is its direct reversal by the enzyme SP lyase, encoded by the splB gene in Bacillus subtilis. SplB protein containing an N-terminal tag of six histidine residues [(6His)SplB] was purified from dormant B. subtilis spores and shown to efficiently cleave SP but not cyclobutane cis,syn thymine-thymine dimers in vitro. In contrast, SplB protein containing an N-terminal 10-histidine tag [(10His)SplB] purified from an Escherichia colioverexpression system was incompetent to cleave SP unless the 10-His tag was first removed by proteolysis at an engineered factor Xa site. To assay the parameters of binding of SplB protein to UV-damaged DNA, a 35-bp double-stranded oligonucleotide was constructed which carried a single pair of adjacent thymines on one strand. Irradiation of the oligonucleotide in aqueous solution or at 10% relative humidity resulted in formation of cyclobutane pyrimidine dimers (Py◊Py) or SP, respectively. (10His)SplB was assayed for oligonucleotide binding using a DNase I protection assay. In the presence of (10His)SplB, the SP-containing oligonucleotide was selectively protected from DNase I digestion (half-life, >60 min), while the Py◊Py-containing oligonucleotide and the unirradiated oligonucleotide were rapidly digested by DNase I (half-lives, 6 and 9 min, respectively). DNase I footprinting of (10His)SplB bound to the artificial substrate was carried out utilizing the 32P end-labeled 35-bp oligonucleotide containing SP. DNase I footprinting showed that SplB protected at least a 9-bp region surrounding SP from digestion with DNase I with the exception of two DNase I-hypersensitive sites within the protected region. (10His)SplB also caused significant enhancement of DNase I digestion of the SP-containing oligonucleotide for at least a full helical turn 3′ to the protected region. The data suggest that binding of SP lyase to SP causes significant bending or distortion of the DNA helix in the vicinity of the lesion.

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Kim, S. W., I. M. Ahn, and P. R. Larsen. "In vivo genomic footprinting of thyroid hormone-responsive genes in pituitary tumor cell lines." Molecular and Cellular Biology 16, no. 8 (August 1996): 4465–77. http://dx.doi.org/10.1128/mcb.16.8.4465.

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We studied the effects of thyroid hormone (T3) on nuclear protein-DNA interactions by using dimethyl sulfate (DMS) and DNase I ligation-mediated PCR footprinting. We examined an endogenous gene the growth hormone (GH) gene, and a stably transfected plasmid containing the chicken lysozyme silencer (F2) T3 response element (TRE) gene, F2-TRE-TK-CAT, both in pituitary tumor (GC) cells. The 235-1 cell line, which expresses prolactin (PRL) and Pit-1, but not the T3 receptor (TR) or GH, was used as a control. DMS and DNase I footprinting identified protected G residues in the Pit-1, Sp1, and Zn-15 binding sites of the GH gene in GC, but not in 235-1, cells. There was no specific protection of the tripartite GH TRE at -180 bp against either DMS or DNase I in the absence or presence of T3 in either cell line. However, T3 increased protection of the Pit-1 and Sp1 binding sites against DMS in GC cells. In GC cells stably transfected with a plasmid containing F2-TRE-TK-CAT or TRalpha, chloramphenicol acetyltransferase expression was T3 inducible and DMS footprinting revealed both F2 TRE TR-binding half sites in a pattern suggesting the binding of TR homodimers before and during T3 exposure. We conclude that the GH gene is accessible to specific nuclear proteins in GC, but not in 235-1, cells and that T3 enhances this interaction, although there is no evidence of TR binding to the low-affinity rat GH TRE. The presence of TR binding to the high-affinity F2 TRE before and during T3 exposure suggests that reversible interaction of T3 with DNA-bound TRs, rather than transient T3-TR contact with TREs, determines the level of T3-stimulated transcriptional activation.

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32

Correa, Nidia E., and Karl E. Klose. "Characterization of Enhancer Binding by the Vibrio cholerae Flagellar Regulatory Protein FlrC." Journal of Bacteriology 187, no. 9 (May 1, 2005): 3158–70. http://dx.doi.org/10.1128/jb.187.9.3158-3170.2005.

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ABSTRACT The human pathogen Vibrio cholerae is a highly motile organism by virtue of a polar flagellum, and motility has been inferred to be an important aspect of virulence. It has previously been demonstrated that the σ54-dependent activator FlrC is necessary for both flagellar synthesis and for enhanced intestinal colonization. In order to characterize FlrC binding, we analyzed two FlrC-dependent promoters, the highly transcribed flaA promoter and the weakly transcribed flgK promoter, utilizing transcriptional lacZ fusions, mobility shift assays, and DNase I footprinting. Promoter fusion studies showed that the smallest fragment with wild-type transcriptional activity for flaAp was from positions −54 to +137 with respect to the start site, and from −63 to +144 for flgKp. Gel mobility shift assays indicated that FlrC binds to a fragment containing the region from positions +24 to +95 in the flaAp, and DNase I footprinting identified a protected region between positions +24 and +85. Mobility shift and DNase I footprinting indicated weak binding of FlrC to a region downstream of the flgKp transcription start site. These results demonstrate a relatively novel σ54-dependent promoter architecture, with the activator FlrC binding downstream of the σ54-dependent transcription start sites. When the FlrC binding site(s) in the flaA promoter was moved a large distance (285 bp) upstream of the transcription start site of either flaAp or flgKp, high levels of FlrC-dependent transcription resulted, indicating that this binding region functions as an enhancer element. In contrast, the relatively weak FlrC binding site(s) in the flgK promoter failed to function as an enhancer element at either promoter, suggesting that FlrC binding strength contributes to enhancer activity. Our results suggest that the differences in FlrC binding to various flagellar promoters results in the differences in transcription levels that mirror the relative requirement for the flagellar components within the flagellum.

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Sullivan, Alessandra M., Kerry L. Bubb, Richard Sandstrom, John A. Stamatoyannopoulos, and Christine Queitsch. "DNase I hypersensitivity mapping, genomic footprinting, and transcription factor networks in plants." Current Plant Biology 3-4 (September 2015): 40–47. http://dx.doi.org/10.1016/j.cpb.2015.10.001.

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Chugani, Sudha A., Matthew R. Parsek, and A. M. Chakrabarty. "Transcriptional Repression Mediated by LysR-Type Regulator CatR Bound at Multiple Binding Sites." Journal of Bacteriology 180, no. 9 (May 1, 1998): 2367–72. http://dx.doi.org/10.1128/jb.180.9.2367-2372.1998.

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ABSTRACT The catBCA operon of Pseudomonas putidaencodes enzymes involved in the catabolism of benzoate. Transcription of this operon requires the LysR-type transcriptional regulator CatR and an inducer molecule, cis,cis-muconate. Previous gel shift assays and DNase I footprinting have demonstrated that CatR occupies two adjacent sites proximal to thecatBCA promoter in the presence of the inducer. We report the presence of an additional binding site for CatR downstream of thecatBCA promoter within the catB structural gene. This site, called the internal binding site (IBS), extends from +162 to +193 with respect to the catB transcriptional start site and lies within the catB open reading frame. Gel shift analysis and DNase I footprinting determined that CatR binds to this site with low affinity. CatR binds cooperatively with higher affinity to the IBS in the presence of the two upstream binding sites. Parallel in vivo and in vitro studies were conducted to determine the role of the internal binding site. We measured β-galactosidase activity ofcatB-lacZ transcriptional fusions in vivo. Our results suggest a probable cis-acting repressor function for the internal binding site. Site-directed mutagenesis of the IBS verified this finding. The location of the IBS within the catBstructural gene, the cooperativity observed in footprinting studies, and phasing studies suggest that the IBS likely participates in the interaction of CatR with the upstream binding sites by looping out the intervening DNA.

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Washbrook, E., and K. R. Fox. "Alternate-strand DNA triple-helix formation using short acridine-linked oligonucleotides." Biochemical Journal 301, no. 2 (July 15, 1994): 569–75. http://dx.doi.org/10.1042/bj3010569.

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We have used DNAse I footprinting to examine the formation of intermolecular DNA triple helices at sequences containing adjacent blocks of purines and pyrimidines. The target sites G6T6.A6C6 and T6G6.C6A6 were cloned into longer DNA fragments and used as substrates for DNAse I footprinting, which examined the binding of the acridine (Acr)-linked oligonucleotides Acr-T5G5 and Acr-G5T5 respectively. These third strands were designed to incorporate both G.GC triplets, with antiparallel Gn strands held together by reverse Hoogsteen base pairs, and T.AT triplets, with the two T-containing strands arranged antiparallel to each other. We find that Acr-T5G5 binds to the target sequence G6T6.-A6C6, in the presence of magnesium at pH 7.0, generating clear DNAse I footprints. In this structure the central guanine is not recognized by the third strand and is accessible to modification by dimethyl sulphate. Under these conditions no footprint was observed with Acr-G5T5 and T6G6.C6A6, though this triplex was evident in the presence of manganese chloride. Manganese also facilitated the binding of Acr-T5G5 to a second site in the fragment containing the sequence T6G6.C6A6. This represents interaction with the sequence G4ATCT6, located at the boundary between the synthetic insert and the remainder of the fragment, and suggests that this bivalent metal ion may stabilize triplexes that contain one or two mismatches. Manganese did not affect the interaction of either oligonucleotide with G6T6.A6C6.

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Peterson, C. L., and K. L. Calame. "Complex protein binding within the mouse immunoglobulin heavy-chain enhancer." Molecular and Cellular Biology 7, no. 12 (December 1987): 4194–203. http://dx.doi.org/10.1128/mcb.7.12.4194.

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We have begun to purify and characterize several proteins which bind to the mouse immunoglobulin heavy-chain enhancer to understand the molecular interactions important for enhancer activity. Three proteins which bind to different sites on the immunoglobulin heavy-chain enhancer have been chromatographically separated and partially purified. One protein binds a site which has not been reported previously and does not bind to other reported protein-binding sites on the immunoglobulin heavy-chain enhancer. Binding-site boundaries for the three partially purified proteins have been precisely mapped by methylation interference, DNase I footprinting, and orthophenanthroline/copper chemical nuclease footprinting. We have also characterized these three proteins with respect to dissociation rate constants.

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Peterson, C. L., and K. L. Calame. "Complex protein binding within the mouse immunoglobulin heavy-chain enhancer." Molecular and Cellular Biology 7, no. 12 (December 1987): 4194–203. http://dx.doi.org/10.1128/mcb.7.12.4194-4203.1987.

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We have begun to purify and characterize several proteins which bind to the mouse immunoglobulin heavy-chain enhancer to understand the molecular interactions important for enhancer activity. Three proteins which bind to different sites on the immunoglobulin heavy-chain enhancer have been chromatographically separated and partially purified. One protein binds a site which has not been reported previously and does not bind to other reported protein-binding sites on the immunoglobulin heavy-chain enhancer. Binding-site boundaries for the three partially purified proteins have been precisely mapped by methylation interference, DNase I footprinting, and orthophenanthroline/copper chemical nuclease footprinting. We have also characterized these three proteins with respect to dissociation rate constants.

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Galasinski, Shelly K., Tricia N. Lively, Alexandra Grebe de Barron, and James A. Goodrich. "Acetyl Coenzyme A Stimulates RNA Polymerase II Transcription and Promoter Binding by Transcription Factor IID in the Absence of Histones." Molecular and Cellular Biology 20, no. 6 (March 15, 2000): 1923–30. http://dx.doi.org/10.1128/mcb.20.6.1923-1930.2000.

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ABSTRACT Protein acetylation has emerged as a means of controlling levels of mRNA synthesis in eukaryotic cells. Here we report that acetyl coenzyme A (acetyl-CoA) stimulates RNA polymerase II transcription in vitro in the absence of histones. The effect of acetyl-CoA on basal and activated transcription was studied in a human RNA polymerase II transcription system reconstituted from recombinant and highly purified transcription factors. Both basal and activated transcription were stimulated by the addition of acetyl-CoA to transcription reaction mixtures. By varying the concentrations of general transcription factors in the reaction mixtures, we found that acetyl-CoA decreased the concentration of TFIID required to observe transcription. Electrophoretic mobility shift assays and DNase I footprinting revealed that acetyl-CoA increased the affinity of the general transcription factor TFIID for promoter DNA in a TBP-associated factor (TAF)-dependent manner. Interestingly, acetyl-CoA also caused a conformational change in the TFIID-TFIIA-promoter complex as assessed by DNase I footprinting. These results show that acetyl-CoA alters the DNA binding activity of TFIID and indicate that this biologically important cofactor functions at multiple levels to control gene expression.

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Wen, Wen, Banghui Liu, Lu Xue, Zhongliang Zhu, Liwen Niu, and Baolin Sun. "Autoregulation and Virulence Control by the Toxin-Antitoxin System SavRS inStaphylococcus aureus." Infection and Immunity 86, no. 5 (February 12, 2018): e00032-18. http://dx.doi.org/10.1128/iai.00032-18.

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ABSTRACTToxin-antitoxin (TA) systems play diverse physiological roles, such as plasmid maintenance, growth control, and persister cell formation, but their involvement in bacterial pathogenicity remains largely unknown. Here, we have identified a novel type II toxin-antitoxin system, SavRS, and revealed the molecular mechanisms of its autoregulation and virulence control inStaphylococcus aureus. Electrophoretic mobility shift assay and isothermal titration calorimetry data indicated that the antitoxin SavR acted as the primary repressor bound to its own promoter, while the toxin SavS formed a complex with SavR to enhance the ability to bind to the operator site. DNase I footprinting assay identified the SavRS-binding site containing a short and long palindrome in the promoter region. Further, mutation and DNase I footprinting assay demonstrated that the two palindromes were crucial for DNA binding and transcriptional repression. More interestingly, genetic deletion of thesavRSsystem led to the increased hemolytic activity and pathogenicity in a mouse subcutaneous abscess model. We further identified two virulence genes,hlaandefb, by real-time quantitative reverse transcription-PCR and demonstrated that SavR and SavRS could directly bind to their promoter regions to repress virulence gene expression.

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Stonehouse, Emily, Gabriela Kovacikova, Ronald K. Taylor, and Karen Skorupski. "Integration Host Factor Positively Regulates Virulence Gene Expression in Vibrio cholerae." Journal of Bacteriology 190, no. 13 (May 2, 2008): 4736–48. http://dx.doi.org/10.1128/jb.00089-08.

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ABSTRACT Virulence gene expression in Vibrio cholerae is dependent upon a complex transcriptional cascade that is influenced by both specific and global regulators in response to environmental stimuli. Here, we report that the global regulator integration host factor (IHF) positively affects virulence gene expression in V. cholerae. Inactivation of ihfA and ihfB, the genes encoding the IHF subunits, decreased the expression levels of the two main virulence factors tcpA and ctx and prevented toxin-coregulated pilus and cholera toxin production. IHF was found to directly bind to and bend the tcpA promoter region at an IHF consensus site centered at position −162 by using gel mobility shift assays and DNase I footprinting experiments. Deletion or mutation of the tcpA IHF consensus site resulted in the loss of IHF binding and additionally disrupted the binding of the repressor H-NS. DNase I footprinting revealed that H-NS protection overlaps with both the IHF and the ToxT binding sites at the tcpA promoter. In addition, disruption of ihfA in an hns or toxT mutant background had no effect on tcpA expression. These results suggest that IHF may function at the tcpA promoter to alleviate H-NS repression.

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41

Peers, B., M. L. Voz, P. Monget, M. Mathy-Hartert, M. Berwaer, A. Belayew, and J. A. Martial. "Regulatory elements controlling pituitary-specific expression of the human prolactin gene." Molecular and Cellular Biology 10, no. 9 (September 1990): 4690–700. http://dx.doi.org/10.1128/mcb.10.9.4690.

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We have performed transfection and DNase I footprinting experiments to investigate pituitary-specific expression of the human prolactin (hPRL) gene. When fused to the chloramphenicol acetyltransferase (CAT) reporter gene, 5,000 base pairs of the 5'-flanking sequences of the hPRL gene were able to drive high cat gene expression in prolactin-expressing GH3B6 cells specifically. Deletion analysis indicated that this pituitary-specific expression was controlled by three main positive regulatory regions. The first was located just upstream from the TATA box between coordinates -40 and -250 (proximal region). We have previously shown that three motifs of this region bind the pituitary-specific Pit-1 factor. The second positive region was located in the vicinity of coordinates -1300 to -1750 (distal region). DNase I footprinting assays revealed that eight DNA motifs of this distal region bound protein Pit-1 and that two other motifs were recognized by ubiquitous factors, one of which seems to belong to the AP-1 (jun) family. The third positive region was located further upstream, between -3500 and -5000 (superdistal region). This region appears to enhance transcription only in the presence of the distal region.

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42

Peers, B., M. L. Voz, P. Monget, M. Mathy-Hartert, M. Berwaer, A. Belayew, and J. A. Martial. "Regulatory elements controlling pituitary-specific expression of the human prolactin gene." Molecular and Cellular Biology 10, no. 9 (September 1990): 4690–700. http://dx.doi.org/10.1128/mcb.10.9.4690-4700.1990.

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We have performed transfection and DNase I footprinting experiments to investigate pituitary-specific expression of the human prolactin (hPRL) gene. When fused to the chloramphenicol acetyltransferase (CAT) reporter gene, 5,000 base pairs of the 5'-flanking sequences of the hPRL gene were able to drive high cat gene expression in prolactin-expressing GH3B6 cells specifically. Deletion analysis indicated that this pituitary-specific expression was controlled by three main positive regulatory regions. The first was located just upstream from the TATA box between coordinates -40 and -250 (proximal region). We have previously shown that three motifs of this region bind the pituitary-specific Pit-1 factor. The second positive region was located in the vicinity of coordinates -1300 to -1750 (distal region). DNase I footprinting assays revealed that eight DNA motifs of this distal region bound protein Pit-1 and that two other motifs were recognized by ubiquitous factors, one of which seems to belong to the AP-1 (jun) family. The third positive region was located further upstream, between -3500 and -5000 (superdistal region). This region appears to enhance transcription only in the presence of the distal region.

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43

Loprasert, Suvit, Wirongrong Whangsuk, James M. Dubbs, Ratiboot Sallabhan, Kumpanart Somsongkul, and Skorn Mongkolsuk. "HpdR Is a Transcriptional Activator of Sinorhizobium meliloti hpdA, Which Encodes a Herbicide-Targeted 4-Hydroxyphenylpyruvate Dioxygenase." Journal of Bacteriology 189, no. 9 (March 2, 2007): 3660–64. http://dx.doi.org/10.1128/jb.01662-06.

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ABSTRACT Sinorhizobium meliloti hpdA, which encodes the herbicide target 4-hydroxyphenylpyruvate dioxygenase, is positively regulated by HpdR. Gel mobility shift and DNase I footprinting analyses revealed that HpdR binds to a region that spans two conserved direct-repeat sequences within the hpdR-hpdA intergenic space. HpdR-dependent hpdA transcription occurs in the presence of 4-hydroxyphenylpyruvate, tyrosine, and phenylalanine, as well as during starvation.

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Cheung, Ambrose L., Koren Nishina, and Adhar C. Manna. "SarA of Staphylococcus aureus Binds to the sarA Promoter To Regulate Gene Expression." Journal of Bacteriology 190, no. 6 (January 4, 2008): 2239–43. http://dx.doi.org/10.1128/jb.01826-07.

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ABSTRACT The 375-bp sarA open reading frame is driven by three promoters, P1, P3, and P2. Using gel shift and DNase I footprinting assays, we found that SarA binds to two 26-bp sequences and one 31-bp sequence within the P1 and P3 promoters, respectively. Together with the results of transcription analyses, our data indicate that SarA binds to its own promoter to down-regulate sarA expression.

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Ogasawara, Hiroshi, Jun Teramoto, Kiyo Hirao, Kaneyoshi Yamamoto, Akira Ishihama, and Ryutaro Utsumi. "Negative Regulation of DNA Repair Gene (ung) Expression by the CpxR/CpxA Two-Component System in Escherichia coli K-12 and Induction of Mutations by Increased Expression of CpxR." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8317–25. http://dx.doi.org/10.1128/jb.186.24.8317-8325.2004.

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ABSTRACT In Escherichia coli K-12 overexpressing CpxR, transcription of the ung gene for uracil-DNA glycosylase was repressed, ultimately leading to the induction of mutation. Gel shift, DNase I footprinting, and in vitro transcription assays all indicated negative regulation of ung transcription by phosphorylated CpxR. Based on the accumulated results, we conclude that ung gene expression is negatively regulated by the two-component system of CpxR/CpxA signal transduction.

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46

Lemaigre, F. P., D. A. Lafontaine, S. J. Courtois, S. M. Durviaux, and G. G. Rousseau. "Sp1 can displace GHF-1 from its distal binding site and stimulate transcription from the growth hormone gene promoter." Molecular and Cellular Biology 10, no. 4 (April 1990): 1811–14. http://dx.doi.org/10.1128/mcb.10.4.1811.

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DNase I footprinting experiments showed that binding activities of Sp1 and of GHF-1 to its distal site on the human growth hormone gene promoter are mutually exclusive. The kinetics of GHF-1 binding were indicative of positive cooperativity. The Sp1 site did not affect promoter activity in cell-free transcription. Still, Sp1 could compensate partially for the decreased stimulation of transcription seen at low GHF-1 concentrations.

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Lemaigre, F. P., D. A. Lafontaine, S. J. Courtois, S. M. Durviaux, and G. G. Rousseau. "Sp1 can displace GHF-1 from its distal binding site and stimulate transcription from the growth hormone gene promoter." Molecular and Cellular Biology 10, no. 4 (April 1990): 1811–14. http://dx.doi.org/10.1128/mcb.10.4.1811-1814.1990.

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DNase I footprinting experiments showed that binding activities of Sp1 and of GHF-1 to its distal site on the human growth hormone gene promoter are mutually exclusive. The kinetics of GHF-1 binding were indicative of positive cooperativity. The Sp1 site did not affect promoter activity in cell-free transcription. Still, Sp1 could compensate partially for the decreased stimulation of transcription seen at low GHF-1 concentrations.

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48

Lee, I. J., L. Tung, D. A. Bumcrot, and E. S. Weinberg. "UHF-1, a factor required for maximal transcription of early and late sea urchin histone H4 genes: analysis of promoter-binding sites." Molecular and Cellular Biology 11, no. 2 (February 1991): 1048–61. http://dx.doi.org/10.1128/mcb.11.2.1048.

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A protein, denoted UHF-1, was found to bind upstream of the transcriptional start site of both the early and late H4 (EH4 and LH4) histone genes of the sea urchin Strongylocentrotus purpuratus. A nuclear extract from hatching blastulae contained proteins that bind to EH4 and LH4 promoter fragments in a band shift assay and produced sharp DNase I footprints upstream of the EH4 gene (from -133 to -106) and the LH4 gene (from -94 to -66). DNase I footprinting performed in the presence of EH4 and LH4 promoter competitor DNAs indicated that UHF-1 binds more strongly to the EH4 site. A sequence match of 11 of 13 nucleotides was found within the two footprinted regions: [sequence: see text]. Methylation interference and footprinting experiments showed that UHF-1 bound to the two sites somewhat differently. DNA-protein UV cross-linking studies indicated that UHF-1 has an electrophoretic mobility on sodium dodecyl sulfate-acrylamide gels of approximately 85 kDa and suggested that additional proteins, specific to each promoter, bind to each site. In vitro and in vivo assays were used to demonstrate that the UHF-1-binding site is essential for maximal transcription of the H4 genes. Deletion of the EH4 footprinted region resulted in a 3-fold decrease in transcription in a nuclear extract and a 2.6-fold decrease in expression in morulae from templates that had been injected into eggs. In the latter case, deletion of the binding site did not grossly disrupt the temporal program of expression from the injected EH4 genes. LH4 templates containing a 10-bp deletion in the consensus region or base substitutions in the footprinted region were transcribed at 14 to 58% of the level of the wild-type LH4 template. UHF-1 is therefore essential for maximal expression of the early and late H4 genes.

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Lee, I. J., L. Tung, D. A. Bumcrot, and E. S. Weinberg. "UHF-1, a factor required for maximal transcription of early and late sea urchin histone H4 genes: analysis of promoter-binding sites." Molecular and Cellular Biology 11, no. 2 (February 1991): 1048–61. http://dx.doi.org/10.1128/mcb.11.2.1048-1061.1991.

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A protein, denoted UHF-1, was found to bind upstream of the transcriptional start site of both the early and late H4 (EH4 and LH4) histone genes of the sea urchin Strongylocentrotus purpuratus. A nuclear extract from hatching blastulae contained proteins that bind to EH4 and LH4 promoter fragments in a band shift assay and produced sharp DNase I footprints upstream of the EH4 gene (from -133 to -106) and the LH4 gene (from -94 to -66). DNase I footprinting performed in the presence of EH4 and LH4 promoter competitor DNAs indicated that UHF-1 binds more strongly to the EH4 site. A sequence match of 11 of 13 nucleotides was found within the two footprinted regions: [sequence: see text]. Methylation interference and footprinting experiments showed that UHF-1 bound to the two sites somewhat differently. DNA-protein UV cross-linking studies indicated that UHF-1 has an electrophoretic mobility on sodium dodecyl sulfate-acrylamide gels of approximately 85 kDa and suggested that additional proteins, specific to each promoter, bind to each site. In vitro and in vivo assays were used to demonstrate that the UHF-1-binding site is essential for maximal transcription of the H4 genes. Deletion of the EH4 footprinted region resulted in a 3-fold decrease in transcription in a nuclear extract and a 2.6-fold decrease in expression in morulae from templates that had been injected into eggs. In the latter case, deletion of the binding site did not grossly disrupt the temporal program of expression from the injected EH4 genes. LH4 templates containing a 10-bp deletion in the consensus region or base substitutions in the footprinted region were transcribed at 14 to 58% of the level of the wild-type LH4 template. UHF-1 is therefore essential for maximal expression of the early and late H4 genes.

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Sivapragasam, Smitha, Anuja Pande, and Anne Grove. "A recommended workflow for DNase I footprinting using a capillary electrophoresis genetic analyzer." Analytical Biochemistry 481 (July 2015): 1–3. http://dx.doi.org/10.1016/j.ab.2015.04.013.

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Journal articles on the topic 'DNase I Footprinting'

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