Relevant bibliographies by topics / DNase I Footprinting

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Academic literature on the topic 'DNase I Footprinting'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "DNase I Footprinting"

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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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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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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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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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Dissertations / Theses on the topic "DNase I Footprinting"

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Keppler, Melanie Dawn. "Strategies for increasing the stability of triple helical DNA." Thesis, University of Southampton, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302353.

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Pilonieta, Maria Carolina. "Transcriptional Regulation of Virulence Genes in Enterotoxigenic Escherichia coli and Shigella flexneri by Members of the AraC/XylS Family." Scholarly Repository, 2008. http://scholarlyrepository.miami.edu/oa_dissertations/111.

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Pathogenesis of enterotoxigenic Escherichia coli (ETEC) and Shigella flexneri relies predominantly on members of the AraC/XylS family of transcriptional regulators, Rns (or its homolog, CfaD) and MxiE, respectively. Rns/CfaD regulate the expression of pili, which allow the bacteria to attach to the intestinal epithelium. Better understanding of the role Rns plays in virulence was attained by expanding our knowledge of the Rns regulon, revealing that it functions as an activator of cexE, a previously uncharacterized gene. By in vitro DNase I footprinting two Rns-binding sites were identified upstream of cexEp, both of which are required for full activation of cexE. The amino terminus of CexE also contains a secretory signal peptide that is removed during translocation to the periplasm. Though the function of CexE remains unknown, these studies suggest that CexE is a novel ETEC virulence factor since it is regulated by Rns/CfaD. In Shigella flexneri, the expression of a subset of virulence genes (including, ipaH9.8 and ospE2) is dependent upon the activator MxiE and a cytoplasmic chaperone IpgC. To define the molecular mechanism of transcriptional activation by this chaperone-activator pair, an in vitro pull down assay was performed revealing that MxiE specifically interacts with IpgC in a complex. Additionally, IpgC recognizes three polypeptide regions in MxiE: within MxiE(1-46), MxiE(46-110) and MxiE(196-216). Furthermore, it seems that MxiE and IpgC regulate transcription of ipaH9.8 and ospE2 promoters differently. In the bacterium, the formation of the MxiE-IpgC complex is initially prevented because IpgC is sequestered in individual complexes with effector proteins, IpaB and IpaC. Upon contact with an eukaryotic host cell the effector proteins are secreted, thereby freeing IpgC to form a complex with MxiE and activate the expression of virulence genes. This new characterization of the role of Rns and MxiE in virulence gene regulation in ETEC and S. flexneri, respectively will give new insights into the pathogenesis of the regulators.
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Yardimci, Galip Gurkan. "Tracking Transcription Factors on the Genome by their DNase-seq Footprints." Diss., 2014. http://hdl.handle.net/10161/9084.

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Transcription factors control numerous vital processes in the cell through their ability to control gene expression. Dysfunctional regulation by transcription factors lead to disorders and disease. Transcription factors regulate gene expression by binding to DNA sequences (motifs) on the genome and altering chromatin. DNase-seq footprinting is a well-established assay for identification of DNA sequences that bind to transcription factors. We developed computational techniques to analyze footprints and predict transcription factor binding. These transcription factor specific predictive models are able to correct for DNase sequence bias and characterize variation in DNA binding sequence. We found that DNase-seq footprints are able to identify cell-type or condition specific transcription factor activity and may offer information about the type of the interaction between DNA and transcription factor. Our DNase-seq footprint model is able to accurately discover high confidence transcription factor binding sites and discover alternative interactions between transcription factors and DNA. DNase-seq footprints can be used with ChIP-seq data to discover true binding sites and better understand transcription regulation.


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Boyle, Alan P. "Studies on Human Chromatin Using High-Throughput DNaseI Sequencing." Diss., 2009. http://hdl.handle.net/10161/1634.

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Cis-elements govern the key step of transcription to regulate gene expression within a cell. Identification of utilized elements within a particular cell line will help further our understanding of individual and cumulative effects of trans-acting factors. These elements can be identified through an assay leveraging the ability of DNaseI to cut DNA that is in an open and accessible state making it hypersensitive to cleavage. Here we develop and explore computational techniques to measure open chromatin from sequencing and microarray data. We are able to identify 94,925 DNaseI hypersensitive sites genome-wide in CD4+ T cells. Interestingly, only 16%-20% of these sites were found in promoters. We also show that these regions are associated with different chromatin modifications. We found that DNaseI data can also be used to identify precise 'footprints' indicating protein-DNA interaction sites. Footprints for specific transcription factors correlate well with ChIP-seq enrichment, reveal distinct conservation patters, and reveal a cell-type specific arrangement of transcriptional regulation. These footprints can be used in addition to or in lieu of ChIP-seq data to better understand genomic regulatory systems.


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Smith, Amy Rhoden. "Advances in DNA binding by threading polyintercalation." Thesis, 2013. http://hdl.handle.net/2152/28690.

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Chemistry
Although molecules that bind DNA have the potential to modify gene expression, the reality of targeting DNA in a sequence-specific manner is still a problematic but worthwhile goal. The Iverson lab has been exploring DNA recognition through a motif known as threading polyintercalation based on connecting intercalating naphthalene diimide (NDI) units, which are molecules that insert themselves between DNA base pairs, together with peptide linkers. These polyintercalators interact with both DNA grooves by “threading” or winding through the DNA, like a snake might climb a ladder. Initially, two different bisintercalator modules with altered sequence specificities and different groove binding topologies were discovered and used to inspire the design of a hybrid NDI tetraintercalator. Surprisingly enough, this tetraintercalator bound sequence-specifically with a dissociation half-life of 16 days to its preferred 14 bp site, a record at the time it was reported for a synthetic DNA-binding molecule. The work reported here expands on the capabilities of this modular threading polyintercalation motif. Chapter 2 describes the ability of a new hybrid NDI tetraintercalator, where the bisintercalator modules are connected together in a different way compared to the previously studied tetraintercalator, to subtly discriminate between similar binding sites. Chapter 3 offers a structural understanding, through NMR analysis, for the sequence recognition abilities of this new tetraintercalator. Chapter 4 analyzes the binding abilities of an un-optimized NDI octaintercalator and proposes how to approach the second-generation design of longer polyintercalators. Chapter 5 describes the optimization of the originally designed NDI tetraintercalator by serially lengthening one of the linkers to produce a tetraintercalator with a 57 day dissociation half-life from its 14 bp sequence, a new record for a synthetic DNA-binding molecule. Using the optimized linker in the context of an NDI hexaintercalator allows for binding to a 22 bp designed site, a record for a synthetic non-nucleic acid molecule. Chapter 6 recounts a focused library screening to search for bisintercalators with new sequence specificities. These efforts have laid the groundwork to progress toward studies aimed at understanding how these molecules might function to prevent transcription in a sequence-dependent manner in vivo.
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Ademi, Irsa. "The Nickel-responsive Binding and Regulation of Two Novel Helicobacter pylori NikR–targeted Genes." Thesis, 2013. http://hdl.handle.net/1807/35577.

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Nickel is an essential transition metal for the virulence and survival of Helicobacter pylori in the acidic human stomach. The nickel– and proton– dependent transcriptional regulator HpNikR is important for maintaining nickel homeostasis inside the cytosol by regulating multiple H. pylori genes. A previous ChIP-sequencing experiment with H. pylori G27 and HpNikR identified two novel genes currently annotated as putative iron-transporters, HpG27_866 and HpG27_1499. In vitro DNA-binding assays with the promoter sequences of the two genes revealed nickel-dependent HpNikR binding with an affinity of ~10-7 M. The recognition site of HpNikR was identified on HpG27_1499 by footprinting assays, which loosely correlates with the HpNikR pseudo-consensus sequence. Furthermore, HpG27_1499 transcription showed nickel-dependent repression in WT H. pylori, and no changes in an isogenic ΔnikR strain. These data suggest that HpG27_1499 could be a nickel importer that is regulated by HpNikR in a nickel-responsive manner.
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Book chapters on the topic "DNase I Footprinting"

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Cardew, Antonia S., and Keith R. Fox. "DNase I Footprinting." In Methods in Molecular Biology, 153–72. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-418-0_10.

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Leblanc, Benoît, and Tom Moss. "DNase I Footprinting." In Methods in Molecular Biology™, 37–47. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-015-1_3.

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Leblanc, Benoît P., and Tom Moss. "In Vitro DNase I Footprinting." In Methods in Molecular Biology, 17–27. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2877-4_2.

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Martino-Catt, Susan J., and Steve A. Kay. "Optimization of DNase I footprinting experiments." In Plant Molecular Biology Manual, 445–57. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0511-8_29.

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Hancock, Matthew, and Elizabeth A. Shephard. "Detection of Regulatory Polymorphisms: High-Throughput Capillary DNase I Footprinting." In Methods in Molecular Biology, 269–82. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-321-3_23.

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Dynan, William S. "DNase I Footprinting as an Assay for Mammalian Gene Regulatory Proteins." In Genetic Engineering, 75–87. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5377-5_5.

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Moyano, Tomás C., Rodrigo A. Gutiérrez, and José M. Alvarez. "Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks." In Modeling Transcriptional Regulation, 25–46. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1534-8_3.

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Baraquet, Claudine, and Caroline S. Harwood. "Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-Binding Proteins." In c-di-GMP Signaling, 303–15. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7240-1_24.

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Krummel, Barbara. "DNase I FOOTPRINTING." In PCR Protocols, 184–88. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-372180-8.50027-5.

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"DNase I Footprinting." In Techniques for Molecular Biology, 127–28. CRC Press, 2006. http://dx.doi.org/10.1201/9781482294460-41.

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