Disease relevance of DNaseII

• This accumulation of DNA in the DNase II mutants caused the constitutive expression of the antibacterial genes for diptericin and attacin, which are usually activated during bacterial infection [1].
• Binding of the GAGA transcription factor on existing nucleosomes leads to nucleosome disruption, DNase I hypersensitivity at the TATA box and heat-shock elements, and rearrangement of adjacent nucleosomes [2].
• The association of integration sites of retroviruses and regions in which DNase I hypersensitive sites exist and the preferential integration of Ty1 at the 5' ends of some genes might suggest that regions which do not have phased nucleosomes are targets for integration [3].
• DNase I footprinting identified two regions of the nucleocapsid promoter, representing three recognition elements, that bound purified Sp1 [4].
• Those mutations are also associated with an elevated frequency of chromosomal aberrations, altered DNA metabolism and the modification of a deoxyribonuclease [5].

High impact information on DNaseII

• We show here that, although in these two cell types the correspondence between DNase I sensitivity and gene transcription holds good for globin and the ribosomal genes, the tRNA and oogenetic 5S genes are DNase I sensitive in both liver and erythrocyte nuclei [6].
• The DNase I sensitivity of Xenopus laevis genes transcribed by RNA polymerase III [6].
• Reconstituted in vitro transcription reactions and deoxyribonuclease I footprinting assays confirmed the ability of TRF1 to bind preferentially and direct transcription of the tudor gene from an alternate promoter [7].
• The expression of these genes was further enhanced in flies lacking both dICAD and DNase II [1].
• In contrast, the deficiency of DNase II enhanced the apoptotic DNA fragmentation in the embryos and ovary, but paradoxically, the mutant flies accumulated a large amount of DNA, particularly in the ovary [1].

Chemical compound and disease context of DNaseII

• Alterations in the pattern of DNase I hypersensitivity were observed on ecdysterone-stimulated transcription of Drosophila melanogaster small heat shock protein genes [8].
• While the patterns of DNase I hypersensitivity are similar in the vicinity of the direct terminal repeats, the patterns revealed by micrococcal nuclease and MPE . Fe(II) are not, indicating a different chromatin organization of these two identical sequences [9].
• Here we present methods for the extraction and quantification of insect RNA and DNA based on the use of N-lauroylsarcosine and sonication for extraction, the nucleases RNase and DNase, and the use of microplate fluorescent assays to quantify nucleic acids as percent of body weight in insects [10].

Biological context of DNaseII

• Interestingly, overexpression of CG7780 both ubiquitously and in specific tissues failed to elicit any discernable phenotype [11].
• Database queries using the C. elegans NUC-1 protein sequence identified a highly homologous open reading frame in Drosophila (CG7780) that could encode a similar enzyme [11].
• Sequence analysis of CG7780 DNA and mRNA revealed that the hypomorphic line contains a missense mutation within the coding region of this gene [11].
• A genetic analysis demonstrated that both the biochemical and cytological phenotypes were the consequences of a single recessive mutation in the DNase-1 gene on chromosome III [12].
• Second, DNase I footprinting and gel retardation assays show that Tc1A binds specifically to the inverted repeats at the ends of the element and that the Tc1A recognition site is located between base pairs 5 and 26 from the ends of Tc1 [13].

Anatomical context of DNaseII

• The constitutive DNase I hypersensitive site at the 5' end of the chicken beta-globin locus marks the boundary of the active chromatin domain in erythroid cells [14].
• Hybridomas secreting monoclonal antibodies have been produced by fusion of NS-1 mouse myeloma cells with the spleen cells of mice inoculated with a 60-65,000-mol wt fraction of proteins released from Drosophila embryo nuclei treated with DNase I [15].
• DmORC displays at best six-fold differences in the relative affinities to DNA from the third chorion locus and to random fragments in vitro, and chemical probing and DNase1 protection experiments did not identify a discrete binding site for DmORC on any of these fragments [16].
• Deletion analysis of the 1.8-kb scs element identified a 220-bp fragment from one of the DNase I-hypersensitive regions that has full blocking activity in the oocyte assay [17].
• DNase I footprinting revealed a region protected by both HepG2 and liver cell nuclear extracts between nucleotides -83 and -112 [18].

Associations of DNaseII with chemical compounds

• The enzyme is a lysosomal DNase, because it is glycosylated and carries 1.8-2.4 mol of mannose-6-phosphate/mol of enzyme [19].
• These nuclei have been further treated with high concentrations of DNase I and RNase A followed by sequential extraction with 2% Triton X-100 and 1 M NaCl to produce a structurally and biochemically distinct preparation designated Drosophila subnuclear fraction I (DSNF-I) [20].
• Drosophila topo II-containing particles were insensitive to EDTA, Triton X-100 and DNase I, but could be disrupted by incubation with 0.3 M NaCl or RNase A [21].
• A factor present in embryonic nuclear extracts specifically protects element I in DNase I footprinting assays [22].
• Both the chemical cleavage reagent methidiumpropyl-EDTA X iron(II) [MPE X Fe(II)] and the nuclease DNase I revealed a complex pattern of four or five hypersensitive sites upstream of each gene before activation [23].

Physical interactions of DNaseII

• It was also determined that the Sp family of transcription factors binds 2 DNase I-footprinted sites at -165 and -195 [24].
• The DNase I footprinting result showed that there are two strong binding sites and five weak binding sites in the fragment between -385 and -675 bp from the transcription start site of the vnd/NK-2 gene [25].
• In contrast, GAGA factor appears to be capable of binding and establishing a DNase I hypersensitive region in the absence of TFIID and polymerase [26].
• We now show that Sp1 and Egr-1 bind specifically to the G+C-rich promoter sequence using in vitro deoxyribonuclease I footprinting [27].

Regulatory relationships of DNaseII

• Despite having different charges as determined by two-dimensional (2D) gel electrophoresis, Act88F expressed in vivo and in vitro in rabbit reticulocyte lysate bind to DNase I with equal affinity and are able to copolymerise with bulk rabbit actin equally well [28].
• Using Xenopus laevis oocyte extracts to assemble chromatin in vitro, we have confirmed that Sp1 and NFkappaB can indeed induce sites hypersensitive to DNase I, micrococcal nuclease, or restriction enzymes on either side of factor binding sites in chromatin but not naked DNA [29].

Other interactions of DNaseII

• We demonstrate that recombinant FTZ-F1 alpha and FTZ-F1 beta proteins produce similar in vitro DNase I footprint patterns on a 14-nucleotide region of the zebra element and bind to this site with similar affinities and sequence specificities [30].
• DNase I footprinting of pol gamma.DNA complexes and initial rate measurements show that mtSSB enhances primer recognition and binding and stimulates 30-fold the rate of initiation of DNA strands [31].
• Consensus analysis and DNase I footprinting assay indicated that P7 contains multiple Sp1- and AP-2-binding sites [32].
• Both the sry beta and delta proteins protect an 18-22 base region from DNase I digestion within each analysed genomic binding site, that includes a 13 bp consensus sequence [33].
• Comparison of the chromatin structure at the Mcp locus in wild-type and dsp1 mutant embryos reveals that the 300-bp DNase I hypersensitive region is absent in a dsp1 mutant context [34].

Analytical, diagnostic and therapeutic context of DNaseII

• As assessed by DNase I footprinting and promoter dissection experiments, two of these elements are potential regulatory targets of Raf-1-activated transcription factors [35].
• Site-directed mutagenesis, DNase I footprinting and deletion analysis of 5276 bp of 5' proximal -1b flanking sequence revealed that this region does not confer tissue-specific expression and that 210 bp of proximal sequence is sufficient for maximal promoter activity [36].
• Cut serial sections, optical serial sections, scanning electron microscopy (SEM) on whole mounts, high-voltage electron microscopy (HVEM) on whole mounts, and pancreatic DNase I digestion monitored by fluorescent microscopy have been used to complement one another in this analysis [37].
• Sucrose velocity gradient ultracentrifugation demonstrated that DNA topoisomerase II solubilized from nuclei by either RNase A or DNase I migrated at about 9 S, as expected for the homodimer [38].
• Binding of Sp1 and Sp3 transcription factors to this region was confirmed by DNase I footprinting, electrophoretic mobility shift assay, super-shift assay, and chromatin immunoprecipitation [39].

References