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1 DNase I and Tn5 transposase assays require thousands to
2 DNase I DNA footprint assays show that AerR containing B
3 DNase I footprint analysis further defined the sequences
4 DNase I footprinting located the most proximal DNA bindi
5 DNase I footprinting showed that the VpsT binding site a
6 DNase I footprinting showed that this sequence lies with
7 DNase I footprinting with these sequences confirmed trip
8 DNase I footprints for these regulators were indicative
9 DNase I hypersensitive sites (DHSs) are a hallmark of ch
10 DNase I hypersensitive sites (DHSs) provide important in
11 DNase I injected into experimental animals, moreover, re
12 DNase I is a secreted enzyme whose function has been pre
13 DNase I is a sequence-specific enzyme, with a specificit
14 DNase I is a useful biomarker.
15 DNase I is an enzyme which cuts duplex DNA at a rate tha
16 DNase I protection assays demonstrated that the CO-assoc
17 DNase I protection studies as well as promoter fusion an
18 DNase I-hypersensitive site I (HSI) of the LCR is essent
19 00 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retin
20 nkyrin 1 (ANK1E) core promoter contains a 5' DNase I hypersensitive site (HS) with barrier insulator
21 e image analysis, electron microscopy, and a DNase I assay to show that hyperosmotic conditions (>400
23 slocation breakpoints in t-AMLs cluster in a DNase I hypersensitive region, which possesses cryptic p
31 saline, provided partial protection against DNase I digestion and exhibited the highest gene transfe
32 trol region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks
33 r, electrophoretic mobility shift assays and DNase I footprinting revealed that OhrR binds directly t
34 l, electrophoretic mobility shift assays and DNase I footprinting showed that the ArcA and IscR bindi
37 re evaluated in DNA thermal denaturation and DNase I footprinting assays, and the ability to inhibit
38 located in GC-rich, nucleosome-depleted, and DNase I sensitive regions, flanked by well-positioned nu
39 , micrococcal nuclease (MNase) digestion and DNase I digestion, followed by deeply sequencing the res
42 results were referenced against enhancer and DNase I hypersensitive regions from ENCODE and Roadmap E
44 pression quantitative trait loci (eQTLs) and DNase I sensitivity quantitative trait loci (dsQTLs) in
49 ree hypothetical protein-encoding genes, and DNase I footprint analysis identified the specific nucle
50 nce of NET-dissolving drugs like heparin and DNase I, already in clinical use, and recent development
53 els of H3K4me2 and H3K27ac histone marks and DNase I hypersensitivity--signifying accessible, permiss
54 ng DNA methylation, histone modification and DNase I hypersensitivity profiling as well as Hi-C to in
59 gel retardation, potassium permanganate and DNase I footprinting, cleavage reactions with protein co
60 d to DNA in combination with DMS probing and DNase I footprinting results supported the CoMA data.
62 hese hypotheses, and promoter resections and DNase I footprinting assays revealed a single CepR2 bind
67 cluding protein-coding genes, enhancers, and DNase-I hypersensitive sites in over 100 tissues and cel
68 ormatic analyses using H3K4Me1, H3K4Me3, and DNase-I hypersensitivity chromatin signatures and evolut
69 occupied by the insulator protein CTCF, are DNase I hypersensitive and represent only a small minori
74 , transcriptional fusions, gel-shift assays, DNase I footprinting, and in vitro transcription, it was
77 exploits information from H3K27ac signal at DNase I hypersensitive sites identified from published h
82 closed conformation of CNS-1, as assessed by DNase I hypersensitivity, along with enhanced accumulati
83 show that the intrinsic rate of cleavage by DNase I closely tracks the width of the minor groove.
85 ologous structural framework as confirmed by DNase I and hydroxyl radical footprinting, the two compl
89 alysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient O-loop forma
94 rved sequence element mapping to a chromatin DNase I hypersensitive site located within intron 1.
95 rivate disruptive mutations within fetal CNS DNase I hypersensitive sites (i.e., putative regulatory
97 m reveals strong enhancer regions containing DNase I hypersensitive sites overlapping the rs874040 li
98 s that cannot be analyzed using conventional DNase I sequencing because of the requirement for millio
100 ucers did not yield identical CbbR-dependent DNase I footprints, indicating that the coinducers cause
101 imarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that corr
102 tors and those within frontal cortex-derived DNase I hypersensitivity sites are significantly enriche
104 e hundred thousand genomic loci that display DNase I hypersensitivity in one or more ENCODE cell line
106 hylogenetic conservation as well as elevated DNase I hypersensitivity (DHS) in ENCODE cell lines.
109 the current high-throughput sequencing era, DNase I has mainly been used to study genomic regions de
110 velopment is illustrated by direct evidence: DNase I added to tumor cells eliminates the structures a
112 rimetric readout would make the lateral flow DNase I test strip a suitable platform for point-of-care
113 we used potassium permanganate footprinting, DNase I footprinting, and in vitro transcription from th
115 riants at the 20 eGFR loci were enriched for DNase I hypersensitivity sites (DHSs) in human kidney ce
116 27 k Illumina array, and with enrichment for DNase-I Hypersensitivity sites across the full range of
118 with a DNA fragment including only its four DNase I hypersensitive sites (lacking the large spacer r
119 er also show a high level of protection from DNase I digestion genome-wide, and likely have important
120 n regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell
135 tify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experi
136 oteins were partially purified and tested in DNase I footprinting experiments with the excisive attac
137 me-widely using chromatin features including DNase I hypersensitivity, 11 histone modifications (HMs)
139 chromatin structure, resulting in increased DNase I sensitivity, the accumulation of DNA damage, and
141 t formation along the gradient of increasing DNase I concentrations is used to determine the accessib
146 tor binding sites are derived from intrinsic DNase I cleavage bias rather than from specific protein-
147 ing CpG site methylation, CGIs, co-localized DNase I hypersensitive sites, transcription factor bindi
149 ained a total of 2.7 billion uniquely mapped DNase I-sequencing (DNase-seq) reads, which allowed us t
151 de maps for 17 TFs, 3 histone modifications, DNase I hypersensitive sites, and high-resolution promot
152 characterization of the most highly mutated DNase I hypersensitive sites in breast cancer (using in
153 NFAT and AP-1 which created thousands of new DNase I-hypersensitive sites (DHSs), enabling ETS-1 and
157 and affects the organization of nucleosomes, DNase I hypersensitivity, and the transcriptional profil
158 nrelated to changes in nucleosome occupancy, DNase I hypersensitivity dynamics are also predictive of
161 In an acidic environment, the activity of DNase I was activated through the acid-triggered sheddin
166 We observed that physiological amounts of DNase I do not suffice to completely degrade NETs in vit
169 tudies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potent
170 We first defined more than 1800 clusters of DNase I hypersensitive sites (DHSs) with similar tissue
171 Both monotherapies and coadministration of DNase I and rhADAMTS13 revealed a cardioprotective effec
172 In contrast, quantitative comparison of DNase I hypersensitivity between states can predict tran
173 erformed the first genome-wide comparison of DNase I sensitivity of chromatin in mitosis and interpha
174 olymeric nanogel to facilitate decoration of DNase I into the NCl by electrostatic interactions.
178 localize with, and maintain the intensity of DNase I hypersensitive sites genome wide, in resting but
180 port consistent patterns of gain and loss of DNase I-hypersensitive sites (DHSs) as cells progress fr
181 s-regulatory elements; therefore, mapping of DNase I hypersensitive sites (DHSs) enables the detectio
183 rate that it enables simultaneous mapping of DNase I hypersensitivity and regional DNA methylation le
184 enerated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and
185 q) method that allows us to generate maps of DNase I-hypersensitive site (DHS) of mouse preimplantati
188 scription start sites, reduces the number of DNase I-hypersensitive sites genome wide, and decreases
189 atory element located in an adjacent pair of DNase I HS located 5.6 kb 3' of the ANK1E promoter at th
192 e, we use a recent comprehensive data set of DNase I sequencing-identified cis-regulatory binding sit
193 gulated by two partially overlapping sets of DNase I hypersensitive sites (HSs) that constitute the p
194 apped the location and allele-specificity of DNase I hypersensitive (DH) sites within the PWS-IC in b
195 c identification of hundreds of thousands of DNase I hypersensitive sites (DHS) per cell type has bee
197 uccess of this strategy is the unique use of DNase I digestion to remove unwanted ssDNA from the memb
201 ion of association tests, prior knowledge of DNase-I hypersensitivity sites or other relevant biologi
203 VM accurately predicts the impact of SNPs on DNase I sensitivity in their native genomic contexts and
204 entified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing
205 Instead, ORC binds nonspecifically to open (DNase I-hypersensitive) regions containing active chroma
206 e of these seven loci lay within enhancer or DNase I hypersensitivity regions in lung fibroblasts or
207 ped, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA mo
208 acing and sequence, and was marked by phased DNase I hyperactivity and protection patterns consistent
212 systemic lupus erythematosus exhibit reduced DNase I activity, and patients with myocardial infarctio
215 Here we demonstrate that high-resolution DNase I cleavage profiles can provide detailed informati
216 oclew (NCl) embedded with an acid-responsive DNase I nanocapsule (NCa) was developed for targeted can
220 Here we profile parental allele-specific DNase I hypersensitive sites in mouse zygotes and morula
221 ntify 76 genes with paternal allele-specific DNase I hypersensitive sites that are devoid of DNA meth
222 ed and exhibits a plasmacytoma cell-specific DNase I-hypersensitive site in chromatin, henceforth ter
226 with several traits, and cell-type-specific DNase-I hypersensitive sites were enriched with SNPs ass
227 tiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of inter
230 modes of interaction with chromatin and that DNase I hypersensitivity dynamics provides a general app
231 vasive bioluminescent imaging confirmed that DNase I treatment was sufficient to suppress tumor metas
233 oximately 40 yr ago it was demonstrated that DNase I also digests with a approximately 10-bp periodic
234 g studies have instead yielded evidence that DNase I plays a central role in newly defined dynamics o
235 Here, we reveal for the first time that DNase I can be used to precisely map the (translational)
237 tructural and biochemical data implicate the DNase I binding loop (D-loop) of actin in such nucleotid
238 nd disulfide cross-linking of Cys-41 (in the DNase I binding loop) to Cys-374 (C-terminal) but increa
242 est strip, we have successfully measured the DNase I activity and determined the factors that influen
243 cleosomal DNA; the oscillatory nature of the DNase I cleavage profile within nucleosomal DNA enables
244 s between receptor loading, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range intera
246 changes in the structure and dynamics of the DNase-I loop, alterations in the structure of the H73 lo
249 il loci drive gene-expression changes though DNase-I hypersensitive sites (DHSs) near transcription s
250 ococcus mutans and DNA binding sites through DNase I footprinting and electrophoretic mobility shift
251 nce and protected against ALI in mice; thus, DNase I may be a new potential adjuvant for ALI therapy.
252 and H3K27me3, an increased accessibility to DNase I and an induction of euchromatic H3 and H4 histon
253 on measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo a
255 rate that a 650-bp sequence corresponding to DNase I hypersensitive sites HS1-2 within the mouse Igka
256 were identified based on hypersensitivity to DNase I digestion and association with H3K4me3-modified
257 d cellular internalization and resistance to DNase I compared to free synthetic nucleic acids, they s
259 ce of nanoparticles were highly resistant to DNase I endonucleases, and degradation was carried out e
263 co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predic
264 ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding,
265 ronic sequence containing an uncharacterized DNase I hypersensitivity (DHS) site located 3' to the si
266 with those of enhancers and exhibited unique DNase I hypersensitivity profiles that reflected the pot
270 ed a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid s
276 s for over 50 years, the potential for using DNase I as a clinical tool to prevent or treat cancer re
278 ved from the membrane containing HBcAg using DNase I digestion and gradient wash with urea buffers.
279 with open chromatin regions identified using DNase I hypersensitivity assays, and are enriched in the
280 based on cuts in linker regions, we utilize DNase I cuts both outside and within nucleosomal DNA; th
284 vely parallel sequencing has enabled in vivo DNase I footprinting on a genomic scale, offering the po
286 eling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcript
293 ngly, treatment of cancer cell cultures with DNase I to degrade DNA nonspecifically reduced metastati
299 Treatment of biofilms formed in urea with DNase I reduced the biofilm, indicating that extracellul
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