ライフサイエンスコーパス: footprinting

1 vel, a method introduced as 'digital genomic footprinting'.

2 ein chemical modification reactions (protein footprinting).

3 ine thiols by differential isotopic chemical footprinting.

4 rophoretic mobility shift assay, and RNase A footprinting.

5 the remaining issues and hurdles for genomic footprinting.

6 physiological salt condition as shown by DMS footprinting.

7 re polyribosome purification or in vitro RNA footprinting.

8 mplex stability assays and DNAse I and KMnO4 footprinting.

9 , has become a powerful approach for protein footprinting.

10 define actively translated ORFs by ribosome footprinting.

11 negative impact on predictive performance of footprinting.

12 fold higher affinity for its own promoter by footprinting.

13 mined by time-resolved hydroxyl (OH) radical footprinting.

14 of 20 amino acid side chains) to fulfill the footprinting.

15 use of gel mobility shift assays and DNase I footprinting.

16 ions of ribosomes on transcripts by nuclease footprinting.

17 tion heretofore unavailable by residue-level footprinting.

18 ckbone amides, is the most common example of footprinting.

19 One of those approaches is protein footprinting.

20 scriminating for specific amino-acid protein footprinting.

21 trophoretic mobility shift assay and DNase I footprinting.

22 olution cryo-electron microscopy and in-cell footprinting.

23 proved properties of this probe make carbene footprinting a viable method for rapid and accurate iden

24 Using genomic DNase I footprinting across 41 diverse cell and tissue types, we

25 Several computational footprinting algorithms have been developed to detect TF

26 Compared with published footprinting algorithms, TRACE has the best overall perf

27 Genomic footprinting allowed us to identify in vivo regulatory e

28 Footprinting also indicated that heparin binding induces

29 DNA-footprinting analyses revealed new transcriptional regul

30 catalytic turnover for EMSA and ribonuclease footprinting analyses.

31 lear magnetic resonance, and dimethylsulfate footprinting analyses.

32 Accordingly, DNase I footprinting analysis confirmed that AbrB bound to the p

33 matin-associated protein binding and genomic footprinting analysis from antibody-targeted CUT&RUN pri

34 DNA footprinting analysis identified unique protein binding

35 Transcription factor (TF) footprinting analysis identifies differences in the regu

36 Footprinting analysis indicated that specific DNA contac

37 we report the results of a hydroxyl radical footprinting analysis of the zinc-selective channel ZIPB

38 Footprinting analysis revealed that immune-related trans

39 Genome-wide footprinting analysis using DNase-seq provides little ev

40 ing a microarray analysis and a phylogenetic footprinting analysis with various biochemical assays, w

41 New methods for footprinting and affinity purification of nucleosomes, R

42 triction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histon

43 Here we used RNA chemical footprinting and binding assays to test this model and f

44 We demonstrate, using chemical footprinting and by monitoring charge-flow-dependent gua

45 dden states, we use rapid mass spectrometric footprinting and confirm our models' prediction that inc

46 oscopy and validation of the structure using footprinting and crosslinking approaches.

47 Footprinting and electrophoretic gel mobility shift anal

48 ith issues concerning the utility of genomic footprinting and is reassessing the proposed approaches

49 ted radical trifluoromethylation for protein footprinting and its broad residue coverage.

50 FPOP platform, the conditions for successful footprinting and its examination by mass measurements of

51 Here we use chemical footprinting and laser-tweezers-based single-molecule ap

52 Further, we applied in vitro RNase footprinting and mapped two binding targets of the prote

53 The method of X-ray footprinting and mass spectrometry (XFMS) on large prote

54 Chemical footprinting and molecular dynamics simulations show tha

55 By footprinting and motif analyses, these regions are predi

56 Subsequent footprinting and mutagenesis analysis indicates that pro

57 ermination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions sho

58 DNA footprinting and purine-base interference assays demonst

59 ndings suggest a revised understanding of TF footprinting and reveal limitations in comprehensive rec

60 We show by dimethyl sulfate footprinting and RNA polymerase arrest assays that at ph

61 thod that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencin

62 Mass spectrometry-based protein footprinting and site-directed mutagenesis studies have

63 Here it is shown, by DNase I footprinting and site-directed mutagenesis, that BreR is

64 chrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering.

65 y-based protein profiling (ABPP), c) protein footprinting, and d) protein cross-linking.

66 Chromatin profiling, phylogenetic footprinting, and functional assays enabled the identifi

67 g electrophoretic mobility-shift assays, DNA footprinting, and in silico analysis, we identified a DN

68 potassium permanganate footprinting, DNase I footprinting, and in vitro transcription from the mitoch

69 riptional fusions, gel-shift assays, DNase I footprinting, and in vitro transcription, it was shown t

70 ne-for-guanine replacement, hydroxyl radical footprinting, and LC-MS/MS were consistent with a cross-

71 ng SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE.

72 at was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy.

73 ee translation assays, quantitative ribosome footprinting, and X-ray crystallography support a model

74 nt to limitations of the DNase-based genomic footprinting approach and call into question the scope o

75 In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in

76 We have developed a phylogenetic footprinting approach for the identification of conserve

77 scribe the application of an oxidative-based footprinting approach inside cells in which hydroxyl rad

78 A third footprinting approach is by reactions with fast, irrever

79 In particular, we use a novel SPR footprinting approach that exploits indirect ligand capt

80 We have now employed a chemical footprinting approach to identify regions on VWF involve

81 In this study a carbene-footprinting approach was developed and applied to ident

82 inants of CCL7, an unbiased hydroxyl radical footprinting approach was employed, followed by a focuse

83 an important mass spectrometry-based protein footprinting approach.

84 Mass spectrometry (MS)-based protein footprinting approaches play an important role in elucid

85 on implementing complementary solution-phase footprinting approaches that differ in time scale, speci

86 uss both prospects and challenges of genomic footprinting, as well as considerations for its applicat

87 ding sites by using a chemical probe reverse-footprinting assay and as the major Gag binding sites by

88 and RNA in combination with the first direct footprinting assay for telomerase association with bound

89 amine this issue using data from a ribosomal footprinting assay in yeast.

90 Using a methyltransferase footprinting assay on isolated nuclei (in vitro), we fin

91 In addition, by exploiting a novel PAR footprinting assay, we obtained evidence that the ALC1 m

92 Gel shift and DNase I footprinting assays confirmed the presence and locations

93 fically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an ad

94 ructural observations together with nuclease footprinting assays indicate otherwise: strand separatio

95 otheses, and promoter resections and DNase I footprinting assays revealed a single CepR2 binding site

96 ts capture some differences from traditional footprinting assays that could suggest that probing in v

97 ated in DNA thermal denaturation and DNase I footprinting assays, and the ability to inhibit binding

98 g electrophoretic mobility shift and DNase I footprinting assays.

99 characterized DNA motifs identified in DNase footprinting assays.

100 By comparing the extent of footprinting between HT3DeltactpADelta27PSII and HT3Delt

101 In addition to RNA transcription, DNAzyme footprinting can be coupled to a wide variety of other n

102 resolution enabled by IM-MS-coupled carbene footprinting can bridge the gap between structural MS an

103 cture, we are investigating whether MS-based footprinting can provide coarse-grained protein structur

104 ative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved

105 ay scattering (SAXS), X-ray hydroxyl radical footprinting, circular dichroism, and H/D exchange mass

106 ardation, potassium permanganate and DNase I footprinting, cleavage reactions with protein conjugated

107 DNA footprinting confirmed that interaction of Dda with a fo

108 Protein cross-linking and radiolytic footprinting coupled with high-resolution mass spectrome

109 Protein footprinting coupled with mass spectrometry has become a

110 Protein footprinting coupled with mass spectrometry is being inc

111 Here hydroxyl radical footprinting coupled with mass spectrometry was employed

112 Single-molecule R-loop footprinting coupled with PacBio sequencing (SMRF-seq) r

113 lied to three model systems where radiolytic footprinting data are reported in the literature.

114 We use allelically resolved genomic DNase I footprinting data encompassing 166 individuals and 114 c

115 The footprinting data further indicate that the conserved Gn

116 Integration of NET-seq with genomic footprinting data reveals stereotypic Pol II pausing coi

117 Protein NMR structural footprinting data show that amodiaquine, chloroquine, an

118 e RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determ

119 roach of mapping protein structures by using footprinting data, but also elevates the use of HRF meas

120 ents of protein synthesis rate with ribosome footprinting data, we here inferred translation initiati

121 0 distinct structural probes from radiolytic footprinting, disulfide trapping, and mutagenesis to map

122 Here we used potassium permanganate footprinting, DNase I footprinting, and in vitro transcr

123 Carbene footprinting efficiently labels proteinaceous residues a

124 Genomic DNase I footprinting enables the quantitative, nucleotide-resolu

125 Using phylogenetic footprinting, epigenetic profiling, and transgenic repor

126 Thermal denaturation studies and footprinting experiments confirm that isolated ES7 is st

127 Binding studies and site-specific footprinting experiments demonstrate the existence of a

128 ntifying the precise positions of ribosomes, footprinting experiments have unveiled key insights into

129 RNA mutagenesis and footprinting experiments indicate that interactions of t

130 nts obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs.

131 nt methods to generate hydroxyl radicals for footprinting experiments rely on the laser photolysis of

132 Footprinting experiments revealed that functional eIF4G

133 Native gel, NMR, and chemical footprinting experiments showed that mutations that dest

134 Molecular docking simulations and DNA footprinting experiments suggest a model where a PC4 dim

135 Footprinting experiments support formation of predicted

136 DNA footprinting experiments were also conducted to further

137 Indeed, footprinting experiments with an enzyme assembled with t

138 ere partially purified and tested in DNase I footprinting experiments with the excisive attachment si

139 By DNase I and hydroxyl radical footprinting experiments, we show that the binding site

140 complexity typically associated with radical footprinting experiments.

141 ated with secondary structure probing by DMS footprinting experiments.

142 d protein cross-linking and hydroxyl radical footprinting experiments.

143 The established workflow combines carbene footprinting, extended liquid chromatographic separation

144 Single-molecule R-loop footprinting following in vitro transcription showed a s

145 light the significance of epigenetic-genetic footprinting for exploring neurologic function in a subj

146 printing" in analogy to the process of DNase footprinting for the detection of protein-DNA interactio

147 nalyses algorithms, including a phylogenetic footprinting framework; (ii) 2125 species with complete

148 This marks the first time protein footprinting has been performed in live cells.

149 Genomic footprinting has emerged as an unbiased discovery method

150 Genomic footprinting has opened unique vistas on the organizatio

151 is of regions protected from cleavage (DNase footprinting) has for many years been used to identify s

152 Using ribosome footprinting, here we perform global translatome profili

153 sed high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measur

154 Hydroxyl-radical footprinting (HRF) of protein-DNA complexes is a chemica

155 Measurements from hydroxyl radical footprinting (HRF) provide rich information about the so

156 Hydroxyl radical protein footprinting (HRPF) by fast photochemical oxidation of p

157 Hydroxyl radical protein footprinting (HRPF) is a powerful technique for probing

158 Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes

159 Transcription factor footprinting implicates cell-specific transcriptional re

160 ether, our results demonstrating in vivo EJC footprinting in Arabidopsis unravel the composition of t

161 has been a growing need for MS-based protein footprinting in both academia and industry owing to its

162 We have now employed chemical footprinting in conjunction with mass spectrometry to id

163 promoter deletion analyses with phylogenetic footprinting in eudicots and in Arabidopsis accessions,

164 ing protein-aptamer complexation as "DNAzyme footprinting" in analogy to the process of DNase footpri

165 RNase footprinting, in vitro binding and stopped-flow fluoresc

166 Hydroxyl radical DNA footprinting indicated that the site-specifically bound

167 This new approach to footprinting is a bridge between trifluoromethylation in

168 DNaseI footprinting is an established assay for identifying tra

169 roteins on damaged DNA by photocross-linking footprinting is consistent with x-ray analysis of the Ra

170 In this method, enzymatic footprinting is coupled to high-throughput sequencing to

171 Another example of footprinting is slow irreversible labeling of functional

172 A basic premise of footprinting is that sequence-specific TF-DNA interactio

173 This could imply that DNase-seq footprinting is too insensitive an approach to identify

174 DNase I footprinting located the most proximal DNA binding site

175 to generate hydroxyl radicals for structural footprinting mass spectrometry experiments to complement

176 The reversed-footprinting mass spectrometry extends the FPOP technolo

177 We developed LiF-MS (ligand-footprinting mass spectrometry), a method to map peptide

178 inase domain heterodimers and carboxyl group footprinting mass spectrometry, we observed that HER2 an

179 Our analysis with X-ray footprinting-mass spectrometry (XFMS) identifies critica

180 In this work, DNase I footprinting measurements were employed to investigate t

181 Overall, DZN labeling emerges as a useful footprinting method capable of shedding light on physiol

182 We have developed a footprinting method to predict TF footprints in active c

183 eins (IV-FPOP) is a hydroxyl radical protein footprinting method used to study protein structure and

184 The hydroxyl radical footprinting method, fast photochemical oxidation of pro

185 a comprehensive and systematic comparison of footprinting methods for specifically identifying which

186 data models for the application of metabolic footprinting methods for wine yeast strain phenotyping a

187 Environmental footprinting methods provide a means to relate the envir

188 Here we describe footprinting of Abeta1-42 by hydroxyl radical-based fast

189 otochemical oxidation of proteins (FPOP) for footprinting of cystic fibrosis transmembrane conductanc

190 aling pathways and chromatin through genomic footprinting of kinase activity and unbiased identificat

191 Genome-wide ribosomal footprinting of MYC(Tg);KRAS(G12) tumors compared with K

192 The single-molecule resolution allows footprinting of protein and nucleosome binding, and dete

193 Metabolic footprinting of supernatants has been proposed as a tool

194 rium exchange and cysteine-specific chemical footprinting of the HBx:DDB1 complex identified several

195 tory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tiss

196 Using DNA footprinting of the regions upstream of the liaXYZ and l

197 g transcript sequencing (NET-seq) with RNase footprinting of the transcripts (RNET-seq).

198 bosome profiling (a technique for the global footprinting of translating ribosomes), we also demonstr

199 allel sequencing has enabled in vivo DNase I footprinting on a genomic scale, offering the potential

200 HDX footprinting on RT +/- aptamer shows strong contacts wit

201 UPF1)-binding sites using transcriptome-wide footprinting or DNA oligonucleotide-directed mRNA cleava

202 profiling of culture supernatants (metabolic footprinting) over the course of growth of both Pseudomo

203 al duplex by 4 nt resulted in a shift in the footprinting pattern for the ssDNA by 4 nt, which is con

204 However, the footprinting pattern in the dsDNA region was shifted by

205 he phosphodiester backbone resulted in a DNA-footprinting pattern similar to that observed with the s

206 Footprinting performed as a function of time indicated t

207 d with a statistically rigorous phylogenetic footprinting pipeline based on precomputed orthologs to

208 The diazirine-based footprinting probe is effectively sequestered by, and in

209 Moreover, the irreversible footprinting probe provides insights into the kinetics o

210 Our data with DNase I footprinting provide mechanistic insights and suggest th

211 , using high-resolution quantitative dynamic footprinting (qDF) microscopy combined with a homogenous

212 a analysis algorithm to convert the measured footprinting rate constant to a protection factor (PF) b

213 comparing the difference in the modification/footprinting rate of a specific site to infer structural

214 Published ribosome footprinting results and the analysis of a frame-shifted

215 The footprinting results indicate that the four active sites

216 in combination with DMS probing and DNase I footprinting results supported the CoMA data.

217 Application of microarray-based genetic footprinting revealed a large number of loci that drasti

218 he protein-DNA interface by quantitative DNA footprinting revealed new minor groove contacts and chan

219 While dimethylsulphate footprinting revealed some evidence for G-quadruplex for

220 Chemical footprinting revealed that Ile-16 is significantly less

221 rophoretic mobility shift assays and DNase I footprinting revealed that OhrR binds directly to a spec

222 DNaseI footprinting reveals that this complex formation corresp

223 integrated data from DNase1 digital genomic footprinting, RNA-seq, and gene expression microarrays t

224 rogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl su

225 for individual templates (MAPit) methylation footprinting showed that nucleosome occupancy and DNA me

226 EMSAs and DNase I footprinting showed that the [4Fe-4S] form of ScNsrR bin

227 rophoretic mobility shift assays and DNase I footprinting showed that the ArcA and IscR binding sites

228 xyl acylation and primer extension) chemical footprinting showed that the rpoS leader is divided into

229 DNase I footprinting showed that the VpsT binding site at the rp

230 DNase I footprinting showed that this sequence lies within the p

231 Ribonuclease V1 footprinting shows that hADAR2-D protects approximately

232 , with reduced SNP density, and with a DNase footprinting signal in all tested cells.

233 Using a combination of site-specific DNA footprinting, single-turnover unwinding assays, and uniq

234 n of membrane proteins by combining MS-based footprinting, specifically fast photochemical oxidation

235 MS-based protein footprinting strategies, including hydrogen/deuterium ex

236 Herein we developed a subresidue footprinting strategy based on the discovery that carben

237 ed a site-specific hydroxyl radical-mediated footprinting strategy to pinpoint the binding sites of P

238 A mass spectrometry-based footprinting strategy was adopted to probe solvent-expos

239 Nevertheless, previous footprinting studies are typically performed at the resi

240 DMS footprinting which, along with previous footprinting studies, helped to explain our probing resu

241 echnologies for protein structure analysis, "footprinting" studies, have improved their sensitivity a

242 A recent chemical footprinting study in our laboratory suggested that regi

243 f Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient O-loop formation and

244 nces in RNA sequencing coupled with chemical footprinting suggested the opposite.

245 is of evolutionary conservation and ribosome footprinting suggests that these protein-coding sequence

246 Here we present a differential protein footprinting technique employing an efficient photo-acti

247 al oxidation of proteins (FPOP) is a protein footprinting technique that is being increasingly used i

248 hese goals were achieved by using a reversed-footprinting technique that monitored the unoxidized pep

249 By deploying this footprinting technique to probe the structure of the nat

250 coupled with mass spectrometry is a protein footprinting technique used to structurally characterize

251 extensive comparison between FPOP and other footprinting techniques gives insight on their complemen

252 Here, we use advanced footprinting techniques to investigate binding between t

253 g, along with co-immunoprecipitation or SecA footprinting techniques to readdress this issue.

254 of translational inhibitors or in vitro RNA footprinting that can alter ribosome protection patterns

255 lectrophoretic mobility shift assays and RNA footprinting, the H. pylori apo-AcnB binds to the 3'-unt

256 DNase1 digital genomic footprinting to a depth of 333,426,353 reads was perform

257 We utilized mutagenesis and DNase I footprinting to characterize YqjI regulation of the yqjH

258 cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP dom

259 scopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the m

260 is perspective, we review the use of protein footprinting to extend our understanding of macromolecul

261 continue to be frustrated by an inability of footprinting to identify the causative variant within a

262 We use transcriptome-scale ribosome footprinting to identify the hallmarks of eIF4A-dependen

263 spatial resolution hydroxyl radical protein footprinting to identify two separate binding sites for

264 ins (FPOP), and site-specific carboxyl group footprinting to investigate the HOS of protein and prote

265 and site-specific hydroxyl radical-mediated footprinting to localize the K-turns.

266 We used protein footprinting to map interdomain interaction surfaces of

267 We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy a

268 Using hydroxyl-radical footprinting to map the structures of RNA molecules in w

269 ere, we used mass spectrometry-based protein footprinting to monitor surface topology changes in full

270 Here, we employed synchrotron X-ray footprinting to probe the solution-state structures of H

271 ing across the genome, and used permanganate footprinting to specifically follow pausing during trans

272 atants (exometabolome analysis, or metabolic footprinting) to compare 179 strains, collected over tim

273 DNA labeling and footprinting, together with cryo-EM studies, were used t

274 Transcription factor (TF) footprinting uncovers putative protein-DNA binding via c

275 Ribosome footprinting using degradome data demonstrated RRGD loci

276 ges in protein conformation include 'protein footprinting,' using mass spectrometry.

277 Lastly, chemical footprinting was employed to examine the nature of ribos

278 Although the initial demonstration of footprinting was for the HOS determination of protein/nu

279 A method of chemical footprinting was used to characterize labile, cross-beta

280 Chemical RNA footprinting was used to compare the secondary structure

281 Through use of DNase I footprinting, we demonstrate that BpaB binds the erp ope

282 Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within

283 Based on footprinting, we find that promoter complexes formed by

284 is and high-resolution copper-phenanthroline footprinting, we have identified the functional toxboxes

285 ene and plant-optimized genome-wide ribosome footprinting, we have uncovered a molecular mechanism li

286 Here, using ribosome footprinting, we show that 2 hr of severe heat stress tr

287 ion assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-E-s

288 CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit linea

289 Some of the protected bases (from footprinting) were localized in proposed stem-loop struc

290 sed protein HOS analysis relies, in part, on footprinting, where a reagent reacts 'to mark' the solve

291 We performed in vivo DMS footprinting which, along with previous footprinting stu

292 spatial resolution hydroxyl radical protein footprinting, which shows great utility for the characte

293 ral diversity, we used MAPit single-molecule footprinting, which simultaneously maps endogenous CG me

294 analyses, nucleotide replacement studies and footprinting with CsrA-FeBABE identified two sites for C

295 The advent of DNA footprinting with DNase I more than 35 years ago enabled

296 In the present study, we used footprinting with Fe-BABE (a protein-labeling reagent th

297 A procedure for in vivo hydroxyl radical footprinting with Fe-EDTA was developed, and, together w

298 of immobilizing the protein in Nanodiscs and footprinting with FPOP is a feasible approach to map ext

299 al oxidation of proteins, and carboxyl group footprinting with glycine ethyl ester, were further appl

300 The extension of these methods for in cell footprinting would open an avenue to study proteins that