ライフサイエンスコーパス: sequence context

1 a strong preference for Tg in the telomeric sequence context.

2 g single molecules 5-19 times depending upon sequence context.

3 glycosylase activity on Gh in the telomeric sequence context.

4 occupation at each base pair from the genome sequence context.

5 is completely dependent on their surrounding sequence context.

6 s and by methylation specifically in the CHH sequence context.

7 that could synergize or compete depending on sequence context.

8 roll of the Pt-GG base pair step in the TGGA sequence context.

9 t to which an adenosine is edited depends on sequence context.

10 nisms were independent of the CEACAM1 intron sequence context.

11 om both microsatellite length as well as the sequence context.

12 iciently to methylated DNA within a specific sequence context.

13 on 7, and the 5' splice site-to-branch point sequence context.

14 ts of conformational coupling that vary with sequence context.

15 ent on both unpaired base identity and bulge sequence context.

16 misincorporated bases is influenced by local sequence context.

17 ivities for particular bases and surrounding sequence context.

18 f the template's secondary structure and the sequence context.

19 mpletion in long DNA segments, regardless of sequence context.

20 base identity but is somewhat contingent on sequence context.

21 nity of HMGB1a for OX-GG adducts in the TGGA sequence context.

22 d over the other three dNTPs in the TG 1*G 2 sequence context.

23 N(2)-dG:N(2)-dG cross-links in the 5'-CpG-3' sequence context.

24 ion patterns than with the underlying genome sequence context.

25 N(2)-dG:N(2)-dG cross-links in the 5'-CpG-3' sequence context.

26 lay of scored features (annotation) within a sequence context.

27 tures of the normal abasic site in a similar sequence context.

28 ures referenced to undamaged DNA in the same sequence context.

29 f DNA methylation outside of the standard CG sequence context.

30 methylation depending on the element and the sequence context.

31 ensitive to protein structure in addition to sequence context.

32 or of 2.3+/-0.3 in the TG*T than in the CG*C sequence context.

33 from trimethyl- to dimethyllysine in an H3K4 sequence context.

34 OX-DNA, CP-DNA and undamaged DNA in the same sequence context.

35 ation termination codon (PTC) in an atypical sequence context.

36 pecificity for phosphopeptides in a specific sequence context.

37 xy-)methyl-cytosines in both CpG and non-CpG sequence context.

38 ty of the DNA polymerase (Pol) and the local sequence context.

39 ion, coding state, nucleosome proximity, and sequence context.

40 dominant substitution types, strand bias and sequence context.

41 compared to a regular guanosine in the same sequence context.

42 ough varied not only with dose but also with sequence context.

43 erved previously for FAF and FAAF in certain sequence contexts.

44 trate of NER than dG-C8-AF in all three NarI sequence contexts.

45 ergy compared with Cp-DNA or Ox-DNA in other sequence contexts.

46 r differences in binding in the AGGC or TGGT sequence contexts.

47 more d5SICS-dNaM pairs in a wide variety of sequence contexts.

48 plicated with high fidelity in virtually all sequence contexts.

49 at uAUGs are functional in a wide variety of sequence contexts.

50 in 5'-d(...G*pT*...) and 5'-d(...G*pCpT*...) sequence contexts.

51 ce contacts was similar in the TGGT and AGGC sequence contexts.

52 kinetic evaluation of OGG1 in alternate DNA sequence contexts.

53 preference for DNA methylation in different sequence contexts.

54 mmodate a variety of mismatches in different sequence contexts.

55 regulation for EAL activity under different sequence contexts.

56 tation rates by small amounts or in specific sequence contexts.

57 rice endosperm DNA is hypomethylated in all sequence contexts.

58 o T:A transversions that occurred within CpG sequence contexts.

59 d DeltaS degrees for duplex formation in all sequence contexts.

60 metrical CG and nonsymmetrical (CHG and CHH) sequence contexts.

61 he error bias for DNA polymerase in specific sequence contexts.

62 ation on a genome-wide scale within specific sequence contexts.

63 transgenes are efficiently methylated in all sequence contexts.

64 proteins prefer methylcytosines in different sequence contexts.

65 ied strand in the B-DNA minor groove in both sequence contexts.

66 g the lesion within the lacZ gene in 4 local sequence contexts.

67 ot trimethylated lysines, in several histone sequence contexts.

68 site-specific recombination in a variety of sequence contexts.

69 een the IQ moieties and the DNA in the three sequence contexts.

70 ate and an increased density of hypermutable sequence contexts.

71 methylated on both strands of DNA at various sequence contexts.

72 ; yet some can be found as partials in other sequence contexts.

73 detecting modifications within specific RNA sequence contexts.

74 of NMPs has been shown to be affected by DNA sequence contexts.

75 NA duplexes containing AP sites in different sequence contexts.

76 target cytosines for methylation in specific sequence contexts.

77 y adjacent objects that belonged to distinct sequence contexts.

78 under identical conditions, using identical sequence contexts.

79 ed because of DNA methylation independent of sequence contexts.

80 f AGT-mediated repair were influenced by DNA sequence context (10-fold differences) but were only wea

81 ed with a normal abasic site (Y) in the same sequence context (2).

82 Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be

83 lently attached to a guanine base in the DNA sequence context 5'-d(CAT[G1Py]CG2TCCTAC) in aerated sol

84 merase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks p

85 NA, imposed by this adduct, in the different sequence contexts 5'-...CGG*C..., 5'-...CG*GC..., 5'-...

86 basic site have been synthesized in the same sequence context (5'-CCA AAG6 XA8C CGG G-3', where X den

87 this study, the human telomere in a complete sequence context, 5'-TAGGG(TTAGGG)3TT-3', was evaluated

88 ith Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G.

89 A...), a lack of consideration of the global sequence context, a response to sound omission, and a se

90 To test if sequence context affects Chi activity, we deep-sequenced

91 ted OG would preferentially form in 5'-GG-3' sequence contexts after exposure to reactive oxygen spec

92 Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of

93 erred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-co

94 e scale SBSs are influenced by the local DNA sequence-context, although the role of flanking sequence

95 ingitidis CRISPR-Cas machinery increases the sequence contexts amenable to RNA-directed genome editin

96 g and the stability are affected by the base sequence context and by the nature of the sugar moiety a

97 study, we investigated the influence of DNA sequence context and endogenous cytosine methylation on

98 is distinct from CC methylation in terms of sequence context and genomic distribution.

99 -GG and undamaged DNA dodecamers in the AGGC sequence context and have compared these structures with

100 aged duplex DNA in the 5'-d(CCTCAGGCCTCC)-3' sequence context and have shown the existence of several

101 ures that epsilonA removal is independent of sequence context and highly efficient despite the relati

102 We then applied the method to determine the sequence context and methylated base identity for three

103 ace area change with [C] shows that both the sequence context and residual structure are important.

104 presentation strongly depends on its larger sequence context and that blocking of the multistep proc

105 V-1 Pol on primer extension is influenced by sequence context and that herpes simplex virus type 1 Po

106 pair; this activity depends strongly on the sequence context and the base opposite to U.

107 main signal for stearate attachment, but the sequence context and the cell type modulate the fatty ac

108 ext provide more information than those from sequence context and the combination of them gives more

109 dition of the DNA template (both in terms of sequence context and the presence of DNA lesions).

110 type and DNA glycosylase tested, (ii) local sequence context and the stagger between opposing strand

111 ying susceptibility influenced by both local sequence context and trans-acting factors.

112 and Tbis1 bind to 5mC-containing DNA in all sequence contexts and have at least a preference of 100

113 unusual error specificity, in four different sequence contexts and in comparison to Pol nu's more acc

114 The analysis of DNA methylation in other sequence contexts and several chromatin modifications re

115 he results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies

116 anding the flexibility of dsDNA and dsRNA in sequence contexts and under mechanical stresses relevant

117 thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners

118 icularly high rates, exceeding 1% in certain sequence contexts, and generates single base substitutio

119 ingle modification type in several different sequence contexts, and identification of isomeric dimeth

120 , preventing polymerase stalling at specific sequence contexts, and overcoming polymerase stalling ca

121 ncy of dNs varied widely among organisms and sequence contexts, and partly reflected the in vitro dis

122 A5 and ATATA sequences in the same flanking sequence context, as models.

123 on the nature of the damage, but also on the sequence context, as revealed from analysis of mutation

124 -linked glycans attach to asparagines in the sequence context Asn-X-Ser/Thr, where X is any amino aci

125 ined by both the substrate structure and the sequence context at the junction point.

126 sses and is predominantly dependent on local sequence context at the meQTL site.

127 enes involves ribosome scanning dependent on sequence context at the multiple initiation sites to con

128 ncy caused severe DNA hypomethylation in all sequence contexts at direct VIM1 targets.

129 makes TH folding extremely sensitive to the sequence context, because the upstream arm easily engage

130 t mutations without chromosome or nucleotide sequence context bias would open the door to identify al

131 of validated variants, albeit with different sequence context biases.

132 r affinity than to OX-GG adducts in the TGGA sequence context but shows much smaller differences in b

133 n gene expression be influenced by the local sequence context, but also by the architecture of the nu

134 -dG-N(2)-dG cross-links in the 5'-CpG-3' DNA sequence context, but the corresponding adduct possessin

135 thways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA met

136 features, such as secondary motifs and local sequence context, by comparing network performance on mu

137 his study examines the extent to which local sequence context can be exploited to improve the quality

138 Our data demonstrate that local sequence context can be strikingly different around moti

139 insic dimerization of a GxxxG motif and that sequence context can control how hydrogen bonds influenc

140 a new, to our knowledge, mechanism by which sequence context can minimize the deleterious properties

141 While this suggests that mCpG sequence context can mostly be ignored in MBD2 binding,

142 ion (RdDM) at cytosine residues in three DNA sequence contexts (CG, CHG, and CHH).

143 e families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, wit

144 ucture and suggest that mutations that alter sequence context commonly affect RBP binding and regulat

145 inucleotides above ~20nM, independent of DNA sequence contexts, concentrations (20-1900nM) and methyl

146 esidues embedded in 16 different neighboring sequence contexts (considering only the 5'- and 3'-neigh

147 at a mismatch embedded in a nearest-neighbor sequence context containing symmetric 3'-purines (2 x 3'

148 What remains enigmatic is how the local DNA sequence context contributes to these differences.

149 number of interface contacts in the CP-TGGA sequence context corresponded to a larger roll of the Pt

150 zyme to misincorporate T opposite C and T in sequence contexts corresponding to mutagenic hot spots.

151 sults demonstrate that, within the same base sequence context, dA-rU base pairs are less stable than

152 diosyncratic features that derive from local sequence context, demonstrating how different genetic se

153 fficiency of deletion formation shows strong sequence-context dependence.

154 Expanding PWMs to include sequence context-dependence will increase the informatio

155 MMR, and quantify the nucleotide-dependence, sequence context-dependence, and strand-dependence of th

156 ining duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilization

157 These effects are consistent with base sequence context-dependent differences in structural dis

158 tum mechanics/molecular mechanics to analyze sequence context-dependent mutagenesis at mononucleotide

159 and amino acid substitution rates are highly sequence context-dependent, e.g., C --> T substitutions

160 oss of RER in B. subtilis causes strand- and sequence-context-dependent GC --> AT transitions.

161 ith the oxaliplatin-GG structure in the same sequence context determined previously in our laboratory

162 alpha iteron for pi-bound gamma and not the sequence context determined whether the origin was activ

163 Our results reveal that local nucleobase sequence context differentially alters the yields of 2,2

164 e and hot piperidine, although GT-containing sequence contexts displayed subtle biases in damage chem

165 natural and artificial RNAs; across multiple sequence contexts, dominantly at but not limited to pyri

166 The sequence context effect was studied for a mutational hot

167 Base sequence context effects for each adduct are caused by d

168 ion signals, and extend our understanding of sequence context effects on NER to the neighbors that ar

169 Again, sequence context effects were profound.

170 However, their activity is affected by sequence context, enzyme concentration and buffer compos

171 the modification to be well tolerated in the sequence contexts examined.

172 hese period-10 motifs, except TA, in certain sequence contexts, facilitates nucleosome formation.

173 onomorphic structure is formed within longer sequence contexts folding into a pearl-necklace structur

174 ed by hPol kappa opposite the adduct in both sequence contexts, followed by dTMP and dGMP.

175 These results highlight the importance of sequence context for alt-EJ repair and have important im

176 unusual base lends credence to and defines a sequence context for the "rare tautomer hypothesis" as a

177 We define the necessary sequence context for the observed cryptic 3' SSs and pro

178 ts mutation rate dependence on the local DNA sequence context for various types of mutations.

179 entified distinct editing site trinucleotide sequence contexts for each APOBEC3 protein and used them

180 des containing all possible three-nucleotide sequence contexts for guanine, the method was used to as

181 hree sites of 3Hyp but at different loci and sequence contexts from those in A-clade collagen chains.

182 Control experiments in one sequence context gave evidence that yyDNA helices, if fo

183 ical function of PT modifications, including sequence context, genomic frequencies, and relationships

184 DNA sequence context has emerged as a critical determinant o

185 be mediated by GxxxG motifs and modulated by sequence context has implications for the signaling mech

186 DNA sequence context has long been known to modulate detecti

187 Nucleotide sequence context has previously been demonstrated to pla

188 However, the nature of the sequence contexts has been poorly understood.

189 Moreover, the impact of larger sequence contexts has not been fully clarified, even tho

190 oxycarbonate, for which different effects of sequence context have been demonstrated by other approac

191 r by targeting cytosine within different DNA sequence contexts; however, the reason for these differe

192 tive polymerase DnaE is mutagenic within the sequence context identified in RER-deficient cells.

193 Finally, sequence context immediately surrounding an abasic site

194 r in the case of the CG*C-II than the CG*C-I sequence context in 135-mer duplexes.

195 he SFS, and they highlight the importance of sequence context in analyses of genome-wide variation.

196 applied this method to quantify the role of sequence context in defining the spectrum of damage prod

197 he method was used to assess the role of DNA sequence context in hydroxyl radical-induced guanine oxi

198 s of the genome, verifying the importance of sequence context in indel mutagenesis.

199 We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase a

200 cine and dibasic motifs located in a defined sequence context in the cytosolic N- and C-terminal doma

201 on the identity of the base and the template sequence context in which it is located.

202 xtracts has been found to depend on the base sequence context in which the lesion is embedded, provid

203 nonwobble pairs observed in different local sequence contexts in crystal and NMR structures.

204 s in 5'- ... CG*GC ... and 5'- ... CGG* C... sequence contexts in otherwise identical 12-mer duplexes

205 ysis of these effects, combined with the DNA sequence contexts in which the reversions take place, su

206 o fully paired 11-mer duplexes with a -G*CN- sequence context, in which G* is a C8-substituted dG add

207 genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which c

208 L84F AGT proteins when contained in multiple sequence contexts, including the twelfth codon of H-ras,

209 Owing to their high specificity and sequence context independence, targeting mismatches with

210 h of a mononucleotide microsatellite and its sequence context influence mutation rate in defective DN

211 Moreover, it is not known whether different sequence contexts influence the preferential access of m

212 s in mammalian cells, or how the surrounding sequence context influences amino acid incorporation.

213 The observation that the sequence context influences the cleavage by the enzymes

214 ially facilitate NER of the BP lesion in the sequence contexts investigated.

215 elected motif, LRLLRWC, was not the fastest; sequence context is also important for translocation eff

216 redicting secondary structure based on local sequence context is an efficient means of breaking the i

217 spontaneous membrane translocation, and that sequence context is important for the contribution of th

218 Therefore, we find local sequence context is the major determinant of mutagenesis

219 repressing transcription depending upon the sequence context it binds.

220 adduct in double-stranded DNA with the TG*T sequence context: its conformational heterogeneity in NM

221 tiation exhibits requirements for start site sequence context known for linear scanning.

222 -base interactions that are sensitive to the sequence context, local DNA conformation and solvent env

223 an other TP53 G:C>T:A hotspot sites and that sequence context more distal to adjacent bases must infl

224 evels, polyadenylation profiles, start-codon sequence context, mRNA half-lives, and RNA polymerase II

225 ethylcytosine (5mC) in the double-strand DNA sequence context of (C/T)(C/G)(5mC)N(C/G) (N = any nucle

226 g modulation is exquisitely sensitive to the sequence context of 3' splice sites and to small structu

227 Importantly, the sequence context of a binding site significantly influen

228 ultiplexing, capable of mapping out the full sequence context of a DNA/ligand interaction in a single

229 ts, and the observation that the surrounding sequence context of a target site affects nick-induced H

230 y was sensitive to the number, position, and sequence context of charged residues.

231 namics estimates enabled us to show that DNA sequence context of CpG sites is informative about methy

232 hylated CpG islands, but the full extent and sequence context of DNA hypomethylation and hypermethyla

233 and also investigate the degree to which the sequence context of key pentaloop point mutations influe

234 er of individual G-tracts and the length and sequence context of linker residues define the diverse t

235 res formed by peptides having the N-terminal sequence context of mutant huntingtin exon 1.

236 Manipulating and controlling the local sequence context of piggyBac elements could be a powerfu

237 bond formation, our findings suggest how the sequence context of polyproline-containing proteins can

238 varies with the drug used and the local DNA sequence context of the adduct.

239 OX-GG adducts are distinct and depend on the sequence context of the adduct.

240 deamination hotspots are defined by both the sequence context of the cytosine dinucleotide target as

241 e alternative outcomes was influenced by the sequence context of the deaminated cytosine, with indivi

242 editing efficiencies varied depending on the sequence context of the editing site consistent with kno

243 The sequence context of the labeling site was systematically

244 n at an ectopic embryonic site; and that the sequence context of the mutation is responsible for a va

245 As with the internal deletions placed in the sequence context of the parental and evolved genome.

246 and OX-GG adducts is highly dependent on the sequence context of the Pt-GG adduct.

247 formations are further influenced by the DNA sequence context of the Pt-GG adduct.

248 g computational approaches employed only the sequence context of the target residue for its predictio

249 The sequence context of this switch tunes the activity of th

250 r mechanisms to indel formation, we analyzed sequence contexts of indels in the non protein- or RNA-c

251 The sequence contexts of indels targeting lineage-defining g

252 translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network

253 tion of nucleobase damage and the effects of sequence context on damage chemistry in DNA.

254 for the rapid determination of the effect of sequence context on mutagenesis called SAMS for serial a

255 te our technique we determined the effect of sequence context on mutations generated by DNA synthesis

256 is known about the effect of methylation and sequence context on the deamination of 5-methylcytosine

257 DTA/H2O2 showed relatively modest effects of sequence context on the proportions of different damage

258 The influence of DNA base sequence context on the removal of a bulky benzo[a]pyren

259 However, the influence of the local sequence context on the structure of the abasic site and

260 ble strategy for uncovering the influence of sequence contexts on the functionalities of primary moti

261 monstrate for the first time that local mRNA sequence context plays a key role in near-cognate aminoa

262 Each displays its own sequence context preference, favoring different nucleoti

263 m ONOOCO(2)(-) did not vary as a function of sequence context, products of riboflavin-mediated photoo

264 ed mutagenesis and its dependence on the DNA sequence context remains unclear.

265 ensity across the genome or correlation with sequence context, replication timing or chromatin struct

266 Experimental results in a 5'-C[BP]G*G-3' sequence context reveal significant selectivity for dGTP

267 simulations of the Pt-GG adducts in the TGGA sequence context revealed that even though the major con

268 ale combinatorial mutagenesis of unfavorable sequence contexts revealed a consistent pattern whereby

269 ns of the HMGB1a-Pt-DNA complex in the three sequence contexts revealed a higher number of interface

270 sults provide insight into how different DNA sequence contexts show variability in DNA distortion at

271 tain base substitutions at high rates within sequence contexts similar to those inferred to be copied

272 promoters that act predictably in different sequence contexts, span two orders of magnitude in stren

273 We analyzed sequence context specificity of mutations in the B cells

274 ed the cleavage site at beta3 Arg(245), in a sequence context (SQLR(245) LQGSCFC) conserved among spe

275 d HsPoleta appeared more processive, but DNA sequence contexts strongly affected termination probabil

276 phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal trans

277 contacts for the CP-DNA complex in the TGGA sequence context than in the OX-DNA complex.

278 riant seems less sensitive to the effects of sequence context than the WT or L84F proteins.

279 h one of gamma without changing the original sequence context that caused enhanced looping in vitro c

280 ially targets TAR RNA by binding to specific sequence contexts that are not present on the final anne

281 kedly variable efficiency in different local sequence contexts that differentially alter the structur

282 acterized by C:G to A:T transversions at CCR sequence contexts that may have arisen due to error-pron

283 ssibility, and NOE connectivity suggest that sequence contexts that provoke improved MSH-activation d

284 serine or threonine residues, which occur in sequence contexts that would not be efficiently glycosyl

285 ur studies support that, besides the primary sequence context, the protein structure is a major deter

286 2 (DRM2), which methylates cytosines in all sequence contexts through an RNA-guided process, the CHR

287 we applied both the spatial context and the sequence context to construct the feature space.

288 ces for an AUG start codon and the canonical sequence context to favor translation initiation appear

289 5 of the cII transgene, which have identical sequence contexts to that of codon 249 of human TP53, co

290 a polymorphic site--the site's trinucleotide sequence context--to study polymorphism levels across th

291 ot observed for sets of TISs with nucleotide sequence contexts unfavorable for translation initiation

292 stalling at PPP motifs is influenced by the sequence context upstream of the stall site.

293 Additionally, the importance of sequence context was highlighted in one region where amp

294 th upon frameshift mutation in gene-specific sequence contexts, we altered the microsatellite length

295 Two predictors based on local sequence context were assessed: (i) single sequence seco

296 In the sequence context where fidelity is highest, k(pol) for c

297 However, in sequence contexts where the error rate is higher, k(pol)

298 ns of DNA methylation, especially in the CHH sequence context, where H is A, C or T.

299 ts with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates i

300 Our study also included different sequence contexts, which suggest the presence of coopera