ライフサイエンスコーパス: sequence context

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

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

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

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

5 dominant substitution types, strand bias and sequence context.

6 plex (G4) folding, both of which depend upon sequence context.

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

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

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

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

11 glycosylase activity on Gh in the telomeric sequence context.

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

13 is completely dependent on their surrounding sequence context.

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

15 ures using an embedding framework for larger sequence context.

16 that could synergize or compete depending on sequence context.

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

18 orm a Watson-Crick (WC) base pair depends on sequence context.

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

20 nisms were independent of the CEACAM1 intron sequence context.

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

22 iciently to methylated DNA within a specific sequence context.

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

24 ts of conformational coupling that vary with sequence context.

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

26 e fidelity of DNA synthesis depends on local sequence context.

27 misincorporated bases is influenced by local sequence context.

28 ivities for particular bases and surrounding sequence context.

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

30 base identity but is somewhat contingent on sequence context.

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

32 indow (positions 5-7) and in a confined TC*N sequence context.

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

34 g the methylation status of cytosines in any sequence context.

35 ance translation, depending on nascent chain sequence context.

36 gies at the base pair steps depending on the sequence context.

37 ce, chromatin structure, promoter shape, and sequence context.

38 pecificity for phosphopeptides in a specific sequence context.

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

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

41 detecting modifications within specific RNA sequence contexts.

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

43 NA duplexes containing AP sites in different sequence contexts.

44 y adjacent objects that belonged to distinct sequence contexts.

45 under identical conditions, using identical sequence contexts.

46 ed because of DNA methylation independent of sequence contexts.

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

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

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

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

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

52 plicated with high fidelity in virtually all sequence contexts.

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

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

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

56 kinetic evaluation of OGG1 in alternate DNA sequence contexts.

57 n complex with DNA substrates with different sequence contexts.

58 preference for DNA methylation in different sequence contexts.

59 mmodate a variety of mismatches in different sequence contexts.

60 regulation for EAL activity under different sequence contexts.

61 rice endosperm DNA is hypomethylated in all sequence contexts.

62 cation of modified RNA residues within their sequence contexts.

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

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

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

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

67 DNA polymerase fidelity within specific DNA sequence contexts.

68 ilters and k-mer embeddings to represent RNA sequence contexts.

69 ar descriptions of binding in representative sequence contexts.

70 APOBEC1 and edits efficiently in all tested sequence contexts.

71 si-A base pair in different nearest-neighbor sequence contexts.

72 ith relatively high efficiency in particular sequence contexts.

73 target cytosines for methylation in specific sequence contexts.

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

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

76 ate and an increased density of hypermutable sequence contexts.

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

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

79 HPV-negative OSCCs, T>C substitutions in the sequence context 5'-ATN-3' correlated with tobacco expos

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

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

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

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

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

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

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

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

88 ing the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR.

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

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

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

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

93 Motif frequency and sequence context analyses show the motifs (PyCG) related

94 AIndel leverages features derived from indel sequence context and biological effect in a machine-lear

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

96 mediated mutations can be dependent on local sequence context and can be predicted by computational m

97 rs both dependent and independent of protein sequence context and caused premature translation termin

98 negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs.

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

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

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 cids of the genetic code can act, in cognate sequence contexts, as destabilizing N-terminal residues.

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 rate was observed robustly for two different sequence contexts at different temperatures, both in the

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

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

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

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

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

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

135 defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of thi

136 rror patterns of NHEJ are strongly biased by sequence context, but these studies were based on relati

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

138 rates of CpG sites in favored and disfavored sequence contexts by forming compensatory interactions t

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

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

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

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

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

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

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

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

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

148 twork can improve m(6)A detection at trained sequence contexts compared to previously published metho

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

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

151 ine base editors (CBEs) that overcome target sequence context constraints of canonical CBEs.

152 t and the replication products for all three sequence contexts contained 85-90% AT and 5-10% TG.

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

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

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

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

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

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

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

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

161 Furthermore, C>T/G>A errors exhibit strong sequence context dependency, sample-specific effects dom

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

163 the 5' end of gRNA influenced unwinding in a sequence-context dependent manner.

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

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

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

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

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

169 The sequence context effect was studied for a mutational hot

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

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

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

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

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

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

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

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

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

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

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

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

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

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

184 ific and is found mainly in two separate DNA sequence contexts: GA and GGC.

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

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

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

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

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

194 The importance of genomic sequence context in generating transcriptome diversity t

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

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

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

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

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

200 ution campaigns is strongly dependent on the sequence context in which mutations are introduced, stem

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

202 s coli (APC) gene is mutated within specific sequence contexts in colorectal carcinomas but the under

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

204 induce C-to-G edits, particularly in AT-rich sequence contexts in human cells.

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

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

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

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

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

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

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

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

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

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

215 repressing transcription depending upon the sequence context it binds.

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

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

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

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

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

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

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

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

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

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

226 uORF use depends on the Kozak sequence context of its start codon, and uORFs with stro

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

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

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

230 In the sequence context of plant EPSPSs, alanine in place of gl

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

232 eporter assays, suggesting that the extended sequence context of tested elements and to a lesser degr

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

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

235 Overall, we show that the location and sequence context of the CpG in the viral genome determin

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

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

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

239 The sequence context of the labeling site was systematically

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

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

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

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

244 nd transcription factor function, and of the sequence context of their promoter motifs, as well as ac

245 ites of embedded rNMPs, study the nucleotide sequence context of these rNMPs and explore their genome

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

247 ded vectors contained an S (p)-Me-PTE in the sequence contexts of 5'-AT-3', 5'-CT-3', or 5'-GT-3', DN

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

249 The sequence contexts of indels targeting lineage-defining g

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

251 single genomic events; (ii) that an extended sequencing context of +/- 2 bp is required to more compl

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

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

254 ranscription factor binding motifs and local sequence context on p53-bound CRE activity.

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

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

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

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

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

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

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

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

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

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

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

266 Analysis of two sequence contexts reveals that DNA containing the UBP is

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

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

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

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

271 lls was A:T->C:G transversion, with a unique sequence-context specificity, i.e. flanking purines at t

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

273 Recently, the sequence context surrounding nuclease-induced double str

274 e maintaining efficient editing in all other sequence contexts tested.

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

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

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

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

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

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

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

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

283 in plant genomes occurs at CG, CHG, and CHH sequence contexts, the comparative roles of the individu

284 2 (DRM2), which methylates cytosines in all sequence contexts through an RNA-guided process, the CHR

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

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

287 ese data, we trained a model that uses local sequence context to predict the distribution of mutation

288 tations, some of which occur within specific sequence contexts to generate mutation hotspots.

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