ライフサイエンスコーパス: DNA motif

1 modular domains in a 42-base single-stranded DNA motif.

2 in reduced affinity of LOB for the consensus DNA motif.

3 their DNA binding domains and bind a common DNA motif.

4 ing a protein (URE3-BP) that recognized this DNA motif.

5 tiation genes that it controls at a CCNNAGGC DNA motif.

6 th two affinity ligands each conjugated to a DNA motif.

7 transcription, regardless of its recognition DNA motif.

8 ated separately through a conserved upstream DNA motif.

9 s involving known architectural proteins and DNA motifs.

10 exposure, thereby distinguishing particular DNA motifs.

11 ional regulators recognize and bind specific DNA motifs.

12 t are programmable for a large repertoire of DNA motifs.

13 lie common functional roles in other RNA and DNA motifs.

14 ining different approaches to discover novel DNA motifs.

15 members of the same subset and bind-specific DNA motifs.

16 b upstream that contains cytokine-responsive DNA motifs.

17 including cell wall components and specific DNA motifs.

18 of VDR.retinoid X receptor-alpha to discrete DNA motifs.

19 roplast DNA, and 15% to the seven repetitive DNA motifs.

20 mmon Pbx1 or E2a-Pbx1 partner bind different DNA motifs.

21 HLH-zip region and recognize the same CACGTG DNA motifs.

22 ubiquitously expressed, and recognize G-rich DNA motifs.

23 dification and DNA methylation patterns from DNA motifs.

24 red regions bind synergistically to adjacent DNA motifs.

25 of the FtsK-orienting polar sequence (KOPS) DNA motifs.

26 n forms homodimers that bind canonical G-box DNA motifs.

27 attenuated the latter's binding to promoter DNA motifs.

28 ion of most abundant double-stranded DNA (ds-DNA) motifs.

29 ents, and the extent of their hard-wiring by DNA motifs; (3) the potential to predict gene expression

30 of dot-blot hybridizations, seven repetitive DNA motifs accounted for >13% (194 kb) of the cucumber m

31 Here we present a new DNA motif and a strategy that has led to the assembly of

32 I hypersensitivity data in conjunction with DNA motif and other genomic features.

33 s were significantly enriched in the AATAATD DNA motif and specific chromatin contexts, including H3K

34 with an overall right-handed, antiparallel B-DNA motif and Watson-Crick base pairing throughout.

35 synthesis to identify candidate NiaR-binding DNA motifs and assess the NiaR regulon content in these

36 mics approach to infer candidate Rex-binding DNA motifs and assess the Rex regulon content in 119 gen

37 ies, TF family members often bind to similar DNA motifs and can confound sequence-based approaches to

38 ically identify 194 nonredundant palindromic DNA motifs and corresponding regulons in S. oneidensis.

39 The DNA motifs and CTP-dependent riboflavin kinase activity

40 ew analysis tools enable users to search for DNA motifs and define genes based on their genomic coloc

41 the target molecule triggers assembly of the DNA motifs and initiates the subsequent DNA strand displ

42 nalis genes was searched for overrepresented DNA motifs and known eukaryotic core promoter elements.

43 and a data yielded all of the four relevant DNA motifs and most of the known a- and alpha-specific g

44 comparative genomics approach, we identified DNA motifs and reconstructed regulons for 40 TunR family

45 parative genomics, we predicted SahR-binding DNA motifs and reconstructed SahR regulons in the genome

46 include transcription factors, their cognate DNA motifs and regulated genes/operons linked to the can

47 d TRP120-bound sequences revealed a G+C-rich DNA motif, and recombinant TRP120 specifically bound syn

48 gical processes, share unique cis-regulatory DNA motifs, and are enriched for binding of specific tra

49 d binding of transcription factors, variable DNA motifs, and bursts in gene expression.

50 Metallic nanoparticles can be attached to DNA motifs, and the arrangement of these particles can b

51 These data support the hypothesis that CpG DNA motifs are a "danger signal" that activates protecti

52 We find that these DNA motifs are also present in the muscle promoters of C

53 ctions between Ap2 and Sp1 and their cognate DNA motifs are critical for basal transcription from the

54 Our data indicate that these two DNA motifs are novel cis -regulatory elements and exhibi

55 n factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcriptio

56 ction in the gene, reveals that these (short DNA motifs) are more prevalent in exons that encode diso

57 HOT regions harbor specific DNA motifs, are enriched for differentially expressed ge

58 Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have hi

59 inity of a transcription factor to different DNA motifs, as it can model complex interactions that ar

60 have been developed for mapping promoters or DNA motifs associated with promoters.

61 This assay allows us to demonstrate G4 DNA motif-associated epigenetic instability in mutants o

62 ies demonstrates that Piwi binds a conserved DNA motif at approximately 72 genomic sites and inhibits

63 ng contrasting functional attributes of this DNA motif at different stages of myogenesis.

64 DNA motifs at several informative loci in more than 500

65 nt a method to measure the DeltaG degrees of DNA motifs at temperatures and buffer conditions of inte

66 ssociating genes frequently contain the same DNA motifs at their promoter regions, suggesting that po

67 is-regulatory sequence here corresponds to a DNA motif bound by a TF.

68 The DNA motif bound by BLIMP1 in vitro overlaps with that of

69 A DNA motif bound by CBP60g and SARD1, GAAATTT, was signif

70 ctly controlled by CviR, in part because the DNA motif bound by CviR is not well characterized.

71 wed that this T372R substitution changes the DNA motif bound by YY1.

72 pparently by disrupting interaction with the DNA motifs bound specifically by the recombinase.

73 we showed that in erythroid K562 cells these DNA motifs bound the following three transcription facto

74 controlled by Stat1/2 and Irf9 and the ISRE DNA motif, but others appeared dependent on non-canonica

75 zed with an ATP-binding aptamer-incorporated DNA motif can selectively release the intercalating doxo

76 Branched DNA motifs can be designed to assume a variety of shapes

77 ore, it has been speculated that these non-B DNA motifs can play regulatory roles in gene transcripti

78 The frequency of these six DNA motifs can predict housekeeping promoters as accurat

79 er activity, and mutagenesis showed that the DNA motif CCCTCCT is essential for GATA-2 promoter activ

80 omoter required a single hybrid MEF-2/GATA-4 DNA motif centered at -1256 base pairs.

81 Trans-acting factor binding to small DNA motifs (cis-elements) underlies regulatory complex a

82 We identified seven conserved DNA motifs (CM), CM1 to 7, that are present in the promo

83 gomeric complex binds to a unique, bipartite DNA motif comprising an E-box, CAGGTG, followed approxim

84 involving Lmo2 which can bind to a bipartite DNA motif comprising two E-box sequences approximately 1

85 by a novel mechanism and identify a specific DNA motif conducive to strong BLM binding and cleavage.

86 based on the predicted transcription-factor-DNA-motif connections.

87 A DNA motif consisting of an inverted repeat was identifie

88 A 6-base DNA motif consisting of an unmethylated CpG dinucleotide

89 n receptor gene rearrangement is directed by DNA motifs consisting of a conserved heptamer and noname

90 ted by a pyknon, a short 20 nucleotide-long DNA motif contained in the N-BLR transcript and is targe

91 inducible hnRNP, which can recognize a novel DNA-motif, controls the expression of the CR2 gene.

92 is footprint, two unrelated 30-bp cis-acting DNA motifs (designated TOAD and FROG) function as positi

93 De novo DNA motif discovery revealed new putative binding sites

94 P-chip experiments followed by computational DNA motif discovery.

95 In contrast, REX1 binds to DNA motifs divergent from YY1, but the binding motifs of

96 The binding-induced DNA TWJ makes use of two DNA motifs each conjugated to an affinity ligand.

97 ene superfamily characterised by a conserved DNA motif encoding the homeodomain.

98 ected a protein that binds specifically to a DNA motif encompassing the cap site.

99 Three DNA motifs enriched in crossover regions and less abunda

100 These factors and their target DNA motifs exhibited a hierarchy of DNA/protein and prot

101 DNA motif finding is one of the core problems in computa

102 promoter and the omlA promoter shared a 5-bp DNA motif for their -10 promoter elements.

103 ere instead characterized by the presence of DNA motifs for AP1 or STAT.

104 h synergistic interactions between consensus DNA motifs for binding of vitamin D receptor, AP1 and EL

105 ters the ability of Ikaros complexes to bind DNA motifs found in pericentromeric heterochromatin (PC-

106 Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprec

107 e physical interaction of Myc with the E-box DNA motif has been extensively characterized, but it is

108 This DNA motif has been identified in many genes that are spe

109 the breakpoint junctions revealed no common DNA motif; however, deletions, duplications, microhomolo

110 ntrinsic biases of SHM targeting on specific DNA motifs (i.e., hot and cold spots).

111 DMINDA (DNA motif identification and analyses) is an integrated

112 nd analyses) is an integrated web server for DNA motif identification and analyses, which is accessib

113 cooperatively bind an evolutionary conserved DNA motif in a target promoter.

114 Unlike most TFs, NF-Y can access its target DNA motif in inactive (nonmodified) or polycomb-represse

115 TFs were shown to bind to the same GCC-like DNA motif in OsRMC promoter and to negatively regulate i

116 hree copies of a conserved 18-bp palindromic DNA motif in the promoter of each ACG family member.

117 shows that PfAP2-I interacts with a specific DNA motif in the promoters of target genes.

118 ed structures self-assembled from individual DNA motifs in 1D, 2D, and finally 3D.

119 to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site data

120 d E2A-Pbx1 exhibit tight binding to specific DNA motifs in conjunction with certain other homeodomain

121 d to connect novel transcription factors and DNA motifs in E. coli.

122 We found an enrichment of some non-B DNA motifs in regulatory regions, and we show that this

123 In total, we obtained 209 unique DNA motifs in S. oneidensis that cover 849 unique transc

124 dentified significant enrichment of specific DNA motifs in the 1000 bp proximal promotor, some of whi

125 matode muscle genes, we identified conserved DNA motifs in the promoter regions using computational D

126 Based on the presence of kappaB-like DNA motifs in the region upstream of the TNF gene, some

127 We compared the distributions of non-B DNA motifs in the regulatory regions of operons with tho

128 d stabilized NF-Y interaction with CCAAT-box DNA motifs in vitro.

129 e predicted regulatory regions identified 31 DNA motifs, including 57.1% of experimentally validated

130 Stimulatory CpG DNA motifs induced B, T, and natural killer cells to sec

131 he integration of noncanonical and canonical DNA motif information yields new hypotheses on cobinding

132 Watson-Crick base pairing rules to assemble DNA motifs into diverse arrangements of geometric shapes

133 ect inverted repeat spaced by one nucleotide DNA motif, inverted repeat-1 (5'-AGGTCAcAGACCT-3'), as a

134 Half of the DNA motifs involved are matched to the existing motif da

135 The identification of the DNA motifs is a vital task for downstream analysis.

136 range coupling information between different DNA motifs is still lacking.

137 ial for binding to the vast majority of GATA DNA motifs, is strictly required for GATA-1-mediated ery

138 use monomeric Hox proteins bind very similar DNA motifs, it is unclear how they activate diverse deve

139 s gene transcription via a sequence-specific DNA motif known as the neuron-restrictive silencer eleme

140 ecombinant PtMYB4 protein is able to bind to DNA motifs known as AC elements.

141 ysis revealed putative Lrp-binding consensus DNA motifs located in P(hilA), P(invF), and P(ssrA).

142 a complicated arrangement of A-box and B-box DNA motifs located on opposite ends of a sharply bent pa

143 plified product strongly suggests that local DNA motifs may have contributed to the generation of thi

144 es of relatively frequent GC-rich cis-acting DNA motifs may offer reiterated binding sites to factors

145 MDscan can be used to find DNA motifs not only in ChIP-array experiments but also i

146 Hot spot-enriched A-rich and CTT-repeat DNA motifs occurred upstream and downstream, respectivel

147 Novel DNA motifs of archaeal DtxR-TFs that have a common palin

148 ding activity to methylated and unmethylated DNA motifs of distinct sequences.

149 CaCse4p-rich regions not only lack conserved DNA motifs of point (<400 bp) centromeres and repeated e

150 searching genomic DNA sequences with genomic DNA motifs (or matrices) that are representative of the

151 It was determined that a 14-bp novel DNA motif (oriLyt promoter activation element), which wa

152 study set of transcription factors and their DNA motifs, our method has a prediction accuracy of 59%

153 99 novel transcription factors and 70 novel DNA motifs, our method predicted 64 transcription-factor

154 er regions were found to contain a conserved DNA motif (p2(bp) box) identical in sequence and positio

155 probability of a given transcription-factor-DNA-motif pair being a true pair.

156 The coupling DNA motif pairs exhibit substantially higher DNase acces

157 to account together, we believe the coupling DNA motif pairs identified in this study can shed lights

158 -kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in

159 our method predicted 64 transcription-factor-DNA-motif pairs.

160 i, where they associate with the TCF-4/LEF-1 DNA motif positioned in the promoters of several importa

161 We identified 17,718 PDIs between 460 DNA motifs predicted to regulate transcription and 4,191

162 n (IL)-2 promoter as well as to a homologous DNA motif present in the proximal segment of the interfe

163 and in vivo to critical homeodomain binding DNA motifs present in the neuronal Pomc enhancers nPE1 a

164 Importantly, the gene sets and associated DNA motifs provide a starting point with which to explor

165 structure predictions available, including Z-DNA motifs, quadruplex-forming motifs, inverted repeats,

166 Because the DNA motif recognized by a transcription factor is typica

167 ns of endosperm cap-enriched genes contained DNA motifs recognized by ethylene response factors (ERFs

168 sults suggest that unique ligands may switch DNA motifs recognized by ligand-dependent transcription

169 from transcription start sites and contained DNA motifs recognized by regulators of cell-type identit

170 The binding-induced assembly of the DNA motifs results in the formation of a highly stable c

171 AC elements are DNA motifs rich in adenosine and cytosine that have been

172 For eukaryotic systems, however, some DNA motif(s) are capable of binding to a family of relat

173 The candidate NrtR-binding DNA motifs showed significant variability between microb

174 ulatory DNA sequences (ISS) containing a CpG DNA motif significantly inhibit airway eosinophilia and

175 n, were distinguished by clusters of a 10-bp DNA motif, suggesting a recruitment-and-spreading mechan

176 promoter region in these strains revealed a DNA motif (TAATGA) that was present in either one or two

177 ly be achieved with well-structured branched DNA motifs tailed by sticky ends.

178 ugh the upstream regulatory element 3 (URE3) DNA motif TATTCTATT.

179 pG (mCpG) sites and a specific nonmethylated DNA motif (TCCTGCNA) and represses transcription by recr

180 hFAST-1 protein was shown to bind to a novel DNA motif, TGT (G/T) (T/G)ATT, an exact copy of which wa

181 f the 100 promoters most enriched revealed a DNA motif that differs from the EBNA1 binding site in th

182 A helical sheets, and reveals a noncanonical DNA motif that has adaptive features that may be useful

183 Using PCR, we identified a specific DNA motif that is bound by Six3 and we demonstrated that

184 me-wide analysis of PGC7 reveals a consensus DNA motif that is recognized by PGC7.

185 nal analysis uncovered a novel homo-trimeric DNA motif that mediates the homo-trimeric DNA binding of

186 We used Gibbs sampling to define a CRP(Mt) DNA motif that resembles the cAMP receptor protein (CRP)

187 stness and potential utility of the many new DNA motifs that are becoming available.

188 Two DNA motifs that are conjugated to specific affinity liga

189 networks of Escherichia coli, we inferred 24 DNA motifs that are conserved in S. oneidensis.

190 sms to maintain epigenetic stability near G4 DNA motifs that are dependent on either REV1 or on the W

191 We have previously identified DNA motifs that are enriched in hot spots, particularly

192 We have previously identified DNA motifs that are enriched in hot spots, particularly

193 r, TCF/Arm mediated repression by binding to DNA motifs that are markedly different from typical TCF-

194 detects and responds to hypo-methylated CpG DNA motifs that are most commonly found in microbial gen

195 ive elements, including L1 and L2 LINEs, and DNA motifs that are significantly enriched around inacti

196 plementation of a novel strategy to identify DNA motifs that bind BLM strongly.

197 te targetting of Pbx heterodimers to related DNA motifs that differ in the sequence of their 3' half-

198 vity, in contrast to that mediated by kappaB DNA motifs that do not efficiently bind p65 homodimers,

199 e tracts of variable-length repeats of short DNA motifs that exhibit high rates of mutation in the fo

200 ties, and this may be useful for identifying DNA motifs that have similar functional properties that

201 (c) The architectures of the DNA motifs that lie adjacent to the G-quadruplex structu

202 network approach called GBNet to search for DNA motifs that may be cooperative in transcriptional re

203 umans and point to novel vertebrate-specific DNA motifs that might play a selective role in TATA-inde

204 do not appear to be demarcated by the usual DNA motifs that punctuate transcription in familiar euka

205 clones carried short (30-53 bp), repetitive DNA motifs that were often degenerate, overlapping, and

206 es of structurally but not textually related DNA motifs, that is, motifs whose consensus sequences ar

207 NF-Y recruits to neighboring DNA motifs the developmentally regulated, erythroid tran

208 proteins into the active ER complex with its DNA motif, the estrogen response element.

209 A new 3D-DNA motif, the ninja star, was self-assembled in quantit

210 bes and 2D arrays assembled from three novel DNA motifs, the 6-helix bundle (6HB), the 6-helix bundle

211 ethylated cytosine-phosphate-guanosine (CpG) DNA motifs through toll-like receptor 9, and we found th

212 ose methods that allow virtually any desired DNA motif to be targeted in vitro.

213 AIR lncRNA preferentially occupies a GA-rich DNA motif to nucleate broad domains of Polycomb occupanc

214 To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel a

215 A conserved DNA motif upstream of many xylose-induced genes was iden

216 are attributable to variation in a specific DNA motif upstream of the cagA transcriptional start sit

217 superstructures consisting of heterogeneous DNA motifs using dsDNA in conjunction with more complex,

218 ion factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regio

219 Nuclear extract binding to kappaB DNA motifs was measured by electrophoretic mobility shif

220 Finally, a preference for some non-B DNA motifs was observed near transcription factor-bindin

221 e signaling and structural features into the DNA motifs, we envision diverse applications in biosensi

222 GATA factors interact with simple DNA motifs (WGATAR) to regulate critical processes, incl

223 DNA with RNA dangling-end motifs shows that DNA motifs with 5' dangling ends contribute to stability

224 te to this goal by combining stable branched DNA motifs with cohesive ends to produce programmed nano

225 ate DNA tessellations by employing multi-arm DNA motifs with low symmetry.

226 This program searches for a given DNA motif within the entire genome of one species and us

227 howed that the distribution of several non-B DNA motifs within intergenic regions separating divergen

228 and IL-4, respectively, and bind to specific DNA motifs within the ECS.

229 on-B DNA transition-susceptible sites (non-B DNA motifs) within the context of the operon structure o

230 mapping indicates both domains bind poly(C) DNA motifs without disrupting the KH1-KH2 interaction.