ライフサイエンスコーパス: core promoter

1 ed, composite Ets/E-box motifs enclosing the core promoter.

2 pre-initiation complex (PIC) assembly at the core promoter.

3 PE), which confer specific properties to the core promoter.

4 a 59-bp sequence immediately upstream of the core promoter.

5 is highly dependent on the RNA polymerase II core promoter.

6 PE), which confer specific properties to the core promoter.

7 DPE]) that confer specific properties to the core promoter.

8 auses a dramatic increase in Mediator at the core promoter.

9 ertional mutagenesis of the Drosophila Hsp70 core promoter.

10 cally acts by enhancing TFIID binding to the core promoter.

11 se) promoter to positions -36 and -11 of the core promoter.

12 th the 5' barrier region including the ANK1E core promoter.

13 ing DNA elements to RNA polymerase II at the core promoter.

14 pression in heart lies within the CpG island core promoter.

15 orm the basal transcription machinery at the core promoter.

16 of a functional FoxO1-binding site in MAO A core promoter.

17 pancy by Sp1 were shown at the natural MAO B core promoter.

18 nce of a nucleosome-free region at the hTERT core promoter.

19 rtner, and through Miz-1 binds to the CDKN1A core promoter.

20 tein-DNA contacts that occurs throughout the core promoter.

21 nization of key subregions in the downstream core promoter.

22 nscription factor (TF) motif profiles at the core promoter.

23 more unified conceptual understanding of the core promoter.

24 as a dynamic bridge between the enhancer and core promoter.

25 ubunits, is among the first GTFs to bind the core promoter.

26 rs to the RNA polymerase II machinery at the core promoter.

27 nate from their own cognate reverse-directed core promoters.

28 esence of both forward- and reverse-directed core promoters.

29 ith PPARgamma at enhancers and TBP/Pol II at core promoters.

30 actor, can robustly activate HBV surface and core promoters.

31 iator (INR) element but not from "TATA-only" core promoters.

32 ailless Mediator nevertheless interacts with core promoters.

33 repeat element (MSR1) adjacent to the PRPF31 core promoter; (2) in vitro, 3-copies of the MSR1 elemen

34 A rare point mutation in the core promoter -270GC-rich box of PIGM, a housekeeping ge

35 The core-promoter, a stretch of DNA surrounding the transcri

36 n the putative KLF15 binding site in the HBV core promoter abolished the ability of KLF15 to activate

37 resulted in a reduction in HBV surface- and core-promoter activities.

38 Deletion analysis revealed that the core promoter activity to be embedded in a region betwee

39 , 27 to 29, and 30 to 33) that contribute to core promoter activity.

40 we found a 75% decrease in activity of Agxt2 core promoter after disruption of the HNF4alpha binding

41 by stabilizing TFIID contacts with both the core promoter and a region within p53's response element

42 1 and c-Myc are both recruited to the CDKN2B core promoter and act in collaboration to repress CDKN2B

43 ontrol of DNA stereochemistry, reshaping the core promoter and making it a better or worse substrate

44 directed mutagenesis studies showed that the core promoter and PAX5 binding region to be between -79

45 The HBV basal core promoter and precore/core gene sequences were also

46 e SAGA pathway located largely distal to the core promoter and regulators of the TFIID pathway locate

47 ction by binding to a DNA site overlapping a core promoter and stimulating isomerization of an initia

48 romotes the binding of purified TFIID to the core promoter and that the TAF6 and TAF9 subunits of TFI

49 , KLF15 binds to DNA probes derived from the core promoter and the surface promoter.

50 Here we analyse the human Pol II core promoter and use machine learning to generate predi

51 ation of pre-initiation complex (PIC) at the core promoter and, consequently, transcriptional initiat

52 machineries recognizing distal enhancers and core promoters and by the high-order spatial organizatio

53 cluding mRNA and long noncoding RNA (lncRNA) core promoters and enhancer RNAs (eRNAs).

54 tal gene regulatory elements, including gene core promoters and enhancers, are important in the contr

55 Empirically, TSSs define the coordinates of core promoters and other regulatory sequences.

56 strongly with the enhancer, but not with the core promoter, and it dissociates from the enhancer upon

57 6% of yeast genes are controlled by multiple core promoters, and alternative core promoter usage by a

58 arily encoded in enhancers and burst size in core promoters, and that allelic single-cell RNA sequenc

59 ing shows that CG dinucleotides in the Cosmc core promoter are hypermethylated.

60 polymerase II transcriptional machinery and core promoter are inherently unidirectional and that rev

61 clic AMP response element (CRE) in the ITGB8 core promoter are required for its expression and that S

62 Core promoters are critical regions for gene regulation

63 Core promoters are crucial for gene regulation, providin

64 results contribute to the emerging view that core promoters are functionally diverse and control patt

65 Notably, core promoters are hypomethylated, and transcript levels

66 Eukaryotic core promoters are often characterized by the presence o

67 tes located immediately upstream of the TERT core promoter, as a cancer-associated epigenetic mechani

68 DNA consensus motifs of early and late ASFV core promoters, as well as a polythymidylate sequence de

69 Precore (PC) (G1896A) and basal core promoter (BCP) (A1762T/G1764A) mutations of the hep

70 res to presence of precore (PC) and/or basal core promoter (BCP) mutants and studied kinetics of hepa

71 ether the presence of precore (PC) and basal core promoter (BCP) mutants before PEG-IFN treatment aff

72 e A1762T/G1764A double mutation in the basal core promoter (BCP) region is associated with HBe antige

73 We also compared the core promoters between YRI (Yoruba in Ibadan, Nigeria) a

74 serve as a docking site for TFIID, the major core promoter-binding factor.

75 es for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficien

76 does not affect Mediator association at the core promoter but increases occupancy at enhancers.

77 confirmed the hypermethylation of the Cosmc core promoter but not for T-synthase.

78 ndicating that nucleosomal deposition at the core promoter, but not histone deacetylation, was the ca

79 ctors and the transcription apparatus at the core promoter, but this process is not well understood.

80 in parallel in two species, indicating that core promoters can be an important natural source of the

81 Constellations of core promoters can generally be reduced to pairs of dive

82 elated factor 2 (Trf2) are components of the core promoter complex required for gene/tissue-specific

83 sults provide evidence for the importance of core promoter composition in the regulation of Dorsal ta

84 bryo extracts, we have demonstrated that the core promoter composition is an important determinant of

85 Core promoters consist of core promoter motifs, e.g. the

86 ooperate to enhance basal transcription from core promoters containing both a TATA box and an Initiat

87 hat the erythroid-specific ankyrin 1 (ANK1E) core promoter contains a 5' DNase I hypersensitive site

88 Core promoter controls the initiation of transcription.

89 In addition, EBV and KSHV late gene core promoters could be activated by MHV-68 lytic replic

90 en by pregenomic RNA, which is controlled by core promoter (CP) and further augmented by enhancer I (

91 Mutations in the hepatitis B virus (HBV) core promoter (CP) have been shown to be associated with

92 al studies have associated hepatitis B virus core promoter (CP) mutations with an increased risk of h

93 ose a hierarchical regulatory model in which core promoters define broad windows of opportunity for e

94 The dissection of overlapping core promoter determinants represents a framework for fu

95 The two classes of core promoters display distinctive patterns in transcrip

96 hich specifically interact with a variety of core promoter DNA sequences.

97 ure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-el

98 TBP binds to core promoter DNA, recognizing the TATA-box.

99 ne assays showed that TDP-43 represses acrv1 core promoter-driven transcription via the N-terminal RR

100 s a strong preference for TATA-like motif in core promoters driving sharp TSS selection, in contrast

101 rs that are dependent on a TCT or downstream core promoter element (DPE) motif.

102 nr), motif ten element (MTE), and downstream core promoter element (DPE) promoter motifs within the T

103 h as the TATA box, initiator, and downstream core promoter element (DPE), which confer specific prope

104 the initiator, TATA box, and the downstream core promoter element (DPE), which confer specific prope

105 eotides 18 to 22 and 27 to 29), a downstream core promoter element (nucleotides 27 to 29 and 30 to 33

106 he TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific proper

107 M1BP binds a core promoter element called Motif 1.

108 that was able to bind to and function via a core promoter element called the Initiator (Inr).

109 NA initiator (Inr) element has been the only core promoter element described in the divergent unicell

110 However, each mutated core promoter element had a distinct effect on expressio

111 The TCT core promoter element is present in most ribosomal prote

112 rDNA transcription factor that binds to the core promoter element of the rDNA.

113 ied directly by the position of a particular core promoter element or the first nucleosome.

114 how that the DPR is a functionally important core promoter element that is widely used in human promo

115 In search of another core promoter element(s), a nonredundant database contai

116 genomic repeat structure constitutes a novel core promoter element, coincides with human evolution, a

117 ensus sequence for the human initiator (Inr) core promoter element.

118 We show that core promoter elements affect burst size and uncover syn

119 e in Pol II pausing correlates with distinct core promoter elements and associates a TATA-enriched pr

120 le in transcription initiation by binding to core promoter elements and directing preinitiation compl

121 ion at many promoters by binding upstream of core promoter elements and interacting with the C-termin

122 criptional activators act at a distance from core promoter elements and work by recruiting RNA polyme

123 All core promoter elements are contacted by subunits of TFII

124 colleagues demonstrate the critical role of core promoter elements at p53 target loci, in that they

125 t, raising interesting possibilities for how core promoter elements contribute to defining promoters

126 hat the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription.

127 ers lack the previously identified canonical core promoter elements except for the Inr.

128 Core promoter elements function beyond initiation, and w

129 The role of core promoter elements in regulating transcription initi

130 of gene promoters is not due to conventional core promoter elements or splicing signals.

131 Furthermore, several core promoter elements that are absent in the slob57 pro

132 The ability of core promoter elements to modulate transcriptional burst

133 requency, but the contribution of individual core promoter elements to transcriptional bursting is no

134 the DNA sequences of BvgA-binding motifs and core promoter elements would indicate the opposite.

135 ough paused Pol II stability correlates with core promoter elements, the contribution of individual s

136 olymerase II (Pol II) is dictated in part by core promoter elements, which are DNA sequences flanking

137 -depleted regions, and are more enriched for core promoter elements, which largely differ between tis

138 vast majority of locations contain the four core promoter elements- upstream TFIIB recognition eleme

139 contributions to bursting of the individual core promoter elements-CCAAT, TATAA-like, Sp1BS, and Inr

140 nal analyses demonstrate that both are novel core promoter elements.

141 rrepresented DNA motifs and known eukaryotic core promoter elements.

142 a 69 bp segment in P(shr) that overlaps the core promoter elements.

143 ally significant local overrepresentation of core promoter elements.

144 te (TSS) at variable distances downstream of core promoter elements.

145 cription can occur in the absence of defined core-promoter elements.

146 Core promoters encompass the RNA start site and consist

147 Here, we report that TAF3, a TBP-associated core promoter factor, is highly enriched in ES cells.

148 istic insights for the role of gene-specific core promoter factors and implications for cell cycle-re

149 vage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-qua

150 o an RNA element named SLC that contains the core promoter for genomic minus-strand RNA synthesis.

151 ciferase assays led to the identification of core promoters for both PRPF31 and TFPT; despite their s

152 omprehensive TSS maps allowed us to identify core promoters for ~96% verified protein-coding genes.

153 Here, we explored the importance of core promoter functions in the dorsal-ventral developmen

154 Core promoters, generally defined as the regions that di

155 Core promoters, generally not thought to play a signific

156 ns but also from non-coding region including core promoters generated by random fragmentation in exom

157 We find that both divergent lncRNA and mRNA core promoters have higher capacities to drive transcrip

158 otic RNA polymerase II on different types of core promoters have remained elusive.

159 s in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and develo

160 ion of the cps genes not only depends on the core promoter immediately upstream of cps2A, but also re

161 provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animal

162 sor non-metastatic 2 (NME2) within the hTERT core promoter in HT1080 fibrosarcoma cells and HCT116 co

163 f DNA transcription(1-5), but the downstream core promoter in humans has been difficult to understand

164 olished the ability of KLF15 to activate the core promoter in luciferase assays.

165 biting the interaction of SP1 with the Fbxl2 core promoter in proliferating myoblasts.

166 RNA polymerase for initiation at a consensus core promoter in vitro and in vivo; we define the TSS-re

167 tor complex associates with the enhancer and core promoter in vivo, indicating that it can physically

168 e results demonstrate the regulatory role of core-promoters in cell-cycle-dependent transcription reg

169 ebrates, the basal machinery recognizing the core promoter includes TATA-binding protein (TBP) and tw

170 responding to environmental cues, we divided core promoters into constitutive class (55%) and inducib

171 The RNA polymerase II core promoter is a diverse and complex regulatory elemen

172 A core promoter is a stretch of DNA surrounding the transc

173 The RNA polymerase II core promoter is a structurally and functionally diverse

174 here the chromatin architecture of the ITGB8 core promoter is altered by nucleosomal repositioning th

175 The core promoter is diverse in terms of its composition and

176 the Salmonella enterica serovar Typhimurium core promoter is more active than previously thought, du

177 itiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex

178 The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of th

179 The RNA polymerase II core promoter is the ultimate target of a multitude of t

180 Therefore, comprehensive characterization of core promoters is essential to understand normal and abn

181 d given the proximity of the -237 SNP to the core promoter, its location within a putative repressor

182 by the dissociation of HDAC2 with the ITGB8 core promoter, leading to increased histone H4 acetylati

183 h) but inhibited SP1 transactivation of its core promoter, localized to bp -160 to +42 within the pr

184 ubunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, w

185 individual, we characterized the features of core promoter-mapped exome sequences, and analysed core-

186 clude that polymorphisms within the NOD Ica1 core promoter may determine AIRE-mediated down-regulatio

187 gene and that polymorphisms within the Ica1 core promoter may partially determine this transcription

188 nt of EVDC (Exome-based Variant Detection in Core promoters) method for genome-scale analysis of core

189 tter observation suggested that an alternate core promoter might be present in the downstream segment

190 nd T-tracts, in combination with a PWM-based core promoter model, accurately predicted promoter stren

191 ng both upstream sequences (UP-elements) and core promoter modules, based on a set of 60 promoters de

192 27 to 29 and 30 to 33), and a novel "bridge" core promoter motif (nucleotides 18 to 22 and 30 to 33).

193 able chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-

194 similarity to the known protein-coding gene core promoter, motif 3 (M3) and motif 5 (M5), were ident

195 nscription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [I

196 hat eQTLs also frequently disrupt some known core promoter motifs but, surprisingly, are not enriched

197 Core promoters consist of core promoter motifs, e.g. the initiator, TATA box, and

198 many human promoters have none of the known core promoter motifs, suggesting that undiscovered promo

199 er the subsequent emergence of A1762T/G1764A core promoter mutations to upregulate replication; effic

200 The A1762T/G1764A core promoter mutations were prevalent in genotype C iso

201 sociated with the more frequent emergence of core promoter mutations, which increase genome replicati

202 Kingdom, HBeAg status, and precore and basal core promoter mutations.

203 served between the promoter distal sites and core promoters occupied by TAF3/CTCF/cohesin.

204 nteraction between this +6-kb region and the core promoter of Cebpe using circular chromosome conform

205 ion factor TFIID recognizes specifically the core promoter of genes transcribed by eukaryotic RNA pol

206 uences that are faithfully integrated at the core promoter of individual genes.

207 escribe two independent mutations within the core promoter of telomerase reverse transcriptase (TERT)

208 orphism at position -1377 (rs2234767) in the core promoter of the CD95 cell death receptor gene in 70

209 upstream IFN response element and downstream core promoter of the class I gene.

210 Here we identified the core promoter of the TDP1 gene, which contains a conserv

211 y and functionally connect the enhancers and core promoters of active genes in murine embryonic stem

212 rs coexist, often physically overlapping, in core promoters of constitutively expressed genes to enab

213 Computer simulations of the core promoters of two pluripotency markers reveal associ

214 activating sequences (UASs) rather than the core promoter or gene body under all conditions tested.

215 c building blocks of divergently transcribed core promoter pairs, in combination with the wealth of T

216 requires additional elements upstream of the core promoter, particularly a 59-bp sequence immediately

217 terminus of Caudal was sufficient to confer core promoter-preferential activation to the heterologou

218 l that enables the co-activation of ftz in a core promoter-preferential manner.

219 n an effort to better understand the role of core promoter recognition and coactivator complex switch

220 s to determine if a novel and as yet unknown core promoter recognition complex takes the place of TFI

221 In addition to its role in the core promoter recognition complex TFIID, genome-wide bin

222 Recent findings implicate alternate core promoter recognition complexes in regulating cellul

223 e points to an unexpected diversification of core promoter recognition complexes that serve as import

224 he general transcription machinery including core promoter recognition complexes, coactivators, and c

225 ing an interaction between a "nonprototypic" core promoter recognition factor (Trf2) and an orphan TA

226 Here we examine the details of core promoter recognition in bacteria that reveal the tr

227 addressed promoter prediction using natural core promoters recognized by the well-studied alternativ

228 human MAPT 5'-flanking region, including the core promoter region (-302/+4), neurospecific domains (-

229 enerate predictive models for the downstream core promoter region (DPR) and the TATA box.

230 cilitates stable nucleosome depletion at the core promoter region and enhances gene expression stabil

231 iguity of the role of methylation within the core promoter region and the subsequent binding of vario

232 Thus, we set out to identify the core promoter region and the transcription factor respon

233 we found that eight CG dinucleotides in the core promoter region are sufficient for strong methylati

234 ates ATP6V1A, we discovered that the ATP6V1A core promoter region contains three YY1 binding sites.

235 sted that epigenetic modulation of the hTERT core promoter region may provide an additional level of

236 ed in a yeast one-hybrid screening using the core promoter region of GluB-1 as bait and cDNA expressi

237 n two accessions of limetta, a change in the core promoter region of Noemi is associated with reduced

238 Surprisingly, deletion of the core promoter region of the major immediate early promot

239 bp deletion (allele frequency 0.76%) in the core promoter region on the other allele.

240 the capsule operon is required and that the core promoter region plays a central role in fine-tuning

241 ption factor M1BP, which associates with the core promoter region, activates transcription of RP gene

242 ability, greater nucleosome depletion at the core promoter region, and more strongly positioned nucle

243 the AT2R transcription start site contain a core promoter region, and regions upstream of 70 bp to 3

244 some, as reflected by the Hmo1 extension and core promoter region.

245 , probably through targeting the polymorphic core promoter region.

246 loser to TSSs, being largely absent from the core promoter region.

247 ional attractive free energy per protein per core-promoter region.

248 Moreover, we find that 22% of common SNPs in core promoter regions have significant regulatory effect

249 nery that binds to TATA boxes located in the core promoter regions of many genes.

250 r levels of binding to interleukins 2 and 10 core promoter regions of the transcription factor cyclic

251 Analysis of core promoter regions shows that eQTLs also frequently d

252 Importantly, core promoter regions tended to have lower H3Ac levels i

253 Our screen identified mutations in core promoter regions, including Sp1 and TATA transcript

254 while RNAPII and MYC preferentially bound to core promoter regions.

255 ght the role of short TRF2 as a preferential core promoter regulator.

256 genome-wide identification of the pri-miRNA core promoter repertoire and its dynamic usage during ze

257 nscription than nondivergent lncRNA and mRNA core promoters, respectively.

258 Instead, deletion of the MIEP core promoter resulted in increased expression of altern

259 Core promoter sequence change can disrupt transcriptiona

260 divergent initiation, similar frequencies of core promoter sequence elements, highly positioned flank

261 On the other hand, replacement of the core promoter sequence of genotype G with genotype A seq

262 tly, most genotype C isolates with wild-type core promoter sequence replicated less efficiently than

263 for genome-wile de novo characterization of core promoter sequence variation.

264 omoters) method for genome-scale analysis of core-promoter sequence variation.

265 depleted at their upstream edges of reverse core promoter sequences and their associated chromatin f

266 apturing enhancer function, and confirm that core promoter sequences are necessary for this activity.

267 cription is generally dependent on the sense core promoter sequences, and that most enhancers and sev

268 of activators that bind close to or overlap core promoter sequences, directing the transcriptional m

269 Most core promoter shifts are coupled with altered gene expre

270 ons in the KLF15 response element in the HBV core promoter significantly reduced viral DNA levels in

271 Our results suggest a core promoter-specific regulation of Mediator and the ba

272 Enhancer-core promoter specificity may provide one solution.

273 tes also utilize similar strategies to alter core promoter specificity, from specificity factor excha

274 also describe conservation of four distinct core promoter structures composed of combinations of ele

275 DNA sequence signals in the core promoter, such as the initiator (Inr), direct trans

276 rongly positioned nucleosomes that flank the core promoter than do head-to-tail genes.

277 dditionally describe an expanded view of the core promoter that comprises the classical DNA sequence

278 We designed a CG-deficient core promoter that is resistant to MeCP2-mediated repres

279 ed that the LTA downstream segment alternate core promoter that produces the LTA TV8 transcript most

280 -related factor 2 (TRF2) activates TATA-less core promoters that are dependent on a TCT or downstream

281 ctivity resides in a small domain of the AGT core promoter; this domain contains binding sites for hy

282 ly, mutp53 is recruited by Sp1 to the ENTPD5 core promoter to induce its expression.

283 of the ATG initiation codon) containing the core promoter, transcription start site, and the TRE wer

284 dx1, mCdx2, and mCdx4) are also preferential core promoter transcriptional activators.

285 by multiple core promoters, and alternative core promoter usage by a gene is widespread in response

286 gene expression, indicating that alternative core promoter usage might play an important role in cont

287 We have systematically varied core promoters, UTRs, operator sequences, and transcript

288 romoter-mapped exome sequences, and analysed core-promoter variation in this individual genome.

289 udy demonstrates in a vertebrate embryo, how core-promoter variations define transcriptional output i

290 tingly, the LTA downstream segment alternate core promoter was active only after specific cellular st

291 To gain a better understanding of the core promoter, we examined the motif 10 element (MTE), w

292 itiate transcription from most tested Pol II core promoters when assayed with crude human nuclear ext

293 r instance, TBP activates TATA-box-dependent core promoters, whereas TBP-related factor 2 (TRF2) acti

294 ption initiates at multiple sites within the core promoter, which contains elements homologous to the

295 7L/JPO2), that down-regulate MAO B via MAO B core promoter, which contains Sp1 sites.

296 of transcription ultimately converge at the core promoter, which is the gateway to transcription.

297 f Mediator is mediated by Head and Middle at core promoters, while Tail and CKM play regulatory roles

298 ave identified and characterized a TATA-less core promoter with an NFAT/IRF-4 composite binding site

299 preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold.

300 d mithramycin A treatment, we identified the core promoters within cCpG-II and tCpG, which contain tw