ライフサイエンスコーパス: transcription start site

1 t deletion (nt -146 to -1008 relative to the transcription start site).

2 ocated proximal to and upstream of the AICDA transcription start site.

3 ly spaced nucleosomes phased relative to the transcription start site.

4 g 91 bp upstream and 60 bp downstream of the transcription start site.

5 f the Il2 gene located 83 kb upstream of the transcription start site.

6 ement located around 2 kb upstream of SQSTM1-transcription start site.

7 nteraction between Ubx enhancers and the Ubx transcription start site.

8 e NF-kappaB-binding elements upstream of the transcription start site.

9 ent (HRE) located at bp -190 upstream of the transcription start site.

10 ine (CpG) dinucleotides proximal to the NOS2 transcription start site.

11 2 binding site in the KLF4 promoter near the transcription start site.

12 bind to a DNA fragment upstream of the bmp2b transcription start site.

13 ve been identified upstream of the rhodopsin transcription start site.

14 ipt levels acquired DNA methylation near the transcription start site.

15 Fn14 promoter contains a CpG island close to transcription start site.

16 d between 3384 and 1560 bp upstream from the transcription start site.

17 ment located 1200 base pairs upstream of the transcription start site.

18 GC-rich regions located within 633 bp of the transcription start site.

19 sitive element located upstream of the major transcription start site.

20 d one approximately 150 kb downstream of the transcription start site.

21 S2 gene is highly methylated around the NOS2 transcription start site.

22 of RNA polymerase II just downstream of the transcription start site.

23 ity factor for the recognition of a specific transcription start site.

24 nwinding of the DNA duplex downstream of the transcription start site.

25 n the promoter region 1.5 kb upstream of the transcription start site.

26 nstitutive promoter, initiated from a single transcription start site.

27 ariants, all of which initiate from a single transcription start site.

28 ospZ gene but over 1 kb upstream of the icsP transcription start site.

29 f vnfDG that was initially identified as the transcription start site.

30 he repressive H3K27me3 modification near its transcription start site.

31 e, which is located downstream of the mapped transcription start site.

32 ions, on the basis of their proximity to the transcription start site.

33 t exons (ALEs) that are more proximal to the transcription start site.

34 histone H4 at tyrosine 88 upstream of the AR transcription start site.

35 d by a function of genomic distance from the transcription start site.

36 in the upstream sequence within 3 kb of the transcription start site.

37 ic location of dCas9 binding relative to the transcription start site.

38 otein production is achieved via alternative transcription start sites.

39 Zta binds mostly to sites that are distal to transcription start sites.

40 nfiguration in which Pol II accumulates near transcription start sites.

41 n, extending tens of kilobases downstream of transcription start sites.

42 ignificance for effective MLV integration at transcription start sites.

43 tural sequence, (GGGGA)4, downstream of many transcription start sites.

44 two main transcripts that utilise different transcription start sites.

45 erns for peaks closer to versus further from transcription start sites.

46 ions and enhanced nucleosome deposition over transcription start sites.

47 by Tip60-p400 in ESCs, binding downstream of transcription start sites.

48 Moreover, OGT associates with TET2 at transcription start sites.

49 anking a nucleosome depleted region (NDR) at transcription start sites.

50 ence, reduced MLV-integration frequencies at transcription start sites.

51 including peaks identified in enhancers and transcription start sites.

52 translated regions and also present multiple transcription start sites.

53 B4-truncated transcripts displaying intronic transcription start sites.

54 e, feed-forward loops and use of alternative transcription start sites.

55 ctivity, a putative initiator element at the transcription start site acts as a target for negative r

56 id amplification of cDNA ends cloning mapped transcription start sites adjacent to the AS promoter.

57 enomic regions upstream or downstream of the transcription start site allows for specific and sustain

58 cant enrichment in G4 sequence motifs at the transcription start site and 5' ends of first introns (f

59 an increase of relative 5(me)C levels at the transcription start site and a decrease in the gene-body

60 arly elongation within 500 base pairs of the transcription start site and akin to its bacterial homol

61 positioning has previously been described at transcription start site and flanking TF binding sites.

62 nds to promoter DNA, melts ~14 bp around the transcription start site and forms a single-stranded "tr

63 evealed itself only with focused analyses of transcription start site and gene body regions (in contr

64 he triplet enrichment and depletion near the transcription start site and identify triplets that have

65 +1 nucleosome which, in yeast, obstructs the transcription start site and is frequently assembled wit

66 pression, we corrected the identified Bcl11b transcription start site and mapped a cell-type-specific

67 fects of nucleotide sequence at and near the transcription start site and spacing between the start s

68 that juxtapose the RARE element with the 5' transcription start site and the 3' end of the genes.

69 ining genes, R-loops are bounded between the transcription start site and the first exon-intron junct

70 ors located many kilobases downstream of the transcription start site and to produce invariably tight

71 creased recruitment of RNA polymerase to the transcription start site and upregulation of target oper

72 between -7585 and -5550 bp ahead of the main transcription start site and via an NF-kappaB-dependent

73 q reveal enrichment of Lin28A binding around transcription start sites and a positive correlation bet

74 eosomes positioned immediately downstream of transcription start sites and at different densities acr

75 EBNA1 binding sites are located proximal to transcription start sites and correlate genome-wide with

76 ted differential regulation of distinct ANK3 transcription start sites and coupling of specific 5' en

77 t in decreasing its integration frequency at transcription start sites and CpG islands, thereby reduc

78 oteins guide gamma-retroviral integration to transcription start sites and enhancers through bimodal

79 es well-positioned nucleosomes downstream of transcription start sites and flanking splice sites.

80 Our systematic study determines 3,570 transcription start sites and identifies 230 small RNAs

81 ugh DNase-I hypersensitive sites (DHSs) near transcription start sites and independently through 3' U

82 f Setd5, histone acetylation is increased at transcription start sites and near downstream regions.

83 lts suggest a model in which MuvB binds near transcription start sites and plays a role in positionin

84 Using 5' RACE, we identified three transcription start sites and several splice variants of

85 nd aligns important genomic features such as transcription start sites and splicing sites from histon

86 at the distribution of distances between the transcription start sites and the translation initiation

87 esignated nucleosome-depleted regions around transcription start sites and transcription termination

88 gulates glucose-induced H3 K9 acetylation at transcription starting site and enhancer regions.

89 pproximately 100 bases upstream of the CEBPA transcription start site, and demonstrated through mutat

90 oth polymerases often initiate from the same transcription start site, and depend on a TATA box or AT

91 racterized the promoter regions, defined the transcription start site, and identified a mechanism of

92 ously thought, due to differences around the transcription start site, and that its expression is rep

93 ximately 44 kb DNA spanning promoter region, transcription start site, and the CAG expansion mutation

94 located in the 177-bp region upstream of the transcription start site, and this region did not contai

95 lity, enhancer activity, and distance to the transcription start site are features of dose-sensitive

96 n RNAP-promoter interactions upstream of the transcription start site are strong and promoter melting

97 s that nucleosomes immediately downstream of transcription start sites are anchored and recapitulates

98 The majority of transcription start sites are associated with distal or

99 shows that, in plants, the vast majority of transcription start sites are TATA free and are defined

100 igher effect size, are located closer to the transcription start site, are more significant, and tend

101 longation complexes or the fate of the short transcription start site-associated (tss) RNAs they prod

102 m ends extend from +3 to +21 relative to the transcription start site at +1.

103 the cps genes are cotranscribed from a major transcription start site at the -25 nucleotide (G) upstr

104 d tup12(+), although the distribution of the transcription start sites becomes broader than that in w

105 stalled state immediately downstream of the transcription start site before productive elongation.

106 ws reduction of occupancy, preferentially at transcription start sites, but occupancy at enhancer sit

107 of naked DNA, and chromatin gave patterns of transcription start sites closely similar to those occur

108 We examined transcription start site consensus NOL plots for maize g

109 significantly clustered near RNA polII-bound transcription start sites, consistent with the reports t

110 nd found that the 70 bp upstream of the AT2R transcription start site contain a core promoter region,

111 fications (H3K4me3 and H3K9/14ac) around the transcription start site correlates with the position of

112 of activation of every cell-cycle regulatory transcription start site, coupled to both the position o

113 m novel first exons consistent with existing transcription start site data.

114 ion, a nucleosome occluding the TATA box and transcription start sites did not impede transcription b

115 growth through utilization of an alternative transcription start site driven by the master filamentat

116 ic disorders, decreases usage of an upstream transcription start site encoding a longer 5'UTR with gr

117 We found that distance to the transcription start site, evolutionary constraint, and e

118 as the presence of epigenetic marks at their transcription start sites, evolutionary conservation amo

119 By moving Zif268 binding sites toward the transcription start site, expression output can be nearl

120 te strand around position -4 relative to the transcription start site facilitates unwinding of the DN

121 uences extending nearly 2 kb upstream of the transcription start site for 68 alleles from 57 major li

122 5' RACE indicates a transcription start site for HYDIN2 outside of the dupli

123 ole of the Ets2 binding site proximal to the transcription start site for LPS responsiveness.

124 isoform of TET1 (TET1ALT) that has a unique transcription start site from an alternate promoter in i

125 uch as ChIP-seq peaks for a given protein or transcription start sites from known gene models.

126 n variant, rs2395471, 800 bp upstream of the transcription start site, gave the most significant asso

127 icating that RNAs synthesized from different transcription start sites have different functions in vi

128 notably that hypomethylated intervals around transcription start sites have evolved to be considerabl

129 ions and the majority were located distal to transcription start sites, highlighting the importance o

130 omatin regions lie within 3 kb upstream of a transcription start site in all species.

131 t several epigenetic factors use alternative transcription start sites in different cell types.

132 sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages

133 of Bacteriology, Thomason and colleagues map transcription start sites in Escherichia coli on an unpr

134 demonstrate structural similarities between transcription start sites in the genomes of four Drosoph

135 's enrichment or biased distribution towards transcription start sites in the promoters of co-express

136 overing about 8000 bp flanking the predicted transcription start sites in Xenopus tropicalis for geno

137 heir roles in nucleosome phasing relative to transcription start sites in yeast.

138 nd DNA mutations allowed us to reprogram the transcription start sites, in a way that can be describe

139 he two nucleosomes immediately distal to the transcription start site, independently of gene length.

140 for example, colocalization of histones and transcription start sites indicate chromatin regulation

141 ture and local sequence composition near the transcription start site influence pausing, with diverge

142 depleted region immediately upstream of most transcription start sites; instead, the -1 nucleosome is

143 SON binds to DNA near transcription start sites, interacts with menin, and inh

144 olymerase II (Pol II) 20-60 bp downstream of transcription start sites is a major checkpoint during t

145 f the human RET gene (-51 to -33 relative to transcription start site) is essential for basal transcr

146 DCL4 expression predominates as a transcription start site isoform encoding a cytoplasmic

147 of the native soybean HPPD gene revealed two transcription start sites, leading to transcripts encodi

148 Alternatively positioned nucleosomes near transcription start sites likely represent different sta

149 ch methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establi

150 The genome-wide identification of microRNA transcription start sites (miRNA TSSs) is essential for

151 e-based methods, CisMapper can predict which transcription start site of a gene is regulated by a par

152 Most notably, immediately upstream of the transcription start site of active promoters, we frequen

153 ow this region physically interacts with the transcription start site of ARID5B, that alleles of rs70

154 in an enhancer element 47 kb upstream of the transcription start site of c-Myc-interacting CDCA7L.

155 s at -9/-10 and -13/-14 kb from the upstream transcription start site of CCR6 that bind PLZF in CCR6(

156 s revealed that TFII-I binds upstream of the transcription start site of expressed genes, both upstre

157 specifically directs H4 acetylation near the transcription start site of highly expressed genes, whil

158 Moreover, two CpG islands near the transcription start site of MYBL1 were identified, and O

159 DRR(eRNA)), is encoded 5 kb upstream of the transcription start site of MyoD, a myogenic transcripti

160 tably, the nucleosome depleted region at the transcription start site of pol III genes extends past t

161 d genes, both upstream and downstream of the transcription start site of repressed genes, and downstr

162 Recruitment of ERalpha upstream of the transcription start site of SUSD3 was demonstrated by ch

163 8584 is located about 170 kb upstream of the transcription start site of the major transcript for the

164 n on RNA polymerase II (RNA Pol II) near the transcription start sites of 625 genes for ALS patient c

165 3NT proteolysis is selectively targeted near transcription start sites of a small group of genes and

166 s a chromatin modification known to mark the transcription start sites of active genes.

167 leosome positioning, particularly around the transcription start sites of affected genes.

168 Around the transcription start sites of endo-MEGs, DNA methylation

169 RF complex were significantly co-enriched at transcription start sites of erythroid genes, and their

170 Enhancer regions and transcription start sites of estrogen-target regulated g

171 fine structural domains, most occur near the transcription start sites of genes.

172 sine 79, with a maximum frequency around the transcription start sites of genes.

173 Furthermore, RNF2 and SALL4 together occupy transcription start sites of germline genes in the stem

174 We also show that some transcription start sites of H3K27me3-repressed injury g

175 Histone marks around transcription start sites of HSV-1-induced and constitut

176 uence motif that is enriched upstream of the transcription start sites of hundreds of testis-expresse

177 ith the distance of Grh-binding sites to the transcription start sites of its targets.

178 cleosome-free regions (NFRs) associated with transcription start sites of most genes.

179 plexes of Pol II are largely absent from the transcription start sites of most mRNA genes but are pre

180 onal cis-regulatory elements adjacent to the transcription start sites of post-natal expressed genes.

181 ned predominantly around 50-500 kbs from the transcription start sites of their nearby genes, and wer

182 We are able to identify the transcription starting site of each of the promoters as

183 uence from -2612 to +682 bp (relative to the transcription start site) of the JDP2 gene was cloned, a

184 gene expression analyses and revealed novel transcription start sites, of which several were validat

185 Spt4/5 is recruited proximal to the transcription start site on the majority of transcriptio

186 hot spots, are enriched near CpG islands and transcription start sites (P<2.2 x 10(-16)), consistent

187 is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing mil

188 ranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR).

189 directly interact with proximal promoter and transcription start sites, potentially bypassing hundred

190 3,552 nucleotides (nt) upstream of the TERT transcription start site, predominantly in the opposite

191 Transcription start site profiling using nano-cap analys

192 ts a valuable resource for identification of transcription start sites, promoters, and novel transcri

193 ation cassette 80 bp downstream of the Lockd transcription start site reduced the entire lncRNA trans

194 cing coverage of plasma DNA fragments around transcription start sites reflects the expression levels

195 an absolute distance to their corresponding transcription start site, regardless of gene length.

196 opulation (HVR3), and downstream of the HSP1 transcription start site required for maximal yield.

197 thesized to control chromatin structure near transcription start sites, requires active remodeling an

198 The analysis of 7678 focused transcription start sites revealed 40% with a perfect ma

199 this unusual regulation results from altered transcription start site selection.

200 P4RNAs exhibit transcription start sites similar to Pol II products and

201 lexed sequencing libraries, offers very high transcription start site specificity, generates accurate

202 ucleotide variants) and transcript isoforms (transcription start sites, splice sites, and polyA sites

203 that GATA4 occupies chromatin near the Dll1 transcription start site suggesting direct regulation of

204 NA targeting the region upstream of the DUX4 transcription start site suppressed DUX4 mRNA expression

205 ally regulated candidate genes and predicted transcription start-site switching and alternative exon

206 pt diversity levels measured by the rates of transcription start-site switching and alternative splic

207 en enrichment levels of epigenetic marks and transcription start-site switching is similar for protei

208 an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcrip

209 Our analysis of foraging's transcription start sites, termination sites, and splici

210 modules located upstream of the SLC13A5 gene transcription start site that are associated with regula

211 ins an E-box located 60 bp downstream of the transcription start site that has been shown to bind tra

212 ifically to a single KLF site near the EphA5 transcription start site that is required for KLF16 tran

213 hisms (SNPs) in sequence regions upstream of transcription start sites, the average length of promote

214 s single-molecule sequencing was used to map transcription start sites throughout the genome in all 3

215 ied an 11-kb genomic region 3' of the Nkx3.1 transcription start site to be responsible for alteratio

216 targeted from -147 to -89-bp upstream of the transcription start sites to induce high activity of luc

217 opoietic cells, Nup98 binds predominantly to transcription start sites to recruit the Wdr82-Set1A/COM

218 In this study, we developed mirSTP (mirna transcription Start sites Tracking Program), a probabili

219 e best region to target gRNAs is between the transcription start site (TSS) and 200 bp upstream of th

220 a peak at 50 base pairs (bp) upstream of the transcription start site (TSS) and 86% of the TFBSs are

221 By mapping global transcription start site (TSS) and chromatin dynamics, w

222 initiation, RNA polymerase (RNAP) selects a transcription start site (TSS) at variable distances dow

223 we present a publicly available, large-scale transcription start site (TSS) data set in plants using

224 The transcription start site (TSS) determines the length and

225 iption factor binding sites (TFBSs) near the transcription start site (TSS) display tight positional

226 l approach for revealing the multiplicity of transcription start site (TSS) events across experiments

227 RT-PCR showed that an alternative transcription start site (TSS) in intron 1 of YAP1 and Y

228 ritable when compared with DNAm sites in the transcription start site (TSS) of a gene expressed in co

229 from six different positions surrounding the transcription start site (TSS) of a reporter gene fusion

230 t, the NF-kB subunit p65 associates with the transcription start site (TSS) of both upregulated and d

231 sertion approximately 160 kb upstream of the transcription start site (TSS) of Foxl2.

232 7ac, H3K9acK14ac, and H3K4me3 at hundreds of transcription start site (TSS) regions and remote regula

233 e categories; 21 in exons of 18 genes, 76 in transcription start site (TSS) regions of 25 genes, and

234 mutations in several promoter regions affect transcription start site (TSS) selection.

235 ements, which are DNA sequences flanking the transcription start site (TSS) that help direct the prop

236 promoter is a stretch of DNA surrounding the transcription start site (TSS) that integrates regulator

237 Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phyt

238 ivated genes have a functional CARE near the transcription start site (TSS), but for others the CARE

239 n a several-kilobase-long region, called the transcription start site (TSS), which is upstream of the

240 NA exosome substrate RNAs include xTSS-RNAs, transcription start site (TSS)-associated antisense tran

241 428 and -525 kb upstream of the MYC oncogene transcription start site (TSS).

242 f the cDNA ends (5'-RACE), we identified one transcription start site (TSS).

243 cells, despite its location 3.5 kb from the transcription start site (TSS).

244 randed 'transcription bubble,' and selects a transcription start site (TSS).

245 loss of binding of RNA Pol II at the Ankrd26 Transcription Start Site (TSS).

246 a template-strand nucleotide to serve as the transcription start site (TSS).

247 A total of 218 transcription start sites (TSS) and 120 polyadenylation

248 hanisms relies on accurate information about transcription start sites (TSS) and polyadenylation site

249 rovides a single base-pair resolution map of transcription start sites (TSS) and their relative usage

250 s cerevisiae RNA polymerase (Pol) II locates transcription start sites (TSS) at TATA-containing promo

251 n assays using ATAC-sequencing show that the transcription start sites (TSS) of ARGs do not change wi

252 logical responses in part through changes in transcription start sites (TSS) or cleavage and polyaden

253 HSI establishes its noncoding transcription start sites (TSS) over a defined distance

254 A mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribut

255 r SMC3 (cohesin components),transcription at transcription start sites (TSS), and the number of CCCTC

256 Tet1 depletion diminishes 5hmC levels at transcription start sites (TSS), whereas Tet2 depletion

257 well-positioned nucleosomes downstream from transcription start sites (TSS).

258 ration is known to prefer regions in or near transcription start sites (TSS).

259 Transcription start-site (TSS) selection and alternative

260 Using MASTER, we define full inventories of transcription start sites ("TSSomes") of Escherichia col

261 ation of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide a

262 Our transcription start sites (TSSs) analysis of Saccharomyc

263 Hypermethylated DMCs were enriched at transcription start sites (TSSs) and in CpG islands, and

264 ial information for gene regulation; namely, transcription start sites (TSSs) and polyadenylation sit

265 hat 119 BbIVET promoters are associated with transcription start sites (TSSs) and validate novel RNA

266 Transcription start sites (TSSs) are bordered by a small

267 eorganization and histone methylation around transcription start sites (TSSs) are highly coordinated

268 The computational identification of gene transcription start sites (TSSs) can provide insights in

269 st MIR loci, which allowed prediction of the transcription start sites (TSSs) for 167 MIR genes in Ar

270 initiation through comprehensive mapping of transcription start sites (TSSs) in human lymphoblastoid

271 his mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at clos

272 efine at nucleotide resolution the divergent transcription start sites (TSSs) near mouse mRNA genes.

273 Whereas RNA polymerase II (Pol II) transcription start sites (TSSs) occur about 30-35 bp do

274 to defined bait DSBs are enriched around the transcription start sites (TSSs) of active genes.

275 The transcription start sites (TSSs) of the divergent transc

276 used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic me

277 In practice, variants near gene transcription start sites (TSSs) or certain histone modi

278 by considering genome locations relative to transcription start sites (TSSs) or enhancer midpoints,

279 15-kb "superenhancer" of Tet1, there are two transcription start sites (TSSs) with different activati

280 end of genes promoting the identification of transcription start sites (TSSs).

281 the assembly of transcriptional machinery at transcription start sites (TSSs).

282 resolution predictions for intergenic miRNA transcription start sites (TSSs).

283 ultiple and in some cases mutually exclusive transcription start sites (TSSs).

284 mIndy located upstream of the most frequent transcription start site was determined by 5'-rapid ampl

285 ted by chromatin immunoprecipitation and the transcription start site was identified by 5' RACE (rapi

286 An active secondary transcription start site was identified within the inter

287 first nucleosome position downstream of the transcription start site, we identified unwrapped interm

288 trong positional preferences relative to the transcription start site were detected based on their pr

289 enic region indicated that all four putative transcription start sites were preceded by possible prom

290 predominantly observed within 1 kb from the transcription start site, where both histone H3 methylat

291 ise to a major distinction downstream of the transcription start site, where nucleosome phasing is hi

292 NAs revealed strong Set1 enrichment near the transcription start site, whereas Set2 was distributed a

293 ongly enriched in repressed regions and near transcription start sites, whereas the genetically regul

294 There is significant flexibility in the transcription start site, which causes variable spacing

295 0 bp sequence, immediately upstream from the transcription start site, which is sufficient to mediate

296 ovirus type 5 in detail and have defined its transcription start site, which our data suggest is posi

297 tain a consensus cis-element upstream of the transcription start site, which was previously identifie

298 ls unique contacts of the iNTPs bound at the transcription start site with the template DNA and also

299 hermore, we detected usage of an alternative transcription start site within intron 1 of the PRTN3 ge

300 These occur in the vicinity of transcription start sites, within gene bodies, and in in