ライフサイエンスコーパス: TSS

1 TSS females died at early larval stages, which makes the

2 TSS improvement correlated with changes in hyperplasia,

3 TSS selection occurs at different positions within the p

4 TSSs showed improvements of 30%, 40%, 68%, and 76% at 2

5 A combination of 27.0% TSS, 1:5 SPI: JSS ratio and 0.3% NBRE-15 was found to be

6 We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing,

7 This study aims to create and characterize a TSS of Lucilia cuprina, which is a major pest of sheep,

8 Here we show the presence of a TSS in epitaxially grown thin films of the half-Heusler

9 s in GRO/PRO-seq data, and provides accurate TSS prediction for human intergenic miRNAs at a high res

10 arked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational h

11 rectional transcription signatures at active TSSs in GRO/PRO-seq data, and provides accurate TSS pred

12 Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive tr

13 quence-specific RNAP-CRE interactions affect TSS selection.

14 ween them reduced promoter strength, altered TSS selection and diminished Pol II recruitment.

15 transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing.

16 RNAs, indicating a wide usage of alternative TSSs.

17 genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typicall

18 using p300 binding sites, as enhancers, and TSS and random non-DHS sites, as non-enhancers.

19 nce-based annotations, such as promoters and TSS windows (25% average increase in enrichment).

20 ular AnEMBR than that in the tubular AnEMBR (TSS = 17 mg/L), likely due to higher current densities t

21 pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces

22 thousands of treatment-induced non-annotated TSSs (TINATs) following DNMTi and HDACi treatment.

23 akpoint junctions indeed are enriched around TSSs that were determined to be active by global run-on

24 tches the enrichment of key features such as TSSs, TTSs, CpG sites and DNA replication timing around

25 Gene ontology analysis of genes with DMCs at TSSs revealed an enrichment of genes involved in develop

26 n marks and aberrant DNA hypermethylation at TSSs in combination with MYC network activation.

27 epression associated with DNA methylation at TSSs was confirmed in multiple tumor types.

28 molecule nanomanipulation, we show bacterial TSS selection exhibits both hallmarks of scrunching and

29 ely required for de novo methylation at both TSS regions and gene bodies of Polycomb group (PcG) targ

30 on, a competition between the top and bottom TSS in contributing to SOT is observed.

31 driven TATA-less promoters that have broader TSS architecture.

32 characterization of the 6042 B. burgdorferi TSSs reveals a variety of RNAs including numerous antise

33 nucleosomal encroachment over the canonical TSS.

34 ipts retain comparable features of canonical TSSs in terms of DNA sequence, directionality, and chrom

35 iption factor commonly used in two-component TSS.

36 The comprehensive TSS maps allowed us to identify core promoters for ~96%

37 L. cuprina TSS with the tTA drivers and tTA-regulated tetO-Lshid ef

38 ers at which RNAP-CRE interactions determine TSS selection.

39 00) consensus promoters containing different TSS region sequences, and we observed that the TSS profi

40 in mitigating excessive tissue injury during TSS.

41 not be essential for assembling an effective TSS as tTA can be repressed by addition of tetracycline

42 ped, ribosome-binding, translation enhancer (TSS) in its 3'UTR that serves as a hub for interactions

43 At equivalent TSS, cluster exposure had little or no effect on malic a

44 of wine from exposed clusters at equivalent TSS.

45 idopsis and compare the accuracy of existing TSS annotations.

46 ly upstream of the TSS that might facilitate TSS selection.

47 Among patients coded for TSS, GAS, and/or S. aureus, IVIG use was still unusual (

48 e higher among IVIG cases, as was coding for TSS and GAS.

49 promoter through DTIE but is dispensable for TSS selection.

50 ial RNAP and suggest a general mechanism for TSS selection by bacterial, archaeal, and eukaryotic RNA

51 ased on our findings, we propose a model for TSS selection in the scanning-model species, as well as

52 tatus and the lack of targeted therapies for TSS emphasize the need to identify key players of the st

53 Distance from TSS appears to be the most important annotation; specifi

54 on quantitative trait loci (eQTL; <1 Mb from TSS, FDR < 1%).

55 RO-seq and 28 PRO-seq experiments identified TSSs for 480 intergenic miRNAs, indicating a wide usage

56 We first identified TSSs at single-nucleotide resolution for 12 yeast specie

57 cans from upstream to downstream to identify TSSs.

58 y for E2-dependent interaction with the Igf1 TSS and induction of uterus-specific Igf1 transcription.

59 act between the distal enhancer and the Igf1 TSS.

60 of TSS and reveal a novel role for IL-17A in TSS immunopathogenesis.

61 Therefore, we explored how alterations in TSS affected expression of genes regulated by the Zap1 t

62 eover, loss of Paf1 triggered an increase in TSS-proximal nucleosome occupancy, which could impose a

63 immunomodulatory properties, participate in TSS is unclear.

64 s indicate that iNKT cells are pathogenic in TSS.

65 results suggest NF-Y is a central player in TSS selection in metazoans and highlight the deleterious

66 II transcription plays an important role in TSS selection but is not required for the scanning react

67 We revealed a distinct sharpening in TSS utilization in genes upregulated in slowly cycling,

68 ential role of yeast Pol II transcription in TSS scanning, HIS4 promoter derivatives were generated t

69 ll-cycle-dynamic-associated transitioning in TSS distribution and differential utilization of alterna

70 Variability in TSS selection has been proposed to involve DNA 'scrunchi

71 isrupts binding of the phosphorylated INCENP TSS motif.

72 nges were TCF dependent, but TCF-independent TSSs exhibited the same hierarchy, indicating that it re

73 transcription machinery locally to influence TSS choice and identify exon gain, loss, and regulatory

74 d across a wide range of values for influent TSS (61-820 mg L(-1)) and COD (384-1505 mg L(-1)), demon

75 hit1 incorporates histone variant H2A.Z into TSS region of genes involved in Lgr5+ stem cell fate det

76 ne also has a CpG island downstream from its TSS, and a NF-kappaB-binding site flanked by CpGs.

77 ation mechanism of each species based on its TSS maps and genome sequences.

78 ated, AURKC and INCENP phosphorylated on its TSS motif, revealing the structural and biochemical mech

79 hways can generate translocations by joining TSS-proximal DSBs to DSBs on other chromosomes.

80 ferent genera, while the ribosome-binding kl-TSS that provides a long-distance interaction with the 5

81 ation, indicating that the combination of kl-TSS and PTE is highly efficient.

82 in cis and in trans in the absence of the kl-TSS by sequestering initiation factor eIF4G.

83 hown that the PTE in conjunction with the kl-TSS did not markedly affect the translation initiation r

84 ansferring the 3'-5' interaction from the kl-TSS to the PTE (to fulfill its functionality as found in

85 vels in protoplasts in the absence of the kl-TSS.

86 leotides of the promoter including all known TSSs and all but 18 nucleotides of the 5'-UTR had virtua

87 h Put and Spd showed lower changes in L( *), TSS and TA and also higher value of chroma in berries.

88 at their 5' ends using the putative lincRNA TSS regions predicted by the TSS proximal region predict

89 here was a statistically significantly lower TSS during the 24-week birch EEC session for 7 DU and 12

90 regions and introns, including several major TSS at unexpected locations.

91 level; (ii) the fractional use of the major TSS increases, but that of each minor TSS decreases, wit

92 sion level; and (iii) cis-elements for major TSSs are selectively constrained, while those for minor

93 rent, low and high, F:M (0.19-0.36 mg COD/mg TSS/d) and C:N (3.5-6.3 mg COD/mg TKN) conditions for a

94 major TSS increases, but that of each minor TSS decreases, with the gene expression level; and (iii)

95 lectively constrained, while those for minor TSSs are not.

96 have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in

97 abilistic model for identifying active miRNA TSSs from nascent transcriptomes generated by global run

98 By integrating predicted miRNA TSSs with matched ENCODE transcription factor (TF) ChIP-

99 of microRNA transcription start sites (miRNA TSSs) is essential for understanding how miRNAs are regu

100 Moreover, TSS selection depends on cell/tissue, development stage

101 t had no effect when upstream of the 5'-most TSS.

102 st 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts sha

103 hkCP enhancers are more likely to form multi-TSS interaction networks and be associated with topologi

104 How multiple TSSs are specified at individual promoters across eukary

105 In stem-like BrCa cells, HDAC7 binds near TSS and to SEs of these oncogenes where it appears to co

106 an also implement H3K4me3 at a subset of non-TSS regulatory elements, a subset of which shares epigen

107 action between location and season (48.6% of TSS).

108 was largely controlled by genotype (40.6% of TSS).

109 interactions are a functional determinant of TSS selection.

110 ly cycling cells carry broad distribution of TSS utilization, coupled with enrichment for the CCAAT-b

111 f these motifs upstream versus downstream of TSS depending on poising status.

112 entify CD4(+) TEM cells as a key effector of TSS and reveal a novel role for IL-17A in TSS immunopath

113 side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional tran

114 B cells revealed that the great majority of TSS-proximal junctions occurred in genes commonly expres

115 The results establish the mechanism of TSS selection by bacterial RNAP and suggest a general me

116 Using a humanized mouse model of TSS and human cells, we herein demonstrate that SAgs eli

117 y addressing the developmental regulation of TSS selection in zebrafish we uncovered a class of dual-

118 l angle values and reveal the unique role of TSS in generating SOT.

119 y, analysis of repair junction signatures of TSS-associated translocations in wild-type versus classi

120 enrichment of G4 sequence motifs upstream of TSS of non-poised active genes suggests a potential role

121 moter sequence determine the distribution of TSSs and their usage.

122 ipt levels (strength) or the distribution of TSSs within a promoter (shape).

123 vely, this is the first comprehensive map of TSSs in B. burgdorferi and characterization of previousl

124 t that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously

125 s (GTFs) assembles and opens DNA upstream of TSSs.

126 ter pairs, in combination with the wealth of TSSs in mammalian genomes, provide a framework with whic

127 nd GTF function and analyze their effects on TSS usage genome-wide.

128 assessed effects of RNAP-CRE interactions on TSS selection in vitro and in vivo for a library of 4(7)

129 e, we propose that each gene has one optimal TSS and that ATI arises primarily from imprecise transcr

130 nsiderable barrier to Pol II elongation past TSS-proximal regions.

131 Here we performed TSS mapping of the translatome following energy stress.

132 With mirSTP, we not only predicted TSSs for 72 miRNAs, but also identified 12 primary miRNA

133 RNA:DNA hybrids are found at both promoters (TSS) and terminators (TTS) of highly expressed genes.

134 Assessing the contribution of cap-proximal TSS nucleotides, we found dramatic effect on translation

135 Higher permeate quality (TSS = 0.05 mg/L) was achieved in the rectangular AnEMBR

136 .Z associates with both active and repressed TSS and is important for priming genes for rapid transcr

137 adenines previously implicated in the RNAP3 TSS motif (CAA).

138 gly, demethylated CpGs downstream from SALL4 TSS are within binding sites of octamer-binding transcri

139 ting CpG demethylation downstream from SALL4 TSS influences SALL4 transcriptional elongation.

140 nd how CpG demethylation downstream of SALL4 TSS regulates SALL4 transcription, we quantified by chro

141 AT3 cis-acting elements, downstream of SALL4 TSS, enables OCT4 and STAT3 binding, recruitment of BRG1

142 on of specific CpG sites downstream of SALL4 TSS.

143 be remarkably prevalent, present at the same TSS downstream location in approximately 20.8% of human

144 inoconjunctivitis (ARC) total symptom score (TSS) after 24 weeks of treatment.

145 endence and by baseline total symptom score (TSS).

146 Changes in total sign scores (TSSs), transepidermal water loss, and tissue biomarkers

147 A-like motif in core promoters driving sharp TSS selection, in contrast with canonical TBP/TFIID-driv

148 NAs is between the transcription start site (TSS) and 200 bp upstream of the TSS.

149 p) upstream of the transcription start site (TSS) and 86% of the TFBSs are in the region from -1,000

150 By mapping global transcription start site (TSS) and chromatin dynamics, we observed the cryptic tra

151 ith respect to the transcription start site (TSS) and strand of occupancy (coding versus non-coding s

152 n relative to KLF9 transcription start site (TSS) and two occurred at distal sites.

153 incorporation of Transcriptional Start Site (TSS) annotations from RIKEN's FANTOM 5 initiative.

154 e (RNAP) selects a transcription start site (TSS) at variable distances downstream of core promoter e

155 The transcription start site (TSS) determines the length and composition of the 5' UTR

156 s (TFBSs) near the transcription start site (TSS) display tight positional preferences relative to th

157 st near the gene's transcription start site (TSS) in human but not mouse adipocytes.

158 Pol II) pausing at transcription start site (TSS) is one of the key rate-limiting steps in regulating

159 Transcription start site (TSS) mapping indicates that TBPL2 has a strong preferenc

160 DNAm sites in the transcription start site (TSS) of a gene expressed in colon tissue.

161 ns surrounding the transcription start site (TSS) of a reporter gene fusion in Arabidopsis thaliana T

162 87 relative to the transcription start site (TSS) of the GM2-synthase gene than in normal kidney epit

163 me3 at hundreds of transcription start site (TSS) regions and remote regulatory sites.

164 nderlying specific transcription start site (TSS) selection in mammals remain unclear.

165 Variations in transcription start site (TSS) selection reflect diversity of preinitiation comple

166 ter regions affect transcription start site (TSS) selection.

167 ences flanking the transcription start site (TSS) that help direct the proper initiation of transcrip

168 investigated their transcription start site (TSS) usage, chromatin organization, and posttranscriptio

169 asure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants af

170 e H3K9me3 at the transcriptional start site (TSS) with methylation-associated, tumor-specific gene si

171 stal from the Igf1 transcription start site (TSS) with multiple E2-dependent ERalpha-binding regions.

172 onal CARE near the transcription start site (TSS), but for others the CARE is downstream.

173 NA surrounding the transcription start site (TSS), is a major integration-point for regulatory-signal

174 occur close to the transcription start site (TSS), or within the gene body.

175 region, called the transcription start site (TSS), which is upstream of the first protein-coding gene

176 g site (CBS) and a transcription start site (TSS)-into 16 ectopic loci across 11 chromosomes, and cha

177 ty as promoter- or transcription start site (TSS)-nucleosomes.

178 ver, TC-NER on the transcription start site (TSS)-proximal half of the +1 nucleosome is largely indep

179 termination of the Transcription Start Site (TSS).

180 tream from SALL4 transcriptional start site (TSS).

181 le,' and selects a transcription start site (TSS).

182 II at the Ankrd26 Transcription Start Site (TSS).

183 de to serve as the transcription start site (TSS).

184 f the MYC oncogene transcription start site (TSS).

185 tream from EpCAM transcriptional start site (TSS).

186 Transcription start-site (TSS) selection and alternative promoter (AP) usage contr

187 tion (H3K27ac) at transcription start sites (TSS) and super-enhancers (SEs) prominently in stem-like

188 he differences in transcription start sites (TSS) and transcription end sites (TES) among gene isofor

189 (Pol) II locates transcription start sites (TSS) at TATA-containing promoters by scanning sequences

190 Transcription start sites (TSS) in eukaryotes are characterized by a nucleosome-dep

191 ing show that the transcription start sites (TSS) of ARGs do not change with neural firing but are al

192 s proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3).

193 hrough changes in transcription start sites (TSS) or cleavage and polyadenylation sites (PAS).

194 ,transcription at transcription start sites (TSS), and the number of CCCTC-binding factor (CTCF)-cohe

195 corresponding to transcription start sites (TSS), as well as 1628 processed 5' ends and 1299 3' ends

196 on by analysing transcriptional start sites (TSS), CRISRPi identified 92% of core cell essential gene

197 eate or disrupt transcriptional start sites (TSS).

198 sites overlapping transcription start sites (TSSs) and CCCTC-binding factor (CTCF) binding sites, and

199 were enriched at transcription start sites (TSSs) and in CpG islands, and depleted in transcriptiona

200 e associated with transcription start sites (TSSs) and validate novel RNA transcripts using Northern

201 Transcription start sites (TSSs) are bordered by a small nucleosome-depleted region

202 ntitative maps of transcription start sites (TSSs) at a single-nucleotide resolution for S. cerevisia

203 we identify ~2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitiv

204 t way of locating transcription start sites (TSSs) has been identified in a budding yeast Saccharomyc

205 alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters suppor

206 curate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulatio

207 with gain of new transcription start sites (TSSs) nearby and increased gene expression.

208 aterial to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleot

209 ariants near gene transcription start sites (TSSs) or certain histone modifications are likely to reg

210 ply peaked around transcription start sites (TSSs), and these peak levels corresponded positively wit

211 with alternative transcription start sites (TSSs).

212 gions upstream of transcription start sites (TSSs).

213 ip are changes in transcription start sites (TSSs).

214 utually exclusive transcription start sites (TSSs).

215 utilize multiple transcription start sites (TSSs).

216 ers to new target transcription start sites (TSSs).

217 gene has multiple transcription start sites (TSSs).

218 s, evidenced by higher total soluble solids (TSS) and proline, and lower malic acid, 3-isobutyl-2-met

219 ocyanin concentration, total soluble solids (TSS) and titratable acidity (TA) were evaluated after 0,

220 endent variables viz., total soluble solids (TSS, 20, 25 and 30 degrees Brix), SPI: JSS (1:1, 1:3 and

221 t with 6 <= pH <= 9, total suspended solids (TSS) < 30 mg L(-1), and chemical oxygen demand (COD) < 1

222 the oocyte transcriptome by using a specific TSS recognition code.

223 otifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a La

224 al to accurately annotate cell type-specific TSS and PAS.

225 let-triplet qubits: a transverse sweet spot (TSS) that enables transitions between qubit states, a st

226 by location (21.5% of Total Sums of Squares [TSS]), plus the interaction between location and season

227 Here a stable TSS of L. cuprina (DH6) that carries two lethal effector

228 The topological surface states (TSS) in topological insulators (TIs) can exert strong sp

229 t in identifying topological surface states (TSSs) in other classes of materials.

230 th 21 models scoring a true skill statistic (TSS) >0.8.

231 Transgenic sexing strains (TSS) that carry conditional female lethal genes are adva

232 Transgenic sexing strains (TSS) using the tetracycline-off control system have been

233 on-coupled eviction of nucleosomes on strong TSSs during intraerythrocytic development and demonstrat

234 and ribosome-binding 3' T-shaped structure (TSS) have been found in viruses of different genera, whi

235 We mapped ~1 million well-supported TSSs, suggesting highly pervasive transcription initiati

236 Toxic shock syndrome (TSS) and other superantigen-mediated illnesses are assoc

237 Toxic shock syndrome (TSS) is caused by staphylococcal and streptococcal super

238 During toxic shock syndrome (TSS), bacterial superantigens trigger a polyclonal T -ce

239 stered for presumptive toxic shock syndrome (TSS), but its frequency of use and efficacy are unclear.

240 pically encountered in toxic shock syndrome (TSS).

241 Although we found that TSS scanning does not require RNA synthesis, our results

242 We propose that TSS selection involves DNA scrunching prior to RNA synth

243 The structures show that TSS motif phosphorylation stabilises the kinase activati

244 Prior results suggest that TSS distributions at promoters where scanning occurs shi

245 ces in Saccharomyces cerevisiae We show that TSSs of chromatin-sensitive internal cryptic transcripts

246 recent theoretical calculations suggest that TSSs may be found in half-Heusler ternary compounds.

247 The TSS motif phosphorylations alter the substrate-binding s

248 ons between distal and proximal GBSs and the TSS correlated with KLF9 induction.

249 an co-localize TFBSs with each other and the TSS.

250 DNA methylation around the TSS was absent in both RCC cell lines and NKE cells.

251 Hypomethylated DMCs were observed at the TSS of transcript variant 2 of alpha-SMA, which correlat

252 correspondingly high DNA methylation at the TSS.

253 the possibility of transitioning between the TSS and symmetric operating points while remaining conti

254 utative lincRNA TSS regions predicted by the TSS proximal region prediction model based on genomic an

255 A-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift

256 n sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative def

257 t be transcribed to increase expression, the TSS changed when the intron was located in the 5'-untran

258 he first nucleosome just downstream from the TSS.

259 This error hypothesis predicts that (i) the TSS diversity of a gene reduces with its expression leve

260 e presence of consensus CRE sequences in the TSS region.

261 ous inflammatory mediators implicated in the TSS-associated cytokine storm.

262 chromatin interactions were centred near the TSS of genes, and, critically, the genes identified as p

263 al mechanisms for replicating an RM near the TSS that binds a particular TF subunit.

264 Furthermore, near the TSS, RMs can co-localize TFBSs with each other and the T

265 pocytes, distinct variants downstream of the TSS have strong effects on PM20D1 expression in human fa

266 hts into the measured contour lengths of the TSS structure elements.

267 nine-rich region immediately upstream of the TSS that might facilitate TSS selection.

268 al intronic region +2.5 kb downstream of the TSS, and this duplication occurred in the primate lineag

269 start site (TSS) and 200 bp upstream of the TSS.

270 bases and centered ~80 bases upstream of the TSS.

271 nal hypoxia response element upstream of the TSS.

272 in these promoters was within ~200 bp of the TSS.

273 Deletions of the CBS or the TSS individually or in combination within inserts reveal

274 SMD recapitulated the TSS unfolding order in the absence of Mg(2+), showed dep

275 r a library of 4(10) promoter sequences, the TSS, the RNAP leading-edge position, and the RNAP traili

276 tion with low ATP concentrations shifted the TSS position downstream.

277 imidine-purine dinucleotides surrounding the TSS.

278 S region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP-CRE

279 urally in a similar location relative to the TSS for possible oxidation-induced gene activation inclu

280 polymerase II enrichment, and looping to the TSS, plausibly underlying constitutive KLF9 expression.

281 with positional preferences relative to the TSS, with 38 preferences tight (+/-5 bp).

282 tight positional preferences relative to the TSS.

283 tight positional preferences relative to the TSS.

284 rom -1,000 bp to +200 bp with respect to the TSS.

285 pression, likely directing RNA pol II to the TSSs within the genome.

286 l DNA mechanics affect transcription through TSS-proximal nucleosomes.

287 n transcriptional profiles are mainly due to TSS mutations and have likely evolved due to differences

288 We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it

289 ethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucle

290 Moreover, by tuning the top TSS carrier concentration, a competition between the top

291 enhancers are more often bound to one or two TSSs and are enriched at chromatin loop anchors.

292 We found hundreds of previously unidentified TSS and PAS which revealed two interesting phenomena: fi

293 esis, suggesting that scrunching and unusual TSS selection contribute to the extraordinary transcript

294 promoters, is also required for the unusual TSS.

295 a consequence of their proximity to upstream TSSs on the opposite strand.

296 The ensemble model performed very well (TSS = 0.898 and ROC = 0.991) and indicated high environm

297 Given the rapidity with which TSS develops, designing timely and truly targeted therap

298 However, current protocols for genome-wide TSS profiling are laborious and/or expensive.

299 T promoters were not found to associate with TSSs.

300 alteration of chromatin accessibility within TSS and enhancer elements gradually decreased as cells p