ライフサイエンスコーパス: polyA

1 synthesis from RNA templates, followed by 3' polyA tailing of the single-stranded cDNA products and d

2 nds on codon usage, requiring the 5' cap, 3' polyA tail and their associated proteins, which suggests

3 ylation complex shortens cytoplasmic mRNA 3' polyA tails to regulate mRNA stability.

4 g the promoter) with the enhancer and the 3' polyA addition site of the target gene.

5 Interaction of 60S subunits with the 3' polyA is suggested.

6 ate an approximately 1-2.5-kb subset of [32P]polyA RNA molecules from a heterogeneous mixture ranging

7 petitive translation assays to native and 5' polyA mutant transcripts generated with promoters that d

8 ith a cytosine located within a conserved 5' polyA element, resulting in formation of an extended 5'

9 nt, resulting in formation of an extended 5' polyA structure as opposed to the hairpin structure form

10 of postreplicative (PR) mRNAs that harbor 5' polyA leaders.

11 We propose that structural plasticity of 5' polyA and other conserved RNA elements place the 5' lead

12 e identified mutations that stabilize the 5' polyA hairpin structure in 3G RNAs, which promote RNA di

13 ted between a cytomegalovirus promoter and a polyA signal to form a transcription cassette.

14 rget mRNAs to possess a 7-methyl G cap and a polyA tail, whereas increasing polyA tail length alone c

15 p mRNA terminating with a 900 bp 3'UTR and a polyA tail.

16 al E1A promoter with a cassette containing a polyA sequence and a human tyrosinase enhancer/promoter

17 mutation, a mononucleotide expansion from a polyA repeat tract (c.132dupA) that causes protein trunc

18 the entire transcript from degradation in a polyA-independent manner.

19 gnal that marks the 3' end of a gene, like a polyA site.

20 Insertion of a polyA signal ablated the Ifng-as1 full-length transcript

21 y conserved stem-loop sequence rather than a polyA sequence.

22 e end in a conserved stem-loop rather than a polyA tail.

23 Supt4h2, a processed intronless gene (with a polyA tail and a tandemly-duplicated 13 bp insertion sit

24 In addition, polyA:tau seeds and fibrils were sensitive to RNase.

25 In recent years, poly adenine (polyA) DNA functionalized gold nanoparticles (AuNPs) fre

26 relies on the incorporation of poly-adenine (polyA) blocks in both nucleic acid probes and antibodies

27 , promoting the synthesis of a poly-adenine (polyA) tail.

28 of human SCAF4 and SCAF8 results in altered polyA selection and subsequent early termination, leadin

29 As alternative polyA sites are common in mammalian genes, several machi

30 Ser5 and are detected at early, alternative polyA sites.

31 A sites, and the specific use of alternative polyA sites (APA) results in isoforms with variable 3'-u

32 The usage of alternative polyA sites in terminal exons is modulated by their rela

33 ification in regulating proximal alternative polyA choice.

34 sites represent uncharacterized alternative polyA events and extensions of known transcripts in huma

35 nuclear mRNA revealed widespread alternative polyA site use (APA) in intestinally expressed genes.

36 and that, among transcripts with alternative polyA (APA) usage in both the brain and the liver, brain

37 ently use an alternative sixth exon (6c) and polyA signals near the middle of the former intergenic r

38 earrangements (21%), 5' truncation (74%) and polyA tails (88%).

39 ch as a splicing acceptor site, TATA box and polyA addition signal sequence, was further tested in si

40 ethyltransferases, ribosomal components, and polyA RNA binding proteins.

41 We show that Cup and polyA-binding protein (PABP) interact physically with Sq

42 data generated by ENCODE in long polyA+ and polyA- fractions in the cell lines K562 and GM12878.

43 transposable elements in their promoter and polyA addition regions, and by the length of a CCA tande

44 ic RNA were greatest when combining rRNA and polyA depletion, and when using a higher MOI.

45 10) and two RNA depletion methods (rRNA and polyA).

46 transcription start sites, splice sites, and polyA sites) are defined and quantified for full-length

47 uman transcriptome, which includes small and polyA RNA as well as total RNA from 300 human tissues an

48 TAR and polyA form extended, coaxially stacked hairpins, consist

49 ction (RT-PCR) assays conducted on total and polyA+ RNA, as well as sequencing of cloned RT-PCR produ

50 Reverse transcription and polyA reverse transcriptase (RT)-PCR was performed, and

51 smsDGE involves a reverse-transcription and polyA-tailing sample preparation procedure followed by s

52 d 62% of protein-coding genes have annotated polyA sites.

53 TR switching directly without relying on any polyA annotations.

54 L1 elements are polyA retrotransposons which inhabit the human genome.

55 ur data suggest expansions in one of the ARX polyA tracts results in nuclear protein aggregation and

56 ed nonpoly(A) mRNA with the same kinetics as polyA(+) mRNA.

57 tor and adapter/linker sequences, as well as polyA/T tails.

58 ases downstream from where CPSF73 cleaves at polyA sites and histone 3' ends.

59 duplications (TSDs) and longer than average polyA-tail length.

60 bases reflect time since loss of MMR because polyA deletions are stepwise.

61 and via an N-terminal zinc finger that binds polyA RNA specifically.

62 ate equivalent expression profiles from both polyA-selected and rRNA-depleted libraries.

63 ACK1/PKCbeta2 associated with polysome-bound polyA-mRNAs.

64 redominantly associated with polysome-bound, polyA-mRNAs that are being actively translated.

65 consecutive adenosine nucleotides, so-called polyA tracks, to the gene coding sequence of interest wi

66 ns that contain adenosine repeats, so-called polyA-leaders.

67 The canonical polyA signal was strongly enriched and positionally cons

68 ript in a domain downstream of the canonical polyA site.

69 e applied LQ-RNAseq to profile S. cerevisiae polyA+ transcripts, demonstrate the reproducibility of t

70 r higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated

71 cts with a central stress granule component, polyA-binding protein (PABP).

72 e direction overlapping gene configurations, polyA read-through is necessary to facilitate transcript

73 domain region, and a variant in a conserved polyA+ signal sequence that alters the length of the 3'

74 models successfully classified constitutive polyA sites from a biologically relevant background (auR

75 mRNAs, enhancing translation and controlling polyA lengths of heterologous mRNAs.

76 elongation and termination, ensuring correct polyA site selection and RNAPII transcriptional terminat

77 In response to developmental cues, polyA tail lengths can vary, affecting the translation e

78 2, forms a complex with PAB-1, a cytoplasmic polyA-binding protein, and that ATX-2 is required for de

79 g translation was, surprisingly, the Cytosol polyA- fraction in both cell lines.

80 rmination of Ube3a-ATS at the vector-derived polyA cassette, or when integrated in the reverse orient

81 s with sum total deletions at four different polyA loci of -32.7 bases in adenomas and -38.4 bases in

82 egulatory mechanisms underlying differential polyA preferences in multiple cell types has been hinder

83 brain transcripts preferentially use distal polyA sites, as reported, and also show higher proximal

84 ssue-specific relative and absolute dominant polyA site prediction.

85 mall amount of polyadenylation to downstream polyA sites when present, however, the majority of the a

86 fferent selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs,

87 y that is specifically related to eukaryotic polyA polymerases is typified by yeast Trf4p and Trf5p p

88 Addition of exogenous polyA RNA to depleted optic nerve extracts yielded incre

89 hese findings further suggest that extensive polyA deletions common in MSI+ tumors likely reflect mul

90 eatures or use relatively old algorithms for polyA site prediction.

91 ate annotation of positional information for polyA tails added posttranscriptionally.

92 CFIA is required for polyA site selection/cleavage targeting RNA sequences th

93 sficantly outperforms the existing tools for polyA site prediction and tissue-specific relative and a

94 Sum total deletions in four polyA repeats were variable (between -17 to -45 bp) in 2

95 e stability through the introduction of free polyA strands or positively charged amino side chains, e

96 ol II to promote termination downstream from polyA sites.

97 f human transcripts have multiple functional polyA sites, and the specific use of alternative polyA s

98 la genes, generating an attP-FRT-SA-T2A-GAL4-polyA-3XP3-EGFP-FRT-attP transgenic library for multiple

99 better understand how these proteins govern polyA site choice, we introduce CPA-Perturb-seq, a multi

100 We found that three RNA homopolymers, polyA, polyU, and polyC, all bound tau, but only polyA R

101 Consistent with this hypothesis, polyA site-sequencing (PolyA-seq) did not detect differe

102 e re-analysed a curated set of 2232 Illumina polyA+ RNA-seq libraries that chart detailed time course

103 ific motif importance and their crosstalk in polyA site formation and cleavage heterogeneity.

104 us 7-methylguanosine (m(7)G) modification in polyA+-purified RNA.

105 n vitro translation of PAD2 was monitored in polyA RNA depleted optic nerve extracts.

106 an N-terminal expanded polyalanine tract in polyA-binding protein nuclear 1 (PABPN1).

107 l G cap and a polyA tail, whereas increasing polyA tail length alone can increase miRNA silencing act

108 Recent studies indicate polyA runs cause ribosome stalling and frameshifting, tr

109 gth and position of TDP-43 binding influence polyA site usage.

110 Our data shows that inflammation influences polyA site choice for SERPINA1 transcripts, resulting in

111 ription in 3' flanking regions by inhibiting polyA site-dependent termination.

112 rimarily adopts conformations with an intact polyA stem, exposed dimerization initiation site, and mu

113 To understand the nature of intergenic polyA transcription, we first assessed its abundance usi

114 Importantly, we found that intestinal polyA sites that undergo APA tend to have U-rich and/or

115 To obtain mechanistic insights into polyA site optimization across the human genome, we deve

116 We find groups of intronic polyA sites regulated by distinct components of the nucl

117 e stability as affected by the length of its polyA anchor was another crucial aspect in our study.

118 ncation of its 3' UTR, including loss of its polyA tail, stabilized Bip1 mRNA, resulting in increased

119 teins, polyA-binding protein 1 and a 130 kDa polyA-mRNA binding protein (KIAA0217).

120 nes encode the only metazoan mRNAs that lack polyA tails, ending instead in a conserved 26-nt sequenc

121 icoid, and with genes encoding eIF4E, Larp1, polyA binding protein (PABP), and Ago2.

122 ling a tantalizing interplay between LARP4A, polyA and PABP.

123 el sequencing of genomic DNA and full-length polyA(+) mRNA from single cells.

124 genes and reporter sequences containing long polyA runs are efficiently and accurately translated in

125 and RNA-seq data generated by ENCODE in long polyA+ and polyA- fractions in the cell lines K562 and G

126 We analyzed the long, polyA-selected, unstranded, deeply sequenced RNA-seq dat

127 Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birt

128 Northern analysis of gastric mucosal polyA+ RNA revealed 7.5- and 4.1-kilobase transcripts, s

129 n human genes that we detected have multiple polyA sites in their 3'UTRs, with 49.3% having three or

130 Most mammalian genes have multiple polyA sites, representing a substantial source of transc

131 ated region (UTR), but not the three natural polyA sites.

132 conferred stability extends to adjacent non-polyA sequences, albeit with diminishing returns relativ

133 ession, the extent of deletions in noncoding polyA sequences were compared between 6 adenomas (all <

134 tumor-derived RNA (total or polyA+, but not polyA- RNA).

135 Expanded NOTCH2NLC-polyG and NOTCH2NLC-polyA could interact with and sequester hnRNPM, while ov

136 an approximately 8-fold increase in nuclear polyA RNA.

137 Analysis of polyA-selected RNAs and cDNA clones from several human c

138 Conventional methods rely on annotation of polyA sites; yet, such knowledge remains incomplete, and

139 Relative depletion of polyA signals in DoG regions correlates with increased l

140 vestigate and quantified the dissociation of polyA DNA on gold nanoparticles in diverse experimental

141 ne and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, he

142 s, we wanted to understand the generality of polyA-expansion cytotoxicity by using yeast as a model o

143 ntiviral functions for the yeast homologs of polyA-binding protein (PABPC1) and the La-domain contain

144 ge remains incomplete, and identification of polyA sites is still challenging.

145 that enables transcriptome-wide inference of polyA site usage.

146 to maintain a good stability of this kind of polyA DNA-AuNPs nanoconjugates.

147 UTR switching without any prior knowledge of polyA annotations.

148 i-miRNA is predicted based on the mapping of polyA signals, and supported by cDNA/EST and ditags data

149 sion (DGE), enabling simultaneous mapping of polyA sites and quantitative measurement of their usage.

150 These quantitative maps of polyA usage in evolutionarily and functionally related s

151 d 8,407 Psi sites from as little as 10 ng of polyA(+) RNA input.

152 ays that were hybridized with populations of polyA+ RNA sequence.

153 otocol to specifically probe the position of polyA sites in three human adult tissue types.

154 Given the prevalence of polyA tracts in eukaryotic proteomes, we wanted to under

155 RNA, termed PUN RNA, which is the product of polyA-templated RNA synthesis.

156 olyalanine tract within the coding region of polyA binding protein nuclear 1 (PABPN1).

157 of single cells; the physical separation of polyA(+) mRNA from genomic DNA using a modified oligo-dT

158 Here we undertake native RNA sequencing of polyA + RNA from two human cell lines, analysing ~5.2 mi

159 io assembly of high-throughput sequencing of polyA(+) RNA (RNA-Seq) from a cohort of 102 prostate tis

160 We generated a series of polyA expansions in Arx and expressed these in cell cult

161 the cleavage of the pre-mRNA at the site of polyA addition.

162 itro, PKCbeta2 can phosphorylate a subset of polyA-mRNA-associated proteins that are also phosphoryla

163 F4), which is important for correct usage of polyA sites for mRNA termination.

164 In general, usage of polyA sites is more similar within the same tissues acro

165 They demonstrate the utility of polyA DNA and real-time PCR for measurement of gene sign

166 Subtractive hybridization was conducted on polyA PCR-amplified RNA to isolate genes expressed by co

167 A, polyU, and polyC, all bound tau, but only polyA RNA triggered seed and fibril formation.

168 -mRNA cleavage and polyadenylation sites, or polyA sites, including more than 3000 sites that have pr

169 DC pulsed with unfractionated RNA (total or polyA+) from OVA-expressing tumor cells were as effectiv

170 h DC pulsed with tumor-derived RNA (total or polyA+, but not polyA- RNA).

171 indicating a requisite role for mRNA in Pab1 polyA-expansion toxicity.

172 Yeast ataxin-2, also known as Pbp1 (polyA binding protein-binding protein 1), is an intrinsi

173 ve AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a no

174 Polyadenine (polyA) serves as an effective anchoring block for prefer

175 rich (81%) genome harbor long polyadenosine (polyA) runs within their ORFs, distinguishing the parasi

176 l loop hybridizes with the 3'-polyadenylate (polyA) tail to sequester it from exonucleolytic attack.

177 s to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic

178 aled widespread alternative polyadenylation (polyA) in eukaryotes, leading to various mRNA isoforms d

179 Alternative polyadenylation (polyA) sites near the 3' end of a pre-mRNA create multip

180 e use of early, alternative polyadenylation (polyA) sites.

181 istribution of cleavage and polyadenylation (polyA) sites should be co-evolutionally optimized with t

182 increased heterogeneity in polyadenylation (polyA) site usage of proliferation-associated genes.

183 and used it to globally map polyadenylation (polyA) sites in 24 matched tissues in human, rhesus, dog

184 f the transactivation (TAR)/polyadenylation (polyA), primer-binding site (PBS), and Psi-packaging dom

185 ation of co-transcriptional polyadenylation (polyA) site choice.

186 expansions in their endogenous polyalanine (polyA) tracts.

187 erinuclear polyglycine (polyG), polyalanine (polyA), and polyarginine (polyR) inclusions, leading to

188 Recently, polyalanine (polyA) tract expansions in the Aristaless-related homeob

189 ions that polyadq uses to evaluate potential polyA signals.

190 cific leader activity that underlie poxvirus polyA-leaders.

191 secondary structures as a feature to predict polyA sites.

192 ning model, called DeepPASTA, for predicting polyA sites from both sequence and RNA secondary structu

193 ing tools have been published for predicting polyA sites from sequence data.

194 In our tests, polyadq predicts polyA signals with a correlation coefficient of 0.413 on

195 We identified predominant polyA sites (herein referred to as pPAS) and putative pr

196 ulin and at least two mRNA-binding proteins, polyA-binding protein 1 and a 130 kDa polyA-mRNA binding

197 with the preferential selection of proximal polyA sites by the 3'end processing complex.

198 n operon of Mycoplasma, a domain of putative polyA polymerases in Synechocystis and Aquifex, PRUNE of

199 ning models to identify genome-wide putative polyA sites at unprecedented nucleotide-level resolution

200 rse transcription polymerase chain reaction, polyA tail, 3' rapid amplification of complementary DNA

201 ion and characterize modules of co-regulated polyA sites.

202 sulin receptor RNA in both total RNA and RNA polyA+ pools relative to normal and myopathic control mu

203 in addition to mRNA and long non-coding RNA, polyA tails can be identified in 16S mitochondrial ribos

204 en reading frames, upstream Kozak sequences, polyA signals, Kozak sequences at the annotated translat

205 ions (maximum of -12 bp) occurred in similar polyA sequences in MMR-deficient mice (mlh1-/-) up to 47

206 itioning transgene element to share a single polyA sequence for termination.

207 rounding the cleavage/polyadenylation sites (polyA sites), which are frequently constrained by sequen

208 signal being nearly absent at brain-specific polyA sites.

209 is then extended to predict tissue-specific polyA sites.

210 while single nucleotides or single-stranded polyA or polyC constructs do not.

211 ng allows Pan3 to supply Pan2 with substrate polyA RNA, facilitating efficient mRNA deadenylation by

212 expression through modulation of a synthetic polyA signal (PAS) cleavage introduced into the 5' UTR o

213 ction lacking PrPSc template seed, synthetic polyA RNA molecules induce hamster HaPrPC to adopt a pro

214 neural network (APARENT-Perturb) for tandem polyA site usage, delineating a cis-regulatory code that

215 a broader fraction of the transcriptome than polyA-selected libraries.

216 Our findings demonstrate that polyA stem stability guides RNA-packaging selectivity.

217 We show that polyA runs do not elicit any response from No Go Decay (

218 The polyA tail is also a convenient handle to enrich binders

219 The polyA tail length is proportional to the binding affinit

220 The polyA-based immobilization approach is a promising alter

221 mble into triple helical fibers known as the polyA/CA motif.

222 siRNAs bind the target messenger RNA at the polyA signal and are capable of redirecting a small amou

223 escently label messenger RNAs locally at the polyA tail.

224 adic tumours that exhibit instability at the polyA tract in the TGFbetaRII gene and to 35% per allele

225 We show that by excluding the polyA tail from the viral reference, ReadItAndKeep preve

226 ovl4, which contained 1794 bp (excluding the polyA tail), including 909 bp of coding region that enco

227 In our initial case, we expanded the polyA tract within the native yeast poly(Adenine)-bindin

228 paration of the transposase element from the polyA sequence after transposition leads to its deactiva

229 hort abnormal (GCN) triplet expansion in the polyA-binding protein nuclear 1 (PABPN1) gene leads to P

230 e to a trinucleotide repeat expansion in the polyA-binding protein nuclear-1 gene.

231 icity that correlated with the length of the polyA expansion.

232 an RNA helicase, and Cid12, a member of the polyA polymerase family, in a complex that has RNA-direc

233 onsistently detect the ATTAAA variant of the polyA signal.

234 dulated by changing sequence features of the polyA tracks.

235 hesize involves stalling of ribosomes on the polyA tail.

236 g by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caen

237 h the ENE's ability to (i) interact with the polyA tail, (ii) inhibit deadenylation in vitro, and (ii

238 ed set of base-pairing interactions with the polyA tail.

239 t with diminishing returns relative to their polyA sections due to hypothesized steric clashes.

240 confirmed by probing a multiple human tissue polyA(+)RNA.

241 ctivated PKCbeta2 to mRNP complexes bound to polyA-mRNAs is involved in activity-triggered control of

242 real-time polymerase chain reaction (PCR) to polyA cDNAs prepared from 106 archived human frozen lymp

243 olyadenylated isoforms and those proximal to polyA sites are more likely to affect gene expression an

244 genes, selected from microarray studies, to polyA cDNAs prepared from 60 archived human frozen lymph

245 knocked down, spliced mRNA, as well as total polyA+ RNA, accumulates in nuclear speckle domains.

246 of a pipeline relying on sequencing of total polyA(+) and polysomal RNA from Arabidopsis grown under

247 Encounter with translated polyA segments by ZNF598 triggered ubiquitination of sev

248 tios, splice junction usage, alternative TSS/polyA usage, and RNA stability) and integrates them with

249 cific tissue and relative dominance when two polyA sites of the same gene are given.

250 es enzyme failure to recognize the unnatural polyA/CA motif, coupled with the motif's propensity to f

251 ontext of viral replication when an upstream polyA was included.

252 ict the most dominant (i.e. frequently used) polyA site of a gene in a specific tissue and relative d

253 Using polyA capture, 3' rapid amplification of complementary D

254 ction of OVA-specific CTL was abrogated when polyA+ RNA from OVA-expressing cells was treated with an

255 t molecular mechanisms mediating genome-wide polyA site expression and characterize their functional

256 NA-binding proteome (RBPome) associated with polyA-tailed RNA species in murine ciliated epithelial c

257 RP with stress granules and colocalizes with polyA binding protein in a variant-dependent manner.

258 nscripts are sequestered in the nucleus with polyA binding protein (PABPC1), and dsRNA is degraded to

259 fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMP

260 f Nano3P-seq in capturing non-A bases within polyA tails of various lengths, and reveal their distrib