ライフサイエンスコーパス: RNA motif

1 es multiple domains of Bvht and the RHT/AGIL RNA motif.

2 ulated expression of genes controlled by the RNA motif.

3 ssential secondary structure of the dominant RNA motif.

4 first calculation of coordinate error for an RNA motif.

5 can form a 'kissing' bulge complex, a unique RNA motif.

6 uman telomerase RNA, which contains an H/ACA RNA motif.

7 e MNV RdRp were found to contact the hairpin RNA motif.

8 ameshift stem-loop, are components of larger RNA motifs.

9 NA than to either single- or double-stranded RNA motifs.

10 be of most interest in attempts to identify RNA motifs.

11 ces to simple graphical objects representing RNA motifs.

12 transcriptionally via cis-regulatory DNA and RNA motifs.

13 bacteria, and identified 22 novel candidate RNA motifs.

14 eration, generation, and prediction of novel RNA motifs.

15 determinants of stability in these important RNA motifs.

16 stimulate the prediction and design of novel RNA motifs.

17 uding naturally occurring and other possible RNA motifs.

18 to be efficient cleavage agents for cognate RNA motifs.

19 dated transcription-factor-binding sites and RNA motifs.

20 condensates from nanostructured, star-shaped RNA motifs.

21 A-binding proteins that recognize additional RNA motifs.

22 nged in tandem, forming multipart modules of RNA motifs.

23 oss 1421 genes, enriched in CU-rich and CAGA RNA motifs.

24 incide with previously identified functional RNA motifs.

25 mited only by the availability of functional RNA motifs.

26 chemotypes allow for specific recognition of RNA motifs.

27 'U-Ubulge and central loop of stem-loop I or RNA motif 3 of 7SK are required for transactivation, sug

28 fied as high-likelihood candidates for novel RNA motifs, 4 were confirmed from the RNA dataset collec

29 rcRNA versions of ribozymes, mimics of viral RNA motifs, a streptavidin aptamer, and protein expressi

30 cilitate the comparison and visualization of RNA motifs across multiple 3D structures.

31 teristic bent conformation and two conserved RNA motifs, an apical hairpin loop and a loop E.

32 f pharmaceutical agents that target specific RNA motifs, an understanding of RNA primary, secondary,

33 the alternative splicing of 505 genes, with RNA motif analysis revealing an enrichment for Aurora-A

34 This study describes an HuR target RNA motif and presents a general strategy for identifyin

35 dy suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA

36 er evolutionary conservation in both DNA and RNA motifs and are enriched in lincRNAs that have been f

37 tudies to elucidate the interactions between RNA motifs and cellular factors that potentiate directio

38 smallest and simplest of the known catalytic RNA motifs and has a unique metal ion specificity for di

39 the discovery of new aminoglycoside-binding RNA motifs and may also have relevance toward understand

40 ediated coactivation is executed by distinct RNA motifs and not by an encoded protein.

41 ow that transient states can remodel distant RNA motifs and possibly give rise to mechanisms for rapi

42 oops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed

43 site Atlas, and RBPSuite enable the study of RNA motifs and RNA-protein interactions, shedding light

44 as to probe the function of conserved viral RNA motifs and secondary structures.

45 tion cycles, emphasizing regulatory roles of RNA motifs and structural dynamics in diverse biological

46 fers a useful graph-based tool for exploring RNA motifs and suggesting large RNA motifs for design.

47 re by designing a cassette of synonymous MS2 RNA motifs and tandem coat proteins for RNA imaging and

48 the functional and structural properties of RNA motifs, and a growing interest in utilising biomolec

49 conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for

50 form abundance analysis, machine learning of RNA motifs, and massively parallel reporter assays.

51 d to quantify the characteristics of a given RNA motif are major goals in the field of RNA research;

52 Many novel RNA motifs are being identified by using bioinformatics

53 All RNA motifs are catalogued by graph vertex number (a meas

54 Double-stranded (ds)RNA motifs are central to immune regulation and block to

55 Several structural principles pertaining to RNA motifs are derived from our analysis.

56 DNA sequences coding for PRC2-binding RNA motifs are enriched at PRC2-binding sites on chromat

57 gest that the stability and folding of small RNA motifs are highly dependent on local context.

58 gions of most if not all segments, but these RNA motifs are poorly defined.

59 pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified.

60 The structures of viral and viroid RNA motifs are studied commonly by in vitro, computation

61 emonstrate the feasibility of using selected RNA motifs as adjuvants in the context of novel aerosol

62 eening strategy to integrate combinations of RNA motifs as architectural joints and DNA building bloc

63 tify alternative protonation states in other RNA motifs, as well as in DNA and proteins.

64 elds and to characterize dynamics in diverse RNA motifs at atomic resolution.

65 n highly accurate covariance models of known RNA motifs based on small numbers of related sequences,

66 It also exemplifies the need of classifying RNA motifs based on their tertiary structural features r

67 -binding activity, with the various proposed RNA motifs being neither necessary for FUS binding nor s

68 in moieties to interact with AU- and UG-rich RNA motifs, binding with low and high affinity, respecti

69 raction depended mainly on a single-stranded RNA motif, but not that of the GFP aptamer, whose intera

70 ases reveals that natural metabolite-sensing RNA motifs can accrue mutations that expand the diversit

71 , these results imply that similar catalytic RNA motifs can arise under fairly simple conditions and

72 While multiple RNA motifs can be bound, recognition of the canonical AU

73 ructures to suggest which hypothetical large RNA motifs can be considered "RNA-like".

74 ularity of 16S and 23S rRNAs by showing that RNA motifs can be constructed from at least 210 building

75 the structural relationships shared by these RNA motifs can be used as a proto-language for assisting

76 e of the selected receptors is a novel 12 nt RNA motif, (CCUGUG ...

77 The U-turn is a well-known RNA motif characterized by a sharp reversal of the RNA b

78 hemical probing data indicate that a modular RNA motif, common to loop E of eucaryotic 5 S ribosomal

79 RNA motifs comprising nucleotides that interact through

80 nd a tree formalism re-define and expand the RNA motif concept, unifying what previously appeared to

81 ization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with

82 A typical RNA motif consists of multiple elements and the running

83 rations, pervasive co-occurrences of DNA and RNA motifs, context-dependent selection for motif avoida

84 Structured RNA motifs create interaction domains for specific prote

85 one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translati

86 To date, however, no unbiased RNA motif definition and clear dissection of nucleic aci

87 d found that among other RNAs, Ro60 bound an RNA motif derived from endogenous Alu retroelements.

88 We use this interaction with an RNA motif derived from this B-repeat region to determine

89 The RNA motifs described here constitute a new paradigm for

90 gner: designs sequences that fold onto novel RNA motifs (described by tree graph topologies).

91 tructures remains a significant challenge in RNA motif design and is crucial for developing RNA-based

92 mplex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF bin

93 d that the engineered ENC inhibits disparate RNA motifs differently, instead of weakening all RNA mot

94 resolve mechanisms by which TERT domains and RNA motifs direct repeat synthesis.

95 ed here will be broadly useful for efficient RNA motif discovery.

96 s enriched at the 3' end of genes, and binds RNA motifs downstream from cleavage sites.

97 y two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein conde

98 ry immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and

99 a GAA-repeat, Exonic Splicing Enhancer-like RNA motif enriched in flanking sequence around HIN1-regu

100 d the identification of conserved structural RNA motifs enriched in each group, suggesting that speci

101 Previous studies identified RNA motifs enriched in Ssd1-associated transcripts, yet

102 additionally, enzymatic activity on certain RNA motifs, especially those flanked by a 5' guanosine i

103 r an almost-exhaustive list of over 50 known RNA motifs ('everything').

104 exity region are required for binding to the RNA motif exposed by m6A methylation.

105 address these issues, we present a universal RNA motif-finding/scanning strategy, termed PRIESSTESS (

106 ion of the 3'-UTR was identified as a target RNA motif for TIAR binding by both RNA gel shift analysi

107 ions (EuPRI), a freely available resource of RNA motifs for 34,746 RBPs from 690 eukaryotes.

108 or exploring RNA motifs and suggesting large RNA motifs for design.

109 ally integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for col

110 In addition to GCAUG, Rbfox1/LASR binds RNA motifs for LASR subunits hnRNPs M, H/F, and C and Ma

111 ogo has been widely used to represent DNA or RNA motifs for more than three decades.

112 protist Trichomonas vaginalis and show that RNA motifs found in yeast and metazoan introns are requi

113 library by extracting validated or predicted RNA motifs from gene-annotated RNA regions.

114 Motif enrichment analysis using DNA or RNA motifs from human, mouse, worm, fly and other model

115 stericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database

116 To determine if this catalytic RNA motif has a wider distribution, we decided to scruti

117 Predictions of the folding patterns of these RNA motifs have been based primarily on sequence and bio

118 Although numerous RNA motifs have been classified and characterized, the i

119 Many simple functional RNA motifs have been found by in vitro selection experim

120 e been implicated and the evidence that such RNA motifs have potential as small molecule target.

121 Atomic structures of small RNA motifs help to provide a better understanding of the

122 ORF57 binds a group of lncRNAs via the RNA motifs identified by ORF57 CLIP-seq to regulate thei

123 We have studied this RNA motif in a 21 nucleotide hairpin containing a GA coa

124 he zebrafish transcriptome, we identified an RNA motif in a variant FurinA transcript harbouring a lo

125 ecific recruitment of PRC2 by a well-defined RNA motif in cells reveals that results are PRC2 indepen

126 ws a widespread distribution of this kind of RNA motif in different sequences suggesting that they mi

127 he sporadic occurrence of this self-cleaving RNA motif in highly divergent organisms could be a conse

128 Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) require

129 analysis identified a functionally enriched RNA motif in the 3' untranslated regions (UTRs) of Brat-

130 Furthermore, an RNA motif in the 5'-untranslated region of RNA1, named t

131 o study the causality between modulating the RNA motif in vitro and the phenotypic outcome in cells.

132 nd highlighted numerous candidate regulatory RNA motifs in 3' untranslated regions.

133 was probed for binding to over 70,000 unique RNA motifs in a high throughput solution-based screen.

134 s to a large number of mRNAs through defined RNA motifs in a sequence-specific manner.

135 We found direct evidence that CpG RNA motifs in a U-rich context control pDC activation an

136 physically separable from the roles of other RNA motifs in establishing a properly defined template.

137 The recognition of cis-regulatory RNA motifs in human transcripts by RNA binding proteins

138 RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternativ

139 ying the structure-function relationships of RNA motifs in other biological processes.

140 Finally, we identified four overrepresented RNA motifs in SARs that likely mediate SR45's recognitio

141 etion analysis, this approach identified six RNA motifs in SRA important for coactivation.

142 novel mechanism of trans-splicing, in which RNA motifs in the 5' intron are sufficient to bring sepa

143 To identify the RNA motifs in the apoB mRNA that support physiological e

144 Here the authors identify short RNA motifs in the parechovirus genome that bind capsid p

145 by structural interactions between identical RNA motifs in the viral leader region.

146 binds p53 and p21 mRNAs via specific C-rich RNA motifs in their 3'-UTRs, enhancing RNA stability and

147 CMfinder is a new tool to predict RNA motifs in unaligned sequences.

148 On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift

149 can now blindly predict energetics of basic RNA motifs, including chemically modified variants, with

150 The RNA motifs, including internal and external loops, are a

151 Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pair

152 the information available on small molecule-RNA motif interactions, which could be useful to design

153 poration of sequences encoding self-cleaving RNA motifs into the transcriptional unit of a gene or ve

154 should be applicable for elucidating minimal RNA motifs involved in many other types of interactions.

155 se candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and

156 An RNA motif is a discrete sequence or combination of base

157 One residue within this RNA motif is only semiconserved and can be an A or C.

158 This sense-antisense RNA motif is used in the regulation of many cellular pro

159 that the thermodynamic contribution of small RNA motifs is independent of both its position in the du

160 a stabilizing and phylogenetically conserved RNA motif, is explored using (31)P NMR spectroscopy and

161 action between the viral protein Rev and the RNA motifs known as Rev response elements (RREs) is requ

162 ified as a DM1 binder through analysis of an RNA motif-ligand database, these studies suggest that le

163 al space simultaneously to identify specific RNA motif-ligand interactions.

164 of gene expression in relation to conserved RNA motifs like OLE RNA as well as in riboswitches and o

165 Specific RNA motifs likely regulate various aspects of this repli

166 The iron-responsive element (IRE) is a 30nt RNA motif located in the non-coding regions of mRNAs of

167 We have identified a highly conserved RNA motif located upstream of genes encoding molybdate t

168 anidine to a previously described, conserved RNA motif located within the gdmH 5'-untranslated region

169 In addition to the classical 3'CSE, other RNA motifs located elsewhere in the SIN genome must play

170 the highly conserved nature of the consensus RNA motif may relate to its tolerance to various mutatio

171 scriptions of a relatively small universe of RNA motifs may lead to predictive models of RNA tertiary

172 We propose that RNA-motif nature and Roquin A- and B-sites jointly steer

173 actions, which identified modules that bound RNA motifs nearby and in the Drosha processing site.

174 cy of the recoding event is regulated by cis RNA motifs, no mechanistic explanation is currently avai

175 (2+) binding properties of a conserved 75mer RNA motif of the internal ribosome entry site (IRES) ele

176 eatures of 5BSL3.2 are present in functional RNA motifs of flaviviruses, suggesting conserved regulat

177 ertiary-structure-function relationships for RNA motifs of general biological significance.

178 Modular RNA motifs of greatly distinct sequence and local second

179 te how RNA condensates formed by star-shaped RNA motifs, or nanostars, can be dynamically controlled

180 opologies and guiding the discovery of novel RNA motifs, perhaps anti-viral therapeutics by subgraph

181 In summary, we have identified an AU-rich RNA motif present in NF90 target mRNAs and have obtained

182 ation on short sequence- and structure-based RNA motifs present within families.

183 an microbiome remains unmined for structured RNA motifs primarily due to computational limitations.

184 ects of Pus4 suggest that the CAM-containing RNA motif provides a regulatory link between RNA replica

185 ution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles and

186 Collectively, the abundance of PRC2-binding RNA motifs rationalizes the promiscuous RNA binding of P

187 olecules that selectively bind to structured RNA motifs remains an important challenge in developing

188 RNA motifs reported in the literature, such as 'Kink tur

189 The pistol RNA motif represents a new class of self-cleaving ribozy

190 the identification of a 17- to 20-base-long RNA motif rich in uracils.

191 oinformatics, we have now discovered a novel RNA motif, ROSE-G, that is closely related to the canoni

192 We have designed a new algorithm for RNA motif search and implemented a new motif search tool

193 In this paper, we study the problem of RNA motif search in long genomic sequences.

194 We have developed a new method for RNA motif search that allows for a significant speedup o

195 Using a hammerhead RNA motif search with relaxed delimitation of the non-co

196 amics simulations explicitly identify target RNA motifs sensitive to magnesium ions and SAM.

197 s of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein ma

198 ms and plants, in contrast to the vertebrate RNA motif set, which has remained relatively stable afte

199 ening program increased the dataset of known RNA motif-small molecule binding partners by 20-fold.

200 d that probes over 3,000,000 combinations of RNA motif-small molecule interactions to identify the pr

201 -96) hairpin precursor against a database of RNA motif-small molecule interactions, which identified

202 tructural motifs that mimic endogenous plant RNA motifs so that they are recognized by cellular facto

203 a variety of RNA motifs) were the preferred RNA motif space that binds small molecules.

204 xperimentally verified that examples of this RNA motif specifically recognize S-adenosylhomocysteine

205 telomerase RNA subunit by demonstrating that RNA motifs stimulate the processivity of nucleotide and

206 l design and suggests a route to investigate RNA motif structures by configuring them into nanoarchit

207 which inducible interactions of noncanonical RNA motif structures with targeting factor heterogeneous

208 efine the highest affinity and most specific RNA motif targets for heterocyclic small molecules.

209 The hammerhead ribozyme is a small RNA motif that catalyzes the cleavage and ligation of RN

210 The guanine quadruplex sequence (GQS) is an RNA motif that folds in the presence of K(+) ions.

211 Twister is a recently discovered RNA motif that is estimated to have one of the fastest k

212 We report here the identification of an RNA motif that is required for PSTVd to traffic from non

213 sis (cob) operon of S.typhimurium carries an RNA motif that matches this consensus sequence.

214 nd in vitro characterization of a MG-binding RNA motif that may enable the same high-resolution analy

215 We have identified a highly conserved RNA motif that occurs upstream of genes involved in S-ad

216 nome contain the same cis-cleaving catalytic RNA motif that plays a crucial role in virus replication

217 Using this method, we discovered an RNA motif that recognizes the U1 small nuclear ribonucle

218 phosphate (ZTP) riboswitch, a ligand-binding RNA motif that regulates bacterial gene expression.

219 at define the functional requirements for an RNA motif that specifies high-affinity binding to the ca

220 go2:miR-122:HCV complex reveals a structured RNA motif that traps Ago2 on the viral RNA, masking its

221 have discovered a large and highly conserved RNA motif that typically resides in a noncoding section

222 viding a comprehensive picture of the DNA or RNA motifs that are enriched in the input sequences.

223 hese studies further establish a database of RNA motifs that are recognized by small molecules that c

224 amers are a class of in vitro selected small RNA motifs that bind a small-molecule ligand with high a

225 of the small molecules that bind RNA and the RNA motifs that bind small molecules.

226 motypes that bind RNA and preferences in the RNA motifs that bind small molecules.

227 tification and characterization of conserved RNA motifs that can be readily used for database search.

228 bozymes comprise a family of small catalytic RNA motifs that catalyze the same reversible phosphodies

229 The IRE fold is representative of many RNA motifs that contain helical domains separated by a b

230 ponents based on utilizing multiple distinct RNA motifs that control N-protein interactions.

231 many non-helical base-pairs are involved in RNA motifs that form a defined set of non-canonical conf

232 At the center of attention are RNA motifs that guide where RBPs bind.

233 Our results led to a genomic map of viroid RNA motifs that mediate single-cell replication and syst

234 onserved but functionally diverse structural RNA motifs that occur in multiple coding regions of the

235 Riboswitches are structured RNA motifs that recognize metabolites to alter the confo

236 Riboswitches are widespread RNA motifs that regulate gene expression in response to

237 iary structures and functional mechanisms of RNA motifs that regulate viroid replication and traffick

238 mework for detecting such regulatory DNA and RNA motifs that relies on directly assessing the mutual

239 The RNA motifs that specifically bind each small molecule we

240 The A-minor junction is a class of RNA motifs that specifically controls coaxial stacking o

241 blind all-atom prediction for a noncanonical RNA motif, the C7.2 tetraloop/receptor, and validated th

242 tains multiple examples of a newly described RNA motif, the extruded helical single strand.

243 irus (HDV) harbors a self-cleaving catalytic RNA motif, the genomic HDV ribozyme, whose crystal struc

244 DV) employs a unique self-cleaving catalytic RNA motif, the HDV ribozyme, during double-rolling circl

245 nome contain a common cis-cleaving catalytic RNA motif, the HDV ribozyme, which plays a crucial role

246 izes in association with a highly structured RNA motif, the Rev response element.

247 ages by re-engineering a natural, biological RNA motif: the packaging RNA of phi29 bacteriophage.

248 mprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiar

249 It utilizes a self-cleaving catalytic RNA motif to process multimeric intermediates in the dou

250 t functions with CNBP through a well-defined RNA motif to regulate cardiovascular lineage commitment,

251 from a single Quaking gene and bind the same RNA motif to regulate splicing, translation, decay, and

252 gRNAs (epegRNAs), which include a structured RNA motif to stabilize and protect pegRNA 3' ends, and t

253 Based on the ability of specific RNA motifs to block tolerance induction and effectively

254 w the intron uses structurally unprecedented RNA motifs to select the 5'- and 3'-splice sites.

255 We incorporated structured RNA motifs to the 3' terminus of pegRNAs that enhance th

256 motifs differently, instead of weakening all RNA motifs to the same extent.

257 -mobile mRNAs, but little is known regarding RNA motifs triggering mobility, the extent of mRNA trans

258 oism experiments show that box C/D and C'/D' RNA motifs undergo conformational changes when magnesium

259 ovide valuable insights into the size of the RNA motif universe and RNA design strategies, offering a

260 These modules can be applied to design novel RNA motifs via build-up-like procedures for constructing

261 nstrated that expression of a short, YFV env RNA motif (vsRNA) was required and sufficient to inhibit

262 Instead, the RNA motif was bound by the ZC3H12B's PilT N terminus (PI

263 Structural analysis revealed that the RNA motif was not bound by the conventional C3H1 RNA-bin

264 Other RNA motifs were also enriched in these transcripts, most

265 approach, hairpin loops (among a variety of RNA motifs) were the preferred RNA motif space that bind

266 This work thus identified multiple novel RNA motifs which appear to contribute to genome packagin

267 me that was bound to an essential telomerase RNA motif, which suggests a role for histones in the fol

268 It seems that simple substructures can build RNA motifs, which combine to establish the fundamental a

269 xamine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridi

270 Unfolding of a RNA motif with internal multiloop, namely, the 109-nucle

271 hairpin ribozyme is a small endonucleolytic RNA motif with potential for targeted RNA inactivation.

272 ved during evolution are good candidates for RNA motifs with posttranscriptional regulatory functions

273 s the three-dimensional (3D) conformation of RNA motifs with small molecule binding partners, directl

274 er, due to challenges in identifying compact RNA motifs with the ability to bind ligands with good ph

275 tudy, we identified a conserved guanine-rich RNA motif within the miR-23b/27b/24-1 cluster that can f

276 structures; we report several occurrences of RNA motifs within larger RNAs.

277 udies provide direct evidence for cis-acting RNA motifs within precursor tRNAs that facilitate the se

278 l advance by defining specific homopolymeric RNA motifs within the genome of HCV and other RNA viruse

279 neered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019).