ライフサイエンスコーパス: RNA motif

1 ssential secondary structure of the dominant RNA motif.

2 first calculation of coordinate error for an RNA motif.

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

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

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

6 ulated expression of genes controlled by the RNA motif.

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

8 ces to simple graphical objects representing RNA motifs.

9 transcriptionally via cis-regulatory DNA and RNA motifs.

10 bacteria, and identified 22 novel candidate RNA motifs.

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

12 determinants of stability in these important RNA motifs.

13 stimulate the prediction and design of novel RNA motifs.

14 uding naturally occurring and other possible RNA motifs.

15 to be efficient cleavage agents for cognate RNA motifs.

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

17 mited only by the availability of functional RNA motifs.

18 chemotypes allow for specific recognition of RNA motifs.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

37 Many novel RNA motifs are being identified by using bioinformatics

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

61 RNA motifs comprising nucleotides that interact through

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

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

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

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

66 Structured RNA motifs create interaction domains for specific prote

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

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

69 The RNA motifs described here constitute a new paradigm for

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

125 Specific RNA motifs likely regulate various aspects of this repli

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

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

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

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

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

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

132 (2+) binding properties of a conserved 75mer RNA motif of the internal ribosome entry site (IRES) ele

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

134 Modular RNA motifs of greatly distinct sequence and local second

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

180 The RNA motifs that specifically bind each small molecule we

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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