ライフサイエンスコーパス: branch site

1 ed for stable interaction between U2 and the branch site.

2 dependent upon its position relative to the branch site.

3 nal extension serving as the major SUMO-SUMO branch site.

4 uires YUA, where Y = pyrimidine and A is the branch site.

5 found a variable distance downstream of the branch site.

6 ntervening sequence, IVS) boundaries and the branch site.

7 valent attachment of a 3' splice site to the branch site.

8 ensus sequences at the intron boundaries and branch site.

9 ts U2 small nuclear ribonucleoprotein to the branch site.

10 ring is involved in marking the prospective branch site.

11 ed for stable interaction between U2 and the branch site.

12 ',5'-branched RNA with any nucleotide at the branch site.

13 nt and is maintained postnatally at arterial branch sites.

14 ryo and is postnatally sustained at arterial branch sites.

15 of EHBP1 and syndapin I at nascent dendritic branch sites.

16 a function for microtubules in selecting new branch sites.

17 calizes preferentially to neuronal dendritic branch sites.

18 ria are often associated with age-associated branch sites.

19 ipheral domains in growth cones and emerging branch sites.

20 ginal alpha-phosphate can be attacked by the branch-site 2'-hydroxyl group; in the latter case, the l

21 ing ligation reaction is between an internal branch-site 2'-hydroxyl nucleophile on one RNA substrate

22 he dynamic associations of proteins with the branch site-3' splice site region during spliceosome ass

23 nitor RNA-protein interactions involving the branch site-3' splice site-3' exon region during yeast p

24 n Prp8p also associates extensively with the branch site-3' splice site-3' exon region.

25 icing occurs via a lariat intermediate whose branch site A residue is predicted to bulge from a duple

26 The 3'-tail emerging from the branch-site A may have indefinite length, but it must be

27 RNA fragments that precisely map to intronic branch sites across the transcriptome.

28 Interactions at the branch site adenosine and requirements for polypyrimidin

29 the discovery that the distance between the branch site adenosine and the acceptor site ranges from

30 on to promote the bulged conformation of the branch site adenosine and to enhance catalysis by snRNAs

31 antisense effect; moreover, only the 3'-most branch site adenosine served as the branch point.

32 complex, and specific interactions with the branch site adenosine.

33 he major groove surrounding the 2'-OH of the branch site adenosine.

34 nd 9F21 deoxyribozymes mediate reaction of a branch-site adenosine 2'-hydroxyl on one RNA substrate w

35 in contact with domain VI that positions the branch-site adenosine for lariat formation during forwar

36 isiae, in which a conserved psi extrudes the branch-site adenosine from the helix.

37 Because the branch-site adenosine is a bulged nucleotide flanked by

38 An unanswered question is whether the use of branch-site adenosine is inherently preferred or a chanc

39 yzes formation of 2',5'-branched RNA using a branch-site adenosine nucleophile and a 5'-triphosphate

40 embles natural RNA splicing instead prefer a branch-site adenosine, although adenosine was never avai

41 role in the selection of the precursor mRNA branch-site adenosine, the nucleophile for the first ste

42 ding the mechanism of the recognition of the branch-site adenosine.

43 Branch-site analyses of the group Q UGT gene tree allowe

44 Previously we showed that when the branch site and 3' splice site AG are supplied by separa

45 A splicing factors in cancer impact intronic branch site and 3' splice site recognition.

46 tranded RNA (ssRNA) sequence adjacent to the branch site and can block the action of debranchase enzy

47 tions were introduced in the vicinity of the branch site and surrounding domains.

48 de or alterations in the spacing between the branch site and the 3' splice site were examined for the

49 question both the fate of its pairing to the branch site and the details of its role in splicing cata

50 domain is required to target U2 snRNP to the branch site and the hU2AF35 RS domain is necessary for p

51 eosome to search for and utilize alternative branch sites and 3' splice sites.

52 ed modulators of epithelial growth to select branch sites and direct branch elongation, but the inter

53 d LR numbers due to the activation of LR pre-branch sites and LR primordia (LRP).

54 sed on the local concentration of spastin at branch sites and the other based on local detachment fro

55 vealed a reduction in the number of tertiary branching sites and increased spine density in Mecp2(WT_

56 icing factors located at the 5' splice site, branch site, and 3' splice site.

57 three obligate signals: a 5' splice site, a branch site, and a 3' splice site.

58 ll RNA containing the sequence of the intron branch site, and activate the branch adenosine to attack

59 en 18 and 40 nucleotides downstream from the branch site, and closer AGs are skipped in favour of AGs

60 e chemical groups on the adenine base at the branch site are differentially recognized during at leas

61 The few reported annotations of branch site are imprecise as reverse transcriptase skips

62 A) nucleotides that form base pairs with the branch site are initially sequestered in a branchpoint-i

63 Branched sites are identified with the FRAGS reagent by

64 snRNP-directed loading of U2 snRNP onto the branch site as well as efficient trans-splicing in these

65 ibit highly diverse structures with multiple branched sites as well as a complex regio- and stereoche

66 3' splice site and recruits U2 snRNP to the branch site at an early step in spliceosome assembly.

67 e 3' splice site and targets U2 snRNP to the branch site at an early step in spliceosome assembly.

68 atalytic step of pre-mRNA splicing, when the branch site attacks the 5' splice site (SS), and the sec

69 ever, other regions which are outside of the branch site base pairing region are not yet characterize

70 components of the U2 snRNP complex following branch site base pairing.

71 nt ATPase involved in monitoring the U2 BSRR-branch site base-pairing interaction.

72 d branch/branch-site models and unrestricted branch-site-based models (BS-REL, BUSTED and RELAX)), ou

73 ion of splicing, such as the position of the branch-site before and after the second step of splicing

74 e-like sequence in the universally conserved branch site-binding region of U2 is used in trans as a 5

75 atalytic step of pre-mRNA splicing, when the branch site (BS) attacks the 5' splice site, and the sec

76 Prp8 directly binds over the 5'SS and the branch site (BS) for the first catalytic step, and the 5

77 The duplex formed between the branch site (BS) of a spliceosomal intron and its cognat

78 ancers and have been shown recently to alter branch site (BS) or 3' splice site selection in splicing

79 (ss), presumably resulting from aberrant U2/branch site (BS) recognition by the mutant spliceosome.

80 association of the U2 snRNP with the intron branch site (BS) sequence during spliceosome assembly.

81 istically, SF3B1-PHF5A binds to the intronic branch site (BS) sequences of all factors, while DLC1 in

82 We now demonstrate that a strong branch site (BS), a long distance to the 3' splice site

83 l1 and Snail2 also promoted cell survival at branch sites, but this was not sufficient to induce bran

84 g the conserved A nucleotide of the intron 2 branch site (c.264-21A>G) was identified in the proband

85 Furthermore, we show that crosslinked branch sites can carry out both steps of splicing, sugge

86 We found RBM5 and RBM10 bound to nearly all branch site complexes and not simply those at regulated

87 RT-PCR across the branch sites confirmed lariat RNAs and circular RNAs in

88 Intron 6 of xTFIIS.oA contains splice and branch site consensus sequences conforming to those of t

89 by highly atypical 5' and 3' splice site and branch site consensus sequences that provide novel targe

90 composition and the presence of three glycan branch sites could be determined from the IRMPD fragment

91 il2, and E47 were transiently upregulated at branch sites; decreasing the expression of these transcr

92 ture reveals that the location of the linker branching site dictates tendency toward albumin associat

93 This branch site does not bear homology to consensus mammalia

94 These structures reveal that the branch-site domain VI helix swings 90 degrees , enabling

95 ic potentials of psi-modified and unmodified branch site duplexes.

96 n (BSRR), which base pairs with the pre-mRNA branch site during splicing.

97 P 155 contacts pre-mRNA on both sides of the branch site early in spliceosome assembly and is therefo

98 The intron downstream of the branch site emerges between the Prp8 reverse transcripta

99 wnstream CUGBP2-binding site and an upstream branch site for U2 snRNP binding.

100 n on endothelial cells at prelesional aortic branch sites from both apo E-deficient and apo E-deficie

101 Using a previously characterized branch site genetic suppression assay, we generated seco

102 In contrast, only a small fraction of branch sites have been identified even once.

103 ntribute to recognition of the spliceosome's branch site helix and activation of the nucleophile for

104 2 small nuclear (sn)RNA to form the pre-mRNA branch site helix.

105 duplex representing the eukaryotic pre-mRNA branch-site helix from Saccharomyces cerevisiae, in whic

106 in VI dynamics closely parallel spliceosomal branch-site helix movement and provide strong evidence f

107 ing formation of the unique structure of the branch-site helix.

108 eins must occur to allow formation of the U2-branch-site helix.

109 uctures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an

110 ation indicates the importance of the lariat branch site in splicing.

111 The branch site is chosen with extraordinarily high fidelity

112 to discern the mechanism by which the proper branch site is chosen.

113 conserved SF3a/SF3b subunits upstream of the branch site is essential for anchoring U2 snRNP to pre-m

114 The branch site is recognized during splicing catalysis and

115 n vivo and in vitro results suggest that the branch site is recognized in the absence of an active 3'

116 se the receptor structure for activating the branch site is unknown.

117 Moreover, we find the single-strandedness of branch sites is also associated with 3' splice site reco

118 a database of positive selection, based on a branch-site likelihood test.

119 nRNP and enhances binding of U2 snRNP to the branch site located upstream of the exon.

120 m single-stranded RNA in the optimal PPT and branch site locations and sequences further upstream.

121 It is the only known branch site marker.

122 A branch-site maximum likelihood model identified three si

123 The branch-site method (BSM) based on a likelihood ratio tes

124 g a variety of approaches (restricted branch/branch-site models and unrestricted branch-site-based mo

125 We used branch-site models to detect genome-wide positive select

126 We also find that branch-site models will incorrectly identify unconverted

127 Furthermore SUMO branch-site mutants suppressed several of the phenotypes

128 The branch site mutation c.6599-20A>T causes type 1 VWD thro

129 ortantly, a missense mutation of ALK-1 and a branch-site mutation of endoglin were also detected.

130 he first time, the effect of a deep intronic/branch-site mutation on exon skipping in PTEN but also f

131 the mitochondria of yeast strains containing branch-site mutations.

132 three-helix-junction structure in which the branch-site nucleotide is located at the intersection of

133 The preference for the branch-site nucleotide is U > C congruent with A > G, al

134 a chemical basis for nature's choice of the branch-site nucleotide, which is almost always adenosine

135 identify the intronic region that binds the branch site of a group IIB intron.

136 The branch site of group II introns is typically a bulged ad

137 region of U12 snRNA, which base pairs to the branch site of minor class introns is well characterized

138 Pairing between U2 snRNA and the branch site of spliceosomal introns is essential for spl

139 and distal frequencies correlated well with branch sites of the pectinate musculature.

140 f mutational variability is tolerated at the branch-site of group II introns, with no apparent loss o

141 reasing delays in activation distal to major branching sites of the crista terminalis and pectinate b

142 f a U2 snRNP-containing complex on a minimal branch-site oligonucleotide.

143 TPX2 condensates, which form the core of the branch site on microtubules.

144 splice sites, a polypyrimidine tract, and a branch site, other splicing-regulatory elements (SREs).

145 streamlined mechanism for recognition of the branch site, pyrimidine tract and 3' splice site at the

146 d both splice sites, we demonstrate that the branch-site receptor is a functional element required fo

147 served Psis (Psi35, Psi42, and Psi44) in the branch site recognition region (BSRR), which base pairs

148 Pseudouridine 35 (psi35) in the branch site recognition region of yeast U2 small nuclear

149 adopts a slightly different structure in the branch site recognition region.

150 s, each containing a point mutation near the branch site recognition sequence, for a synthetic growth

151 Inhibition of the branch-site recognition complex SF3B rapidly diminished

152 e to the overall recognition of the pre-mRNA branch site region by other components of the splicing r

153 inimal alpha-tubulin 3'SS, from the putative branch site region to the AG dinucleotide, is not suffic

154 U12 interaction with the 5' splice site and branch site regions of a U12-dependent intron, respectiv

155 urements suggest that the 5' splice site and branch site remain physically separated throughout splic

156 es of mutant and modified nucleotides at the branch-site reveal that adenine is recognized primarily

157 ynthesized by joining the 2'-hydroxyl of the branch-site ribonucleotide of a DNA or RNA strand to the

158 bozymes newly selected to use uridine as the branch-site RNA nucleotide in a structural context that

159 n important restriction for 7S11 is that the branch-site RNA nucleotide must be a purine (A or G), be

160 lice site selection by promoting alternative branch site selection.

161 fsK regulates hyphal branching by modulating branch-site selection and some aspect of the underlying

162 tructural determinants that appear to govern branch-site selection by group II introns.

163 s did not alter the high fidelity for proper branch-site selection.

164 g the need for initial nucleation or de novo branch-site selection.

165 nalogous to the pairing of US snRNA with the branch site sequence of the major class of introns.

166 equences are similar in S. pombe; however, a branch site sequence was not found in the P. carinii gen

167 tified approximately 80-kDa protein near the branch site sequence, suggesting a potential role for th

168 highly conserved adenosine in the consensus branch-site sequence, which is required for lariat forma

169 introns with noncanonical splice (AT-AC) and branch site sequences exists in metazoan protein coding

170 oes not bear homology to consensus mammalian branch site sequences.

171 pproach for defining high-resolution maps of branch-site sequences and intronic elements on a genomic

172 ution structure of the spliceosomal pre-mRNA branch site showed that a phylogenetically conserved pse

173 The classical splice site and putative branch site signals are completely conserved across the

174 Branch-site-specific analysis shows that the evolution o

175 ycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase.

176 involved in pre-mRNA splicing, including the branch site, splice sites, and polypyrimidine tract show

177 he WAVE regulatory complex (WRC) to dendrite branching sites, stimulating the Arp2/3 complex to polym

178 ins interact with pre-mRNA very close to the branch site, suggest that the SF3b complex plays a criti

179 several combinations of mutations moved the branch site systematically to new positions along the do

180 The branch-site test identified positive selection on T. inu

181 improved the computational efficiency of the branch-site test implementation, allowing larger data se

182 A reduced its affinity for Arp2/3 complex at branching sites that were stabilized by phalloidin.

183 An adenosine at the branch site, the nucleophile for the first transesterifi

184 terminates six nucleotides downstream of the branch site through an assembly of PPIL4, SKIP and the a

185 osine at nt 385 (underlined) in the BPS as a branch site to dictate the selection of the nt 409 3' ss

186 A branch site-to-3' splice site spacing of less than 10 or

187 Finally, matching branch site usage with isoform selection across the exte

188 ces, the epithelium axially aligns fibers at branch sites via RhoA/ROCK-mediated contractions.

189 With label at the branch site, we detected three distinct proteins, design

190 with identical sequence that emerge from the branch site, we developed strategies to control which of

191 traditional splicing signals, including the branch site, we tested whether auxiliary elements in Alu

192 irst description of a mutation at the lariat branch site, which plays a pivotal role in the splicing

193 e and higher eukaryotes, this boundary and a branch site within the intron are conserved.