ライフサイエンスコーパス: cotranscriptional

1 ip1) gene-specific splicing is predominantly cotranscriptional.

2 demonstrating that they are not exclusively cotranscriptional.

3 gesting that splicing is more efficient when cotranscriptional.

4 phosphorylation by Ctk1 recruits factors for cotranscriptional 3' end processing in vivo.

5 lts indicate that Rpb4 contributes to proper cotranscriptional 3'-end processing in vivo.

6 a sensitive readout of genetic influences on cotranscriptional 3'-processing and termination and a to

7 I (Pol II) transcription sites to facilitate cotranscriptional 5'-capping of pre-mRNA and other Pol I

8 Eukaryotic mRNAs undergo cotranscriptional 5'-end modification with a 7-methylgua

9 Here we assess cotranscriptional A-to-I editing in Drosophila by isolat

10 tivity by KLFs reflects sequestration of the cotranscriptional activator CBP/p300, making this cofact

11 9 increases the affinity of a well-described cotranscriptional activator of nuclear hormone receptors

12 EADs) are transcription factors that bind to cotranscriptional activators like the yes-associated pro

13 tructure-based drug design to interfere with cotranscriptional activity of CtBP in cancer.

14 o acid reduces beta-catenin phosphorylation, cotranscriptional activity, and stability.

15 y MPRAs, particularly those that interrogate cotranscriptional and post-transcriptional processes: al

16 The snRNPs display patterns that indicate a cotranscriptional assembly model: U1 first, then U2, and

17 the inner and outer layers and to chart the cotranscriptional assembly of each subunit.

18 These results suggest a mechanism for cotranscriptional assembly of the export competent mRNP

19 tylation and deacetylation facilitate proper cotranscriptional association of spliceosomal snRNPs.

20 analysis suggests that Spt6 is required for cotranscriptional association of the factor Ctr9, a memb

21 ing in the ribD riboswitch provides time for cotranscriptional binding of flavin mononucleotide, whic

22 ulation of transcription by Abd1 may enhance cotranscriptional capping and also act as a checkpoint t

23 inal domain results in a drastic decrease in cotranscriptional capping efficiency but is reversed by

24 d have suggested a checkpoint model in which cotranscriptional capping is a necessary step for the ea

25 Cotranscriptional capping of HIV mRNA is strongly stimul

26 nt phosphorylation of RNAP II CTD stimulates cotranscriptional capping of HIV-1 mRNA.

27 ation factor Spt5 are thought to orchestrate cotranscriptional capping of nascent mRNAs.

28 ind the phosphorylated pol II CTD permitting cotranscriptional capping of nascent pre-mRNAs.

29 and functions as an important checkpoint in cotranscriptional capping of RNA polymerase II (Pol II)

30 f the Pol II largest subunit (CTD), allowing cotranscriptional capping of the nascent pre-mRNA.

31 The process uncouples cotranscriptional chromatin remodeling by dTip60 complex

32 bp4 compromised SSU processome formation and cotranscriptional cleavage of the pre-rRNA.

33 als, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by

34 cleavage at the poly(A) site or at a second cotranscriptional cleavage site (CoTC).

35 Following depletion of Rrp5, cotranscriptional cleavage was lost and preribosome comp

36 been demonstrated or suggested to involve a cotranscriptional component.

37 s within a key hairpin to engender efficient cotranscriptional conformational rearrangement into the

38 ntitatively modulate gene expression through cotranscriptional coupling mechanisms.

39 Regulated cotranscriptional decapping near promoter-proximal pause

40 Cotranscriptional degradation of nascent RNA has not bee

41 nucleases, Rat1 and Xrn1, both contribute to cotranscriptional degradation of nascent RNA, but this d

42 cues within nascent transcripts, specify the cotranscriptional engagement of the relevant RNA process

43 mRNA capping is a cotranscriptional event mediated by the association of c

44 n yeast, histone H2B monoubiquitination is a cotranscriptional event regulating histone H3 methylatio

45 The function of cotranscriptional events in the selection of alternative

46 of different poly(A) sites, suggesting that cotranscriptional events may influence the decision betw

47 ce YSPTSPS and coordinates transcription and cotranscriptional events through dynamic phosphorylation

48 eptapeptides and connects transcription with cotranscriptional events.

49 ting alternative RNA folds, are sensitive to cotranscriptional events.

50 C-terminal binding proteins (CtBPs) are cotranscriptional factors that play key roles in cell fa

51 The prp8 mutation perturbs a cotranscriptional feedback mechanism linking COOLAIR pro

52 consistent with the experimental data and a cotranscriptional folding and assembly hypothesis were g

53 show that TECprobe-VL identifies coordinated cotranscriptional folding events that mediate transcript

54 chemical probing experiments that study RNA cotranscriptional folding generate nucleotide-resolution

55 Moreover, a cotranscriptional folding intermediate could be cleaved

56 res methods for determining the structure of cotranscriptional folding intermediates.

57 oped an optical-trapping assay to follow the cotranscriptional folding of a nascent RNA and used it t

58 econd crucial ingredient of the model is the cotranscriptional folding of the RNA transcript, sterica

59 The profiling of the cotranscriptional folding pathway and identification of

60 oswitch designed to perturb steps within its cotranscriptional folding pathway.

61 new antiviral drug designs targeting kinetic cotranscriptional folding pathways in viral RNAs.

62 known RNA structural transitions within the cotranscriptional folding pathways of the Escherichia co

63 well with RNA folding energies obtained from cotranscriptional folding simulations.

64 table to predict structures that result from cotranscriptional folding, as they can only calculate pr

65 luence dynamic conformational changes during cotranscriptional folding.

66 y and that modulates RNA conformation during cotranscriptional folding.

67 hat lattices can be made by annealing and/or cotranscriptional folding.

68 enable the precise mapping of events during cotranscriptional folding.

69 of early folding stem-loop structures in the cotranscriptional formation of complex RNA molecules inv

70 nce of CGI promoters that is revealed by the cotranscriptional formation of R loop structures.

71 ite of phosphorylation important for EBNA2's cotranscriptional function in mitosis.

72 identify ERI-1 as an important regulator of cotranscriptional gene silencing and post-transcriptiona

73 s, contributing to a paradigm shift from the cotranscriptional gene silencing observed in fission yea

74 ns in deacetylating histones and suppressing cotranscriptional histone eviction.

75 de changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H

76 Cotranscriptional histone methylations by Set1 and Set2

77 of the Paf1 complex, which regulates several cotranscriptional histone modifications, and Chd1, a chr

78 maintaining chromatin structure, regulating cotranscriptional histone modifications, and controlling

79 s, ranging from RNA Polymerase II pausing to cotranscriptional histone modifications.

80 ral mechanisms, including the stimulation of cotranscriptional histone modifications.

81 d, but are generally accepted to be post- or cotranscriptional in character.

82 ng frame, gives rise to the C protein, while cotranscriptional insertion of an extra base gives rise

83 imize transcription elongation, coordinating cotranscriptional interactions of many factors/snoRNAs w

84 RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead t

85 Cotranscriptional loading of RNA processing factors onto

86 calized on the HBV minichromosome to achieve cotranscriptional m(6)A modification of viral RNAs.

87 t did not impair RNA Pol II transcription or cotranscriptional m(7)G capping.

88 provide instructions to transcriptional and cotranscriptional machinery allowing genome expansion in

89 g from an insufficiency in components of the cotranscriptional machinery.

90 UAP56 and NXF1, essential components of the cotranscriptional machinery.

91 gest that Naf1p and Cbf5p are recruited in a cotranscriptional manner during H/ACA snoRNP assembly, p

92 atin establishment at piRNA target loci in a cotranscriptional manner.

93 In this issue, Munoz et al. uncover a cotranscriptional mechanism for activating alternative p

94 together, our results are consistent with a cotranscriptional mechanism for generating the cap 4 str

95 ense splicing increases FLC expression via a cotranscriptional mechanism involving capping of the FLC

96 ice site selection, these findings support a cotranscriptional mechanism to recognize paired 3' and 5

97 binding of Spt6 to Ser2-P RNAPII provides a cotranscriptional mechanism to recruit Iws1, REF1/Aly, a

98 Such cotranscriptional mechanisms are emerging as important r

99 Cotranscriptional methylation of histone H3 lysines 4 an

100 Impaired cotranscriptional microprocessor assembly was accompanie

101 We show that cotranscriptional microprocessor assembly, regulated by

102 The cotranscriptional mRNA processing and packaging reaction

103 ssociates with genes to facilitate efficient cotranscriptional mRNA processing.

104 rase II initiation and elongation as well as cotranscriptional mRNA processing.

105 Additional experiments suggest cotranscriptional PCPA counteracted by U1 association wi

106 The cotranscriptional placement of the 7-methylguanosine cap

107 el mouse models to further examine roles for cotranscriptional/post-transcriptional gene regulation d

108 a critical role for H2B deubiquitination in cotranscriptional pre-mRNA processing events.

109 Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate

110 APII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termi

111 omoters over gene bodies, thereby modulating cotranscriptional pre-mRNA splicing.

112 criptional elongation is required for normal cotranscriptional pre-mRNA splicing.

113 at the rDNA in Seb1-deficient cells impaired cotranscriptional pre-rRNA processing and the production

114 ferentially inhibits super-enhancer-directed cotranscriptional pri-miRNA processing.

115 gnaling pathway controls transcriptional and cotranscriptional processes could provide new insights i

116 ted an evolutionarily conserved function for cotranscriptional processes in the maintenance of genome

117 Transcriptional output is influenced by cotranscriptional processes interconnected to chromatin

118 mics have uncovered its diverse functions in cotranscriptional processes, including chromatin remodel

119 ring the coordination of DNA replication and cotranscriptional processes.

120 Taken together, cotranscriptional processing and stability of a set of s

121 d mRNA production is potentially affected by cotranscriptional processing as well as RNAi and Polycom

122 The role of cotranscriptional processing by RNA interference and by

123 Finally, we present evidence that cotranscriptional processing events determine the recrui

124 tes chromatin modifications and suggest that cotranscriptional processing events play a primary role

125 a model in which hypoxia-induced changes to cotranscriptional processing lead to selective retention

126 ude that CDK11 plays a critical role for the cotranscriptional processing of all HIV mRNA species.

127 Thus, CDK12 plays an important role in cotranscriptional processing of c-FOS transcripts.

128 ription complex for efficient elongation and cotranscriptional processing of mRNA.

129 the transcription cycle and ensure efficient cotranscriptional processing of mRNAs.

130 stimulates RNA polymerase II elongation and cotranscriptional processing of pre-mRNA.

131 of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly o

132 plants, microRNA (miRNA) biogenesis involves cotranscriptional processing of RNA polymerase II (RNAPI

133 on of serine 7 was shown to be important for cotranscriptional processing of two snRNAs in mammalian

134 ranscription, DNA repair, mRNA splicing, and cotranscriptional processing.

135 binant E. coli RNase P, suggesting potential cotranscriptional processing.

136 iated transcription-replication conflicts by cotranscriptional protein engagement of nascent RNA is e

137 RNAs is regulated, their propensity to form cotranscriptional R loops, and how they modulate rRNA tr

138 We here report real-time observations of cotranscriptional R-loop formation at single-molecule re

139 The FLC antisense transcripts form a cotranscriptional R-loop that is dynamically resolved by

140 an TH1- or TH2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced

141 In this study, we found that cotranscriptional R-loops formed at a CAG-70 repeat inse

142 re probing (TECprobe-LM), which assesses the cotranscriptional rearrangement of RNA structures by seq

143 clin T components of P-TEFb are required for cotranscriptional recognition of the 3' box RNA 3' end p

144 S) and Set3C deacetylation activities, their cotranscriptional recruitment is stimulated by the phosp

145 otein (TBP) block mRNA export, implying that cotranscriptional recruitment of Npl3 is required for ef

146 Cotranscriptional recruitment of pre-mRNA splicing facto

147 These findings support a model whereby cotranscriptional recruitment of Rnf20 at MLL-fusion tar

148 However, how the cotranscriptional recruitment of splicing factors is reg

149 that Npl3 promotes splicing by facilitating cotranscriptional recruitment of splicing factors.

150 provide evidence that the mechanism involves cotranscriptional recruitment of SR proteins to RNAP II

151 longation complex, which functions in direct cotranscriptional recruitment of the mRNA export protein

152 In contrast, the cotranscriptional recruitment of the RNA-binding protein

153 this as a fail-safe mechanism to ensure the cotranscriptional recruitment of TRAMP before or during

154 riptional snRNP recruitment and suggest that cotranscriptional recruitment of U2 or the tri-snRNP is

155 ospho-CTD is likely involved directly in the cotranscriptional recruitment of Yra1.

156 dies of active genes, arguing against simple cotranscriptional recruitment to RNA substrates.

157 imulating the degradation process upon their cotranscriptional recruitment.

158 domains of life and plays many key roles in cotranscriptional regulation and in recruiting other fac

159 This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in

160 Together these data reveal that antagonistic cotranscriptional regulation through AGO1 or THO/TREX in

161 ion of nascent COOLAIR and RNA 3' processing/cotranscriptional regulators and enhances COOLAIR proxim

162 gulation, but how the functions of different cotranscriptional regulators are integrated is poorly un

163 Opposing functions of cotranscriptional regulators during an early embryonic d

164 The involvement of these conserved cotranscriptional regulators suggests similar mechanisms

165 Our approach allows the investigation of cotranscriptional regulatory mechanisms in bacterial and

166 (dGsw-int) to evaluate the possibility of a cotranscriptional regulatory role.

167 ONAUTE1 (AGO1) genetically functions in this cotranscriptional repression mechanism.

168 ed a platform for performing high-throughput cotranscriptional RNA biochemical assays, called Transcr

169 TT) identifies RNA structural transitions in cotranscriptional RNA chemical probing datasets.

170 Cotranscriptional RNA chemical probing methods accomplis

171 Here, we describe a concise, high-resolution cotranscriptional RNA chemical probing procedure called

172 ignal is required for efficient termination, cotranscriptional RNA cleavage at the poly(A) site is no

173 urthermore, the phenomena of termination and cotranscriptional RNA cleavage can be uncoupled, and the

174 g establish the roles of the poly(A) signal, cotranscriptional RNA cleavage events, and 5'-3' exonucl

175 resulting in termination and, in some cases, cotranscriptional RNA cleavage.

176 lish TECprobe-LM as a strategy for observing cotranscriptional RNA folding events directly using chem

177 aches that can be used to rationally program cotranscriptional RNA folding for biotechnology applicat

178 However, the experimental study of cotranscriptional RNA folding has been limited by the la

179 Cotranscriptional RNA folding is crucial for the timely

180 Cotranscriptional RNA folding is widely assumed to influ

181 Cotranscriptional RNA folding pathways typically involve

182 probe-VL as an accessible method for mapping cotranscriptional RNA folding pathways.

183 data (R2D2), a method to uncover details of cotranscriptional RNA folding.

184 Cotranscriptional RNA processing and surveillance factor

185 ng chromatin recruitment and activation of a cotranscriptional RNA processing enzyme, Xrn2.

186 majority of genes seemed normal in terms of cotranscriptional RNA processing events, although there

187 splicing to transcript elongation and other cotranscriptional RNA processing events.

188 he conserved THO complex in association with cotranscriptional RNA processing factors including the R

189 ation, Pol II escape, productive elongation, cotranscriptional RNA processing, and termination.

190 ctor for RNA polymerases I and II to control cotranscriptional RNA processing.

191 role in the regulation of transcription and cotranscriptional RNA processing.

192 ggest a role for CBX3 in aiding in efficient cotranscriptional RNA processing.

193 onents, suggesting its function in efficient cotranscriptional RNA processing.

194 ted DNA-RNA hybrid; and (iii) changes in the cotranscriptional RNA secondary structure upstream of th

195 Existing methods for cotranscriptional RNA structure probing map the structur

196 a key helicase required to eliminate harmful cotranscriptional RNA structures that otherwise would bl

197 898-912) identify UAP56 as a cotranscriptional RNA-DNA helicase that unwinds R loops.

198 r DNA structures, 'G-loops', which contain a cotranscriptional RNA: DNA hybrid on the C-rich strand a

199 imilar handoff occurs at tRNA 3' ends, where cotranscriptional RNase Z cleavage generates novel Xrn2

200 activity, thus suggesting a transcriptional/cotranscriptional role for IFN-gamma/IFNGR1 as well as a

201 ing that Bur1 is not a significant source of cotranscriptional Rpb1 phosphorylation.

202 w these properties are crucial for efficient cotranscriptional rRNA processing and ribosome assembly.

203 To address this, we previously developed cotranscriptional selective 2-hydroxyl acylation analyze

204 We further demonstrate cotranscriptional self-assembly of tiles based on branch

205 Herein, we use full-length RNA and cotranscriptional self-cleavage assays to compare reacti

206 Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-ind

207 ributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the

208 strengths of each transcription roadblock in cotranscriptional SHAPE-Seq.

209 with the gene promoter, suggestive of their cotranscriptional sharing of a nuclear microenvironment.

210 ddition of a 5' ribozyme to W(CES) to enable cotranscriptional shedding of the 5' cap promoted W(CES)

211 i-piRNA complexes in Drosophila, facilitates cotranscriptional silencing as a homodimer.

212 volved from an RNA transport receptor into a cotranscriptional silencing factor.

213 t protein complex required for Piwi-mediated cotranscriptional silencing in Drosophila.

214 to nascent messenger RNA transcripts causes cotranscriptional silencing of the source locus and the

215 RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitiv

216 while the RNA binding protein Nxf2 licenses cotranscriptional silencing.

217 at splicing efficiency has a major impact on cotranscriptional snRNP recruitment and suggest that cot

218 Although splicing catalysis is frequently cotranscriptional, some introns are excised after polyad

219 wever, the influence of chromatin factors on cotranscriptional splice site usage remains unclear.

220 ociated with prespliceosome formation during cotranscriptional spliceosome assembly.

221 These studies show that cotranscriptional spliceosome rearrangements are driven

222 des DIRAS3, provides an example of imprinted cotranscriptional splicing and a potential model system

223 lowed elongation, was associated with faster cotranscriptional splicing and proximal splice site use,

224 RNA polymerase II elongation increases both cotranscriptional splicing and splicing efficiency and t

225 fficiency and that faster elongation reduces cotranscriptional splicing and splicing efficiency in bu

226 These results suggest that the cotranscriptional splicing apparatus influences establis

227 However, evidence for cotranscriptional splicing as well as for coupling betwe

228 Importantly, introns with low cotranscriptional splicing efficiencies are present in t

229 Cotranscriptional splicing has been shown to influence M

230 To determine the prevalence of cotranscriptional splicing in Drosophila, we sequenced n

231 The analysis also indicates that cotranscriptional splicing is less efficient for first i

232 munoprecipitation (ChIP) assay, we show that cotranscriptional splicing occurs approximately 1 kb aft

233 itination by USP49 is required for efficient cotranscriptional splicing of a large set of exons.

234 e data suggest that H2A.Z occupancy promotes cotranscriptional splicing of suboptimal introns that ma

235 rains Deltadst1 and Deltapaf1 show different cotranscriptional splicing phenotypes, suggesting that d

236 The kinetic model of cotranscriptional splicing suggests that slow elongation

237 ups for intron retention, including complete cotranscriptional splicing, complete intron retention in

238 n contrast, U2 snRNP recruitment, as well as cotranscriptional splicing, is deficient on short second

239 Consistent with the kinetic model of cotranscriptional splicing, the rapid RNAPII elongation

240 g is imposed by a checkpoint associated with cotranscriptional splicing.

241 efficient splicing signals are critical for cotranscriptional splicing.

242 ndependent spliceosome assembly steps during cotranscriptional splicing.

243 ome sites of IEG transcription and efficient cotranscriptional splicing.

244 percent of the introns assayed manifest >50% cotranscriptional splicing.

245 Cold thus changes cotranscriptional splicing/RNA Pol II functionality in a

246 epletion of individual components shows that cotranscriptional SSU processome formation is a sensitiv

247 transient RNA structures, its application to cotranscriptional studies has been limited to nonnative

248 Riboswitches undergo cotranscriptional switching in the context of transcript

249 st cellular genes but has a modest effect on cotranscriptional termination.

250 Because RNA editing is cotranscriptional, the mtRNAP is implicated in RNA editi

251 Such a placement would enable efficient cotranscriptional translation and facile transertion of

252 ts of DNA replication, RNA transcription and cotranscriptional translation of membrane proteins cause

253 This two-level control mechanism prevents cotranscriptional translation of the toxin and allows it

254 spatial separation of DNA and ribosomes with cotranscriptional translation.

255 recruitment from transcription, suggest that cotranscriptional U1 recruitment contributes to optimal

256 Cotranscriptional ubiquitination of histone H2B is key t