ライフサイエンスコーパス: co-transcriptional

1 R loops, which are mainly co-transcriptional, abundant RNA/DNA hybrids, form natur

2 Here we show that, in yeast, co-transcriptional acetylation is achieved in part by hi

3 l component of E-cadherin junctions and as a co-transcriptional activator of the Wnt/beta-catenin sig

4 Enhancers are typically marked by the co-transcriptional activator protein p300 or by groups o

5 Saccharomyces cerevisiae, we tested whether co-transcriptional activator Sub1, recently identified a

6 d HLA-A*0101 restricted peptide derived from co-transcriptional activator Vestigial-like 1 (VGLL1) as

7 crosslinking of extracellular matrix via the co-transcriptional activator YAP.

8 The WW domain-containing co-transcriptional activator Yes-associated protein (YAP

9 Here we report the identification of four CO transcriptional activators, named FLOWERING BHLH 1 (F

10 conformation and prevents the recruitment of co-transcriptional activators, thus defining the mechani

11 Co-transcriptional activities are deemed commonplace in

12 opose that pairing requires Ctcf binding and co-transcriptional activity of Tsix and Xite.

13 teasome resistance and increased protein and co-transcriptional activity.

14 ssed antisense transcripts (SRATs) since the co-transcriptional addition of the H3K36 methyl mark by

15 ome to affect target mRNA expression through co-transcriptional alternative splicing (AS) and linked

16 nt ligand-dependent regulatory activity in a co-transcriptional and cellular context.

17 me activity in regulating experience-induced co-transcriptional and local translational processes req

18 portant insights into the relative amount of co-transcriptional and post-transcriptional processing,

19 ar compartments in transcription regulation, co-transcriptional and post-transcriptional RNA processi

20 utside the context of transcription and that co-transcriptional approaches are essential for developi

21 ings suggest convergence of epigenetics with co-transcriptional AS, whether epigenetic dysregulation

22 cripts using single-molecule co-localization co-transcriptional assembly (smCoCoA).

23 Co-transcriptional assembly is an integral feature of th

24 on determined by native gel-shift assays and co-transcriptional assembly is correlated to the G/C con

25 To visualize co-transcriptional assembly of ribosomal protein-RNA com

26 The structure supports the hypothesis of co-transcriptional assembly, centered around L24 in doma

27 Our work demonstrates that extended co-transcriptional association is an important determina

28 The subsequent co-transcriptional association of ribosome assembly fact

29 Thus, Sfp1's co-transcriptional binding imprints the mRNA fate, servi

30 mity of the transcription site, thus seeming co-transcriptional by most assays.

31 rm identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp

32 bing elongation complex and in the form of a co-transcriptional capping complex that contains the vir

33 r, causes defects in Pol II phosphorylation, co-transcriptional capping, promoter proximal pausing, a

34 polymerase II transcription by coordinating co-transcriptional chromatin modifications and helping r

35 vement of RNAPII through the nucleosome with co-transcriptional chromatin modifications during transc

36 ient transcription termination machinery for co-transcriptional chromatin targeting and genome survei

37 DNA-damaging agents trigger the shutdown of co-transcriptional chromatin-associated 3'-end processin

38 in gene poly(A) signal are associated with a co-transcriptional cleavage (CoTC) activity that acts wi

39 r terminator classes described so far is the Co-Transcriptional Cleavage (CoTC) element.

40 curs post-transcriptionally, i.e., through a co-transcriptional cleavage (CoTC) event downstream of t

41 beta-globin gene revealed a new phenomenon--co-transcriptional cleavage (CoTC).

42 Co-transcriptional cleavage and transcription terminatio

43 Co-transcriptional cleavage data were simulated successf

44 s in part post-transcriptionally following a co-transcriptional cleavage event.

45 microprocessor to the MIRNA loci, prompting co-transcriptional cleavage of primary miRNA substrates.

46 the absence of additional factors, efficient co-transcriptional cleavage of the full-length genomic H

47 PR RNA (crRNA)-guided nucleases that perform co-transcriptional cleavage of the viral target DNA and

48 , cleaves pre-rRNA at so-called site A(2), a co-transcriptional cleavage step that separates rRNAs de

49 ian development, and interacts with the PAF1 co-transcriptional complex and other proteins.

50 d reconstitute the EVI1 chromatin-associated co-transcriptional complex merging on the role of prolif

51 ulatory processes in the transcriptional and co-transcriptional control of immune-responsive genes an

52 each cell, with no evidence for simultaneous co-transcriptional coupling of all or specific subsets o

53 AR inhibition also induces co-transcriptional CPSF recruitment to gene promoters, p

54 Although the co-transcriptional deacetylation pathway is well charact

55 cytoplasmic localization displayed enhanced co-transcriptional degradation of lacZ mRNA.

56 cations to chromatin, providing evidence for co-transcriptional deposition and function in gene regul

57 wtooth-like binding pattern, consistent with co-transcriptional deposition of FUS/TLS.

58 d-specific mapping for DNA-bound RNA reveals co-transcriptional dual-strand DNA:RNA hybrids present a

59 arum: editing is distinct from that of other co-transcriptional editing systems.

60 witches; our analysis of RS3 suggests strong co-transcriptional effects for this riboswitch.

61 ation of histone H3 at Lys 36 (H3K36me) is a co-transcriptional event that is necessary for the activ

62 Pre-mRNA splicing is a predominantly co-transcriptional event which involves a large number o

63 RNA polymerase II coordinates co-transcriptional events by recruiting distinct sets of

64 ic regulation and possible functions of such co-transcriptional events remain poorly understood.

65 ynthesis itself or because of alterations to co-transcriptional events that are responsive to or coup

66 the recruitment of factors and regulation of co-transcriptional events, from RNA processing to chroma

67 ing platform for factors involved in various co-transcriptional events.

68 gation complexes to allow time for necessary co-transcriptional events.

69 We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a su

70 HAT)-mediated chromatin remodeling function, co-transcriptional factor, p300, is also known to play a

71 Elongation, termination, and recruitment of co-transcriptional factors are not directly affected.

72 nes on the template DNA strand, suggesting a co-transcriptional feedback to siRNA biogenesis by DNA m

73 olding behind elongating ribosomes resembles co-transcriptional folding behind Pol II.

74 ggest the possibility of co-replicational or co-transcriptional folding of G-quadruplex inside the po

75 In particular, the co-transcriptional folding of nascent RNA of all classes

76 Our results emphasize the importance of co-transcriptional folding of RNA tertiary structure for

77 optical tweezers to follow in real time the co-transcriptional folding of SRP RNA.

78 In these studies, co-transcriptional folding of the genomic ribozyme was a

79 iary interactions that promote high-fidelity co-transcriptional folding of the riboswitch but are onl

80 Moreover, co-transcriptional folding of the RNA at a physiological

81 Yet, rapid co-transcriptional folding of the RNA can mask sRNP site

82 e basis of these results and modeling of the co-transcriptional folding of the ROSE element, we propo

83 A transcripts provided justification for the co-transcriptional folding of these species.

84 ental to the cell, altogether showing that a co-transcriptional folding pathway underpins the proper

85 Co-transcriptional folding using superhelicases shows re

86 anostructures that can self-assemble through co-transcriptional folding with applications in nanomedi

87 Successful co-transcriptional formation of condensates from single-

88 bonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containin

89 This mechanism requires YAP co-transcriptional function and involves the activation

90 l that IQGAP1 binds to YAP and modulates its co-transcriptional function, suggesting that IQGAP1 part

91 ered by topoisomerase 1 (TOP1), which limits co-transcriptional G4 formation, and by factors promotin

92 recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes an

93 Clr4(SUV39H1), promoting the transition from co-transcriptional gene silencing (H3K9me2) to transcrip

94 state that is sufficient for RNAi-dependent co-transcriptional gene silencing at pericentromeric DNA

95 guards genome integrity in part through the co-transcriptional gene silencing of transposon insertio

96 roteins to nascent RNA transcripts to induce co-transcriptional gene silencing.

97 ve a prominent function in the resolution of co-transcriptional genotoxic R-loops, which can cause th

98 nt or function, although significant loss of co-transcriptional H3K36 trimethylation is observed.

99 t discovery that the majority of splicing is co-transcriptional has led to the finding that chromatin

100 Our results reveal an elaborate co-transcriptional histone crosstalk pathway involving t

101 e results uncover novel interactions between co-transcriptional histone modification pathways, which

102 Rpb1 and Spt5 CTD phospho-sites in directing co-transcriptional histone modifications in the fission

103 Our results elaborate the CTD 'code' for co-transcriptional histone modifications.

104 e topology in the formation and stability of co-transcriptional hubs.

105 This work uncovers the co-transcriptional inhibition of translation as an addit

106 luding co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 2

107 Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the

108 Our results uncover a co-transcriptional layer of NLR control with implication

109 remains largely unknown, particularly at the co-transcriptional level.

110 mature RNAs are inefficiently spliced at the co-transcriptional level.

111 ly equilibrating RNA structures, but rather, co-transcriptional ligand binding kinetically traps the

112 e-mRNA processing; however, the mechanism of co-transcriptional m(6)A-dependent alternative splicing

113 ur results reveal an integrated mechanism of co-transcriptional m(6)A-mediated splicing regulation, i

114 ed by the LARP7-free MePCE and in probably a co-transcriptional manner prior to its sequestration int

115 These data strongly support a co-transcriptional mechanism of Physarum: RNA editing in

116 ich silences transcription, can proceed by a co-transcriptional mechanism that also promotes sRNA gen

117 However, molecular details of such co-transcriptional mechanisms remain obscure, partly bec

118 enetic and epigenetic regulatory mechanisms, co-transcriptional mechanisms, such as alternative polya

119 However, the molecular mechanism of co-transcriptional miRNA processing is poorly understood

120 , these studies suggest that HP1BP3 promotes co-transcriptional miRNA processing via chromatin retent

121 f chromatin retention factors for widespread co-transcriptional miRNA processing.

122 potential of RNA and broadens the exclusive co-transcriptional models that pervade the field.

123 ructures unravel the basis for synthesis and co-transcriptional modification of poxvirus RNA.

124 provide a structural basis for understanding co-transcriptional modification of SARS-CoV-2 mRNA but a

125 rtance of co-transcriptional RNA folding and co-transcriptional modifications that have yet to be cha

126 Despite the critical role of co-transcriptional mRNP assembly in gene expression, the

127 for understanding protein recruitment during co-transcriptional mRNP assembly, providing mechanistic

128 hed light on the order of events for Dbp2 in co-transcriptional mRNP assembly.

129 SHM involves co-transcriptional mutagenesis of immunoglobulin variabl

130 system has provided further support for the co-transcriptional nature of editing in Physarum polycep

131 The co-transcriptional nature of mRNA processing has permitt

132 R-loops are dynamic, co-transcriptional nucleic acid structures that facilita

133 chromatin remodeling complex is required for co-transcriptional nucleosome remodeling that leads to L

134 Little is known about co-transcriptional or post-transcriptional regulatory me

135 Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPI

136 on to its previously described modulation of co-transcriptional polyadenylation (polyA) site choice.

137 otein interactions and provides insight into co-transcriptional, post-transcriptional and cytoplasmic

138 We propose a model for co-transcriptional pre-mRNA processing that incorporates

139 AP III (POLR3A) is not sufficient to enhance co-transcriptional pre-mRNA splicing or capping in vivo.

140 erasure of the ubiquitin mark from ubH2B and co-transcriptional pre-mRNA splicing.

141 strating functional coupling between the two co-transcriptional processes as a determinant of product

142 lts can help understand other time sensitive co-transcriptional processes in pro- and eukaryotes.

143 in orchestrates eukaryotic transcription and co-transcriptional processes, including transcription in

144 f transcription speed, which influences many co-transcriptional processes, is poorly understood.

145 ter understand its role in transcription and co-transcriptional processes.

146 polymerase II, regulating transcription and co-transcriptional processes.

147 d factor that functions in transcription and co-transcriptional processes.

148 Here we describe nanopore analysis of co-transcriptional processing (nano-COP), a method for p

149 We developed nanopore analysis of co-transcriptional processing (nano-COP), in which nasce

150 II (Pol2) movement through chromatin and the co-transcriptional processing and fate of nascent transc

151 n this review, we discuss recent advances in co-transcriptional processing and how it contributes to

152 ical kinase for transcription elongation and co-transcriptional processing of eukaryotic genes.

153 D) is essential for normal transcription and co-transcriptional processing of mRNA precursors.

154 ates the elongation of RNA polymerase II and co-transcriptional processing of nascent transcripts.

155 se II, P-TEFb facilitates the elongation and co-transcriptional processing of nascent transcripts.

156 , and alternative splicing in the context of co-transcriptional processing of pre-mRNA.

157 ex can be recruited to chromatin to catalyze co-transcriptional processing of primary microRNAs (pri-

158 echanistic model predictions, revealing that co-transcriptional processing sets the level of producti

159 Ribosomal RNA gene transcription, co-transcriptional processing, and ribosome biogenesis a

160 of all classes has the potential to regulate co-transcriptional processing, RNP (ribonucleoprotein pa

161 RNAs with 5' caps prior to their removal by co-transcriptional processing.

162 phosphorylated CTD is required for efficient co-transcriptional processing.

163 ligand-dependent termination is obligatorily co-transcriptional, providing a clear readout of the fol

164 etic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mech

165 with their DNA template via the formation of co-transcriptional R-loop structures.

166 onic low levels of SMN cause accumulation of co-transcriptional R-loops and DNA damage leading to gen

167 1 is critical for preventing accumulation of co-transcriptional R-loops and DNA damage to avert genom

168 has shown that replication forks stalled by co-transcriptional R-loops can be restarted by a mechani

169 ns between the DNA replication machinery and co-transcriptional R-loops can impede DNA synthesis and

170 Co-transcriptional R-loops could aggravate such conflict

171 Co-transcriptional R-loops were recently reported to be

172 study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors an

173 This interaction is implicated in co-transcriptional recruitment of the EZL1 complex.

174 These findings suggest that co-transcriptional recruitment of the RNA processing mac

175 Together with CO transcriptional regulation, FKF1 protein controls rob

176 tive splicing (AS) is emerging as a critical co-transcriptional regulation for plants in response to

177 Post-transcriptional and co-transcriptional regulation is a crucial link between

178 We report herein that an additional layer of co-transcriptional regulation is required for exopolysac

179 d a novel functional approach to demonstrate co-transcriptional regulation of alternative splicing.

180 (3-11), forming a signal-integration hub for co-transcriptional regulation that includes translation-

181 The interconnections between co-transcriptional regulation, chromatin environment, an

182 olyadenylation (APA) is an important part of co-transcriptional regulation, which is crucial in devel

183 at this results in increased level of TAZ, a co-transcriptional regulator downstream of the Hippo sig

184 FBXO7 bound and stabilized SIX1 co-transcriptional regulator EYA2, stimulating mesenchym

185 icago truncatula, a homeotic mutation in the co-transcriptional regulator gene NODULE ROOT1 (MtNOOT1)

186 hancer factor 2C), functioning as its potent co-transcriptional regulator.

187 densates in the cold is affected by specific co-transcriptional regulators and cold induction of a sp

188 eling and deacetylation (NuRD) complexes are co-transcriptional regulators implicated in differentiat

189 s by either activating or inhibiting YAP/TAZ co-transcriptional regulators of the Hippo pathway via u

190 We show that YAP and TAZ, the co-transcriptional regulators of the Hippo signalling pa

191 termind-like) proteins are a family of three co-transcriptional regulators that are essential for Not

192 To relate these findings to co-transcriptional regulatory activity, we have investig

193 36me) is thought to participate in a host of co-transcriptional regulatory events.

194 we show that ASAP and PRC1 are necessary for co-transcriptional repression and chromatin regulation a

195 A-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi.

196 nscriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly, is abunda

197 In an in vitro co-transcriptional ribosome assembly assay, 10 assembly

198 More broadly, it establishes co-transcriptional RNA binding as a cis-acting mechanism

199 Co-transcriptional RNA binding by Trf4 may link RNA and

200 We performed co-transcriptional RNA chemical probing, allowing us to

201 a 'torpedo' mechanism for Pol I termination: co-transcriptional RNA cleavage by Rnt1 provides an entr

202 y Rnt1 inactivation in vivo reveals a second co-transcriptional RNA cleavage event at T1 which provid

203 We also show that a lincRNA-specific co-transcriptional RNA cleavage mechanism acts to induce

204 hadowing the likely regulatory importance of co-transcriptional RNA folding and co-transcriptional mo

205 We simulated co-transcriptional RNA folding dynamics to identify comp

206 Hence, co-transcriptional RNA folding modulates post-transcript

207 ains nascent RNA secondary structures from a co-transcriptional RNA folding software, and computes th

208 Post- and co-transcriptional RNA modifications are found to play v

209 Numerous links exist between co-transcriptional RNA processing and the transcribing R

210 s show how modulation of R-loop stability by co-transcriptional RNA processing can trigger chromatin

211 m loops or more complex structures may alter co-transcriptional RNA processing or its efficiency.

212 tion genome-wide profiles of nascent RNA and co-transcriptional RNA processing that are associated wi

213 is FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation

214 I-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing.

215 afford full dissection of the complexity of co-transcriptional RNA processing.

216 RNA polymerase (RNAP) is the central step in co-transcriptional RNA proofreading.

217 with SMA pathogenesis cause accumulation of co-transcriptional RNA-DNA hybrids (R-loops) and DNA dam

218 Co-transcriptional RNA-DNA hybrids can not only cause DN

219 global increase in the formation of R-loops, co-transcriptional RNA-DNA products, which in some insta

220 eins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin function

221 ess and DNA damage depend on the presence of co-transcriptional RNA/DNA hybrids (R-loops) that form i

222 ent on active transcription and formation of co-transcriptional RNA:DNA hybrids (R-loops).

223 RNA-DNA helicase that mediates resolution of co-transcriptional RNA:DNA hybrids (R-loops).

224 Co-transcriptional RNAi releases RNA polymerase II (Pol

225 we review insights gained from studying the co-transcriptional roles of RNA modifications, and their

226 We find that co-transcriptional rRNA folding is complicated by the fo

227 Surprisingly, co-transcriptional self-cleavage occurs when the number

228 ribozyme was assayed in vitro by monitoring co-transcriptional self-cleavage of transcripts having v

229 therefore likely to affect the efficiency of co-transcriptional self-cleavage.

230 atin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing

231 These co-transcriptional silencing mechanisms form powerful RN

232 orm a complex with Panx and are required for co-transcriptional silencing of transposons in somatic a

233 results support a model of piRNA-associated co-transcriptional silencing while also suggesting addit

234 As splicing is co-transcriptional, slower recycling increases the likel

235 We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in

236 ole in splicing is dependent on the cellular co-transcriptional splicing activators Tat-SF1 and CA150

237 ol II CTD phosphorylation states reveal weak co-transcriptional splicing and poly(A) signal-independe

238 for the homeostatic regulation of efficient co-transcriptional splicing by chromatin-bound U2AF2.

239 RNA polymerase II (Pol II) facilitates co-transcriptional splicing by recruiting the U1 small n

240 Sequencing (SKaTER-seq) method, analysis of co-transcriptional splicing demonstrated that PRMT inhib

241 two predominant features that correlate with co-transcriptional splicing efficiency, and introns with

242 d features that may affect or be affected by co-transcriptional splicing efficiency.

243 Furthermore, POINT-nano reveals that co-transcriptional splicing either occurs immediately af

244 nscribing RNA polymerase II over introns and co-transcriptional splicing events.

245 o investigate the timing and determinants of co-transcriptional splicing genome wide.

246 However, co-transcriptional splicing has not yet been explored in

247 y, our results not only uncovered widespread co-transcriptional splicing in Arabidopsis but also iden

248 for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silen

249 Recent evidence supports co-transcriptional splicing in plants, hence the chromat

250 ng, but this mutation could be suppressed by co-transcriptional splicing in the presence of Cbp2.

251 Together, our work establishes a system for co-transcriptional splicing in vitro, in which the splic

252 we established an efficient model system for co-transcriptional splicing in vitro.

253 elongation through a chromatin template and co-transcriptional splicing including alternative splici

254 Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon m

255 To determine how co-transcriptional splicing is integrated with transcrip

256 Surprisingly, co-transcriptional splicing kinetics did not correlate w

257 eosome binding to their pre-mRNAs and higher co-transcriptional splicing levels than genes that are l

258 bozyme-dependent intron cleavage is tuned to co-transcriptional splicing of the Cpeb3 mRNA.

259 promotes their transcription associated with co-transcriptional splicing of the first introns in the

260 ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano), and p

261 on, regulate RNA polymerase II processivity, co-transcriptional splicing, and stability and translati

262 pates in DNA replication, transcription, and co-transcriptional splicing, where DNA is undamaged.

263 a and showed that nearly all introns undergo co-transcriptional splicing, which occurs with higher ef

264 icity of FGFR2 alternative splicing requires co-transcriptional splicing.

265 surveyed the effect of epigenetic context on co-transcriptional splicing.

266 ition complex SF3B rapidly diminished global co-transcriptional splicing.

267 t splice sites are associated with efficient co-transcriptional splicing.

268 RNAPII with a K1246R mutation showed reduced co-transcriptional splicing.

269 reports, we show that HSV-1 does not inhibit co-transcriptional splicing.

270 These co-transcriptional states remain mostly unknown.

271 advance our insight into the significance of co-transcriptional structure formation are discussed.

272 Here, we develop co-transcriptional structure tracking (CoSTseq), which d

273 strong promoters; however, it might require co-transcriptional synthesis of a polypeptide.

274 es and conformational switching in a limited co-transcriptional timeframe, make them ideal model syst

275 mosomal expansion due to transertion enables co-transcriptional translation throughout the nucleoids.

276 ese results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.