ライフサイエンスコーパス: transcription bubble

1 -bp hybrid (thereby generating an artificial transcription "bubble").

2 ingle-stranded DNA (ssDNA) in the genome as 'transcription bubbles'.

3 bution: folding energy and GC content in the transcription bubble.

4 A, and (ii) expansion and contraction of the transcription bubble.

5 ly affects an early step in formation of the transcription bubble.

6 ds of the DNA segment that opens up into the transcription bubble.

7 ate DNA strand in the region of the terminal transcription bubble.

8 bed DNA strand near the upstream edge of the transcription bubble.

9 of the base pair at the upstream edge of the transcription bubble.

10 strand separation at the upstream end of the transcription bubble.

11 fficient to trigger expansion of the initial transcription bubble.

12 catalytic active site have melted to form a transcription bubble.

13 e-opened by unpairing a short segment of the transcription bubble.

14 free energy required to maintain an extended transcription bubble.

15 ed separation of the DNA strands to form the transcription bubble.

16 requires sigma factors for nucleation of the transcription bubble.

17 d upstream DNA, presumably with an enlarging transcription bubble.

18 osition the -10 element for formation of the transcription bubble.

19 e non-template DNA (ntDNA) strand within the transcription bubble.

20 ons between sigma(54) and DNA strands in the transcription bubble.

21 and especially the B' rudder, stabilise the transcription bubble.

22 d especially the beta' rudder, stabilise the transcription bubble.

23 interacts with promoter DNA to stabilize the transcription bubble.

24 the unpaired non-template strand within the transcription bubble.

25 nd of DNA both upstream of RNAPII and in the transcription bubble.

26 am portion of the non-template strand in the transcription bubble.

27 bits backtracking by stabilizing the minimal transcription bubble.

28 emplate DNA (ntDNA) strand within the paused transcription bubble.

29 stranded/single-stranded DNA junction of the transcription bubble.

30 zyme and promoter DNA that includes the full transcription bubble.

31 exes, revealing the upstream duplex and full transcription bubble.

32 the nontemplate DNA strand within the paused transcription bubble.

33 ded DNA junction at the upstream edge of the transcription bubble.

34 PIC, or the collapse of the initially formed transcription bubble.

35 element located at the upstream edge of the transcription bubble.

36 leave RNA transcripts, but not ssDNA, at the transcription bubble.

37 of the RNA transcript and the closing of the transcription bubble.

38 pproximately 12 base-pair region to form the transcription bubble.

39 lder and contacts the nontemplate DNA in the transcription bubble.

40 a CAP site at position -61.5 and a premelted transcription bubble.

41 processively within a stalled or backtracked transcription bubble.

42 ivity sufficient for expansion of the NER or transcription bubble.

43 which interacts with the DNA template in the transcription bubble.

44 lves structural changes in both the RNAP and transcription bubble.

45 otein/DNA interactions and generate the same transcription bubbles.

46 binding is to pre-melted dsDNA, as found in transcription bubbles.

47 n initiation complexes containing a complete transcription bubble and de novo synthesized RNA oligonu

48 te; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol

49 ction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at

50 a promoter DNA fragment corresponding to the transcription bubble and downstream double-stranded DNA

51 se (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP act

52 he lid may be important for holding open the transcription bubble and may help displace the RNA from

53 TPs) favor the downstream propagation of the transcription bubble and strongly stimulate the RP(-1) t

54 here double-stranded DNA is opened up into a transcription bubble and template strand DNA is position

55 ex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DN

56 t inhibits the downstream propagation of the transcription bubble and thereby increases the concentra

57 on, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA.

58 al and slippage pathways with fully resolved transcription bubbles and RNA transcripts starting from

59 h duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing com

60 hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (

61 n complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucl

62 eractions with nucleic acids upstream of the transcription bubble, and this mechanism may confer robu

63 cts also explains YY1 binding to a preformed transcription bubble, and YY1 binding to a DNA/RNA hybri

64 complex (RPo) containing a single-stranded 'transcription bubble,' and selects a transcription start

65 tions with DNA immediately downstream of the transcription bubble are particularly important for init

66 nealing of DNA in the upstream region of the transcription bubble, as is also true for termination by

67 esults suggest that proper resolution of the transcription bubble at its trailing edge and/or displac

68 plexes preferentially bind to ssDNA of small transcription bubbles at SHM 'hotspots', leading to AID-

69 Nucleic acid, in all likelihood the "transcription bubble" at the active center of the enzyme

70 IH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompani

71 a structural model of Pol II with a complete transcription bubble based on multiple sources of existi

72 olymerase interactions with the promoter and transcription bubble, but the absence of DNA downstream

73 actions with single-stranded segments of the transcription bubble by gp2 is a novel effect, which may

74 After expanding the transcription bubble by one base (T7A1), the nontemplate

75 of NusG with the ntDNA strand rearranges the transcription bubble by positioning three consecutive T

76 at may be involved in maintaining the melted transcription bubble, clamping onto the RNA product and/

77 hey likely facilitate DNA bending and impede transcription bubble collapse.

78 romoter complexes considerably by preventing transcription bubble collapse.

79 pparently binds near the upstream end of the transcription bubble, competes with sigma(A), and favors

80 recombination protein to target and resolve transcription bubbles containing R-loops, leading to gen

81 h involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscru

82 cription-bubble expansion ("scrunching") and transcription-bubble contraction ("anti-scrunching").

83 stream part of the nontemplate strand of the transcription bubble ("core recognition element," CRE).

84 e PNAs can bind to accessible DNA within the transcription bubble created by RNA polymerase.

85 Probing the edges of the DNA transcription bubble demonstrates that termination hairp

86 llular genome at replication forks or within transcription bubbles depending on the physiological sta

87 from -11A to +3 to form the single-stranded transcription bubble DNA during isomerization.

88 late and non-template strand segments of the transcription bubble downstream of the -10 promoter elem

89 cess, a local change in the structure of the transcription bubble drives a large change in the archit

90 However, the structure and stability of the transcription bubble during elongation are not altered i

91 stablishment of the upstream boundary of the transcription bubble during promoter complex formation,

92 The progress of transcription bubbles during inhibition in vitro was fol

93 Our data show that initially, the transcription bubble enlarges, DNA strands scrunch, redu

94 This indicates that the transcription bubble expands at its leading edge in the

95 ereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble c

96 ith the proposal that TSS selection involves transcription-bubble expansion ("scrunching") and transc

97 In the absence of C53 and C37, the transcription bubble fails to stably propagate to and be

98 pol III on B"; the favored placement of the transcription bubble for B"-independent transcription by

99 At the upstream transcription bubble fork, rudder and fork loop 1 residu

100 cription, sensing the DNA conformation where transcription bubble formation initiates.

101 y from the -10 element occurs first then the transcription bubble formation is slow involving reforma

102 2-aminopurine in place of adenine to monitor transcription bubble formation, and gamma-fluorophore-la

103 to initiate the DNA distortions required for transcription bubble formation, and how the activator in

104 for studying protein/DNA complex formation, transcription bubble formation, and mRNA production.

105 r specificity to E and playing a key role in transcription bubble formation.

106 ibitory structures of sigma(N) to allow full transcription bubble formation.

107 ed for nucleic acid remodeling that leads to transcription bubble formation.

108 al important insights into the initiation of transcription bubble formation.

109 f promoter spacing, the upstream edge of the transcription bubble forms 20 bp from TATA.

110 sembled on promoters containing a pre-melted transcription bubble from -9 to +3.

111 cally prepared by constructing an artificial transcription bubble from synthetic oligonucleotides and

112 ible loop, juxtaposed at the leading edge of transcription bubble, has been proposed to participate i

113 translocational and size fluctuations of the transcription bubble; (ii) changes in the associated DNA

114 e contacts with duplex DNA downstream of the transcription bubble in initiation and elongation comple

115 The DNA bulges that form within the transcription bubble in RPITC are positioned differently

116 te the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS se

117 template strand of the open promoter complex transcription bubble in the context of model non-templat

118 ture, and the absence of DNA upstream of the transcription bubble in the elongation complex structure

119 complex and to the upstream boundary of the transcription bubble in the elongation complex, providin

120 ork in the initiation state and the complete transcription bubble in the elongation state.

121 chitecture of the duplex DNA that flanks the transcription bubble in the T7 RNAP initiation and elong

122 Sub1 localizes near the transcription bubble in vitro and binds to promoters in

123 th 30 base pairs of duplex DNA containing a "transcription bubble" interacting with a 17-nucleotide R

124 Our results indicate that the transcription bubble is approximately nine bases long an

125 either the nontranscribed DNA strand nor the transcription bubble is essential for rho-independent te

126 According to this hypothesis, the transcription bubble is formed in the -10 region, and co

127 A smaller transcription bubble is observed during productive reite

128 bble showed that the upstream portion of the transcription bubble is required for efficient NPH I-med

129 Proper organization of the transcription bubble is required for maintaining the cor

130 (template) strand within the confines of the transcription bubble is seen as indicating that the nont

131 The open galP1 promoter complex, whose transcription bubble is very AT-rich, also closes revers

132 ges in the sequence and length of DNA in the transcription bubble just upstream of the start site (+1

133 RNAP contacts with the upstream edge of the transcription bubble lead to read-through of various typ

134 onstant number of base pairs, similar to the transcription bubble maintained by RNA polymerase.

135 h in the template strand of a replication or transcription bubble may prevent mutations associated wi

136 second step, apparently independent of ATP, transcription bubbles move into the initial transcribed

137 By contrast, the mechanism of transcription bubble nucleation and formation during the

138 ter upstream sequence (beyond -35) stimulate transcription bubble nucleation and tune the reaction pa

139 ubunits of Pol III being positioned near the transcription bubble of actively transcribing Pol III, a

140 tiation, eventually attaining a steady-state transcription bubble of approximately 19 base-pairs.

141 bservation of conformational dynamics in the transcription bubble of RP(o) and indicates that DNA dyn

142 nds physically to single-stranded DNA in the transcription bubble of the OC and increases its stabili

143 binds and unwinds promoter DNA, forming the transcription bubble of the open promoter complex (RPo).

144 short (3 or 5 bp) DNA segments spanning the transcription bubble of the open promoter complex.

145 We find that the DNA in the single-stranded transcription bubble of the rrnB P1 promoter complex exp

146 NA reanneal, resulting in the formation of a transcription "bubble" of approximately 10 bp.

147 tional changes, including the formation of a transcription bubble on the promoter and the loading of

148 RNA polymerase cannot form a transcription bubble on these templates; thus, the Yager

149 airpin may also be important for holding the transcription bubble open during transcript elongation,

150 A break or invades the displaced strand of a transcription bubble or R-loop, followed by DNA synthesi

151 xibility may occur in the positioning of the transcription bubble prior to RNA synthesis and may refl

152 val of the non-template strand also disrupts transcription bubble reannealing.

153 y in the TATA-element region but also in the transcription-bubble region, near the transcription star

154 -terminal domain in the interaction with the transcription-bubble region.

155 ibed by repositioning of the single-stranded transcription bubble relative to the RNAP active site wi

156 ation state of RNAPII was unaltered, and the transcription bubbles remained open.

157 NA, with their activity and the integrity of transcription bubbles remaining intact.

158 rtions of the non-template strand within the transcription bubble showed that the upstream portion of

159 thesized RNA oligonucleotide, and a complete transcription bubble (sigma(S)-TIC) at about 3.9-A resol

160 d limit backtracking, whereas high GC in the transcription bubble slows elongation.

161 xes are also different with respect to their transcription bubble stability.

162 nalysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong s

163 i and is dependent on the length of time the transcription bubble stays open during elongation.

164 is not important for RNA displacement or for transcription bubble structure or stability during elong

165 defect that can be bypassed with a preformed transcription bubble, suggesting a mechanism to explain

166 during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID

167 P beta' subunit near the upstream end of the transcription bubble suppress Nun binding and arrest.

168 e unpaired non-template DNA part of the full transcription bubble (TB) is still unknown.

169 r factors and a DNA substrate analogous to a transcription bubble terminating at a cyclobutane thymin

170 merase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric i

171 ce changes trigger global alterations in the transcription bubble that modulate the RPo lifetime and

172 n, we have identified the sites inside these transcription bubbles that are accessible for hybridizat

173 Within this transcription bubble the growing 3'-end of nascent RNA f

174 uding the formation and translocation of the transcription bubble, the formation and unwinding of the

175 stranded DNA-binding site (DBS) ahead of the transcription bubble, the RNA-DNA heteroduplex-binding s

176 e two complexes do differ in the size of the transcription bubble: the open complex contains a 10.4 +

177 be sharply bent at the upstream edge of the transcription bubble, thereby allowing formation of upst

178 rand order in the single-stranded DNA of the transcription bubble; these differences propagate beyond

179 nterferes with downstream propagation of the transcription bubble to and beyond the transcriptional s

180 interact with the nontemplate strand of the transcription bubble to drive promoter melting.

181 e mechanism of downstream propagation of the transcription bubble to include the transcription start

182 cks with a double-stranded DNA branch of the transcription bubble to potentially attenuate elongation

183 lymerase, and how RNA polymerase rewinds the transcription bubble to release RNA and then DNA.

184 nor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription init

185 oring the hyperreactivity of thymines in the transcription bubble toward potassium permanganate.

186 ed by the nontemplate DNA strand of the open transcription bubble, we conclude that RNA polymerase co

187 nhibit rewinding of the upstream part of the transcription bubble, we show that transcript release in

188 eam base pairs sequentially open to form the transcription bubble, which results in strain build up.

189 spot motifs within the confines of a moving transcription bubble while introducing clusters of multi

190 concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of

191 RNA polymerase near the middle of the melted transcription bubble with the bases oriented away from t

192 tion start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP