ライフサイエンスコーパス: palindrome

1 organization as large inverted duplications (palindromes).

2 re polyadenylated in the right-hand terminal palindrome.

3 n the half-site, as well as in the full-site palindrome.

4 lf-sites couple to form a higher order 20 bp palindrome.

5 human p53REs of 3 bp enhances the half-site palindrome.

6 ely followed by the formation of a large DNA palindrome.

7 le copy sequence is duplicated to generate a palindrome.

8 protein did not demonstrate binding with the palindrome.

9 legitimate nucleotide incorporation into the palindrome.

10 ircular DNA molecule with an origin-flanking palindrome.

11 inverted repeats that form a nearly perfect palindrome.

12 ired for extrusion of the underlying perfect palindrome.

13 s located on the A-A' region of the terminal palindrome.

14 the idiA regulatory region that included the palindrome.

15 hat their translocations are within the same palindrome.

16 ized within an ATRR that is part of a larger palindrome.

17 inding site occupying the inboard arm of the palindrome.

18 a 20 bp spacer to form a 480 bp interrupted palindrome.

19 not bind the mutated half-sites of the G-box palindrome.

20 mechanism to specifically unwind the central palindrome.

21 ructure determines the location of large DNA palindromes.

22 specific mutations into oriL and other large palindromes.

23 f older Sireviruses reflects their conserved palindromes.

24 ectious progeny viruses with restored or new palindromes.

25 ny viruses containing longer and more stable palindromes.

26 ng motifs that organize as four spaced C/EBP palindromes.

27 is of duplex linear plasmids containing long palindromes.

28 ally applicable mechanism for generating DNA palindromes.

29 cells undergoing telomere losses and forming palindromes.

30 bination events occur at nearly all Y-linked palindromes.

31 t2 promoter but not cut1 promoter unless its palindrome 1 is mutated, unlike CTF1 alpha which transac

32 rotein (PBP) previously cloned binds only to palindrome 1 of cut1 promoter but not palindrome 1 of cu

33 Because PBP cannot bind palindrome 1 of cut2, this gene is not repressed.

34 nly to palindrome 1 of cut1 promoter but not palindrome 1 of cut2/3 which contains two base substitut

35 transcription factor, CTF1 beta, that binds palindrome 2 was cloned and sequenced.

36 ngly and specifically to the double-stranded palindrome 5'-TATGCATTATTTCATA-3' that matches the conse

37 hat it promoted the formation of a large DNA palindrome after an adjacent DNA double-strand break.

38 Altogether, we hypothesize that the palindromes aid the silencing of active elements and inf

39 ed that proteins recognizing a consensus ERE palindrome also bind GGTCA-like sequences in the CAV pro

40 GOLGA8-flanked palindromes also demarcate the breakpoints of recurrent

41 elected DIS sequence is a 4- or 6-nt GC-rich palindrome, although not all sequences with these charac

42 of kilobases) 'head-to-head' inverted repeat palindromes (amplicons).

43 We found that a 160-bp palindrome (an inverted repeat of 80 bp) conferred a mit

44 Msh3p was involved in recognition of the palindrome and all loops, but also had an unexpected ant

45 erization of RNA molecules carrying both the palindrome and G-rich sequences was completely inhibited

46 substitutions that break the symmetry of the palindrome and generate activator or repressor motifs cr

47 The full-site palindrome and half-site palindrome are controlled by in

48 ovirus with deletions in the origin-flanking palindrome and incapable of forming any cruciform struct

49 he p53 DNA-binding motif consists of a 10-bp palindrome and most commonly a second related palindrome

50 replication (oriS) contains a 46-bp AT-rich palindrome and three consensus binding sites for the VZV

51 Finally, LexA bound to the dinJ-yafQ palindrome and triggered module transcription after DNA

52 wn how a DSB is resolved to form a large DNA palindrome and whether any local DNA structure determine

53 es and primary tumors to spatially associate palindromes and copy-number gains.

54 st unique Y-linked genes are not situated in palindromes and have no gene conversion partners.

55 Perfect palindromes and IRs with short spacers can extrude as cr

56 In several cases, LCRs, AT-rich palindromes and pericentromeric repeats are located at s

57 Genetic instability at palindromes and spaced inverted repeats (IRs) leads to c

58 nd break leads to the formation of large DNA palindromes and that DNA inverted repeats in the genome

59 copies of the cDNA insert in a head-to-head palindrome, and insertion of the construct downstream of

60 ed by HPNikR do not contain any identifiable palindromes, and the exact mechanism(s) of the HPNikR-DN

61 he number of CANT repeats, their presence in palindromes, and their positions relative to the RBP-Jk

62 ty and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component o

63 replicated chromosome containing the perfect palindrome are cleaved, resulting in the formation of an

64 The full-site palindrome and half-site palindrome are controlled by insertions between the two

65 l analysis reveals that sequences within the palindrome are critical for binding and activation by OR

66 The imperfections in the palindrome are sequentially incorporated into the crucif

67 H-palindromes are an important class of such DNA sequences

68 howed that the majority of intergenic CACGTG palindromes are bound by Cbf1p.

69 The palindromes are constructed from six distinct families o

70 These results suggest that origin-flanking palindromes are essential for termination but not for in

71 We previously proposed that the palindromes are formed by invasion and break-induced rep

72 Large DNA palindromes are frequent and nonrandomly distributed in

73 DNA palindromes are hotspots for DNA double strand breaks, i

74 Inverted chromosome duplications or palindromes are linked with genetic disorders and malign

75 However, long DNA palindromes are not normally found in bacterial or human

76 Our evidence supports a model in which palindromes are primarily formed by an intermolecular re

77 DNA palindromes are rare in humans but are associated with m

78 f these C/EBP motifs showed that these C/EBP palindromes are required for both K8 binding and ori-Lyt

79 Long DNA palindromes are sites of genome instability (deletions,

80 The resulting palindromes are stable in sae2Delta cells, but unstable

81 s containing long adjacent inverted repeats (palindromes) are inherently unstable and are associated

82 ty could be interpreted as evidence that the palindromes arose through duplication events that occurr

83 r, and forks moving toward the center of the palindrome arrest at a developmentally regulated replica

84 Here we have explored the role of the palindrome as a silencer of the ldhc gene in somatic tis

85 the importance of the formation of large DNA palindromes as a very early event in gene amplification

86 fer the potential to evaluate the utility of palindromes as prognostic markers, particularly in prema

87 himpanzee MSY contains twice as many massive palindromes as the human MSY, yet it has lost large frac

88 otif of the globin-2 gene promoter, a CACGTG palindrome at position -146, functions as a docking site

89 ore mutilated inverted-repeat sequences to a palindrome at the Ori of circular DNAs or at the termini

90 Thus, a flanking palindrome at the Ori was not essential for initiation o

91 remaining terminal sequences generated large palindromes at some chromosome termini.

92 The palindromes at the two ends of the minute virus of mice

93 gate the importance of the inverted repeats (palindrome) at the origin of DNA replication (Ori) of po

94 st prominent features here are eight massive palindromes, at least six of which contain testis genes.

95 T-box proteins, the resulting sequence is a palindrome based around near-perfect copies of AGGTGTGA.

96 A small internal palindrome (BB'), necessary for optimal Rep-inverted ter

97 A palindrome binding protein (PBP) previously cloned binds

98 hilles' heel in the mechanism that preserves palindrome-borne genes.

99 The hotspot activity of the palindrome, but not the basal level of recombination, wa

100 We show here that the perfect palindrome can form hairpin DNA structures on the templa

101 The molecular mechanisms by which palindromes can cause gene amplification are largely unk

102 s that the 1p21.2 breakpoint splits a 278 nt palindrome capable of forming stem-loop secondary struct

103 n the proximal and distal arms of the 445 bp palindrome (cis-morphisms) that correspond to five polym

104 duces RpoS is by repressing cspE at the LexA palindrome; cold-shock protein CspE enhances translation

105 Eight palindromes comprise one-quarter of the euchromatic DNA

106 on start site from -9 to +11 is an imperfect palindrome; consequently, this motif is referred to as t

107 deletions and often display large junctional palindromes, consistent with a hairpin coding end openin

108 Treatment of the palindrome-containing DNA with sodium bisulfite at high

109 The center of symmetry of this palindrome contains an inverted repeat consisting of two

110 Each palindrome contains two head-to-head CCAAT consensus mot

111 ary to the palindrome; molecules lacking the palindrome could not dimerize in the presence of oligome

112 The palindrome couplings between the half-sites are stronger

113 Accordingly, the formation of palindrome-dependent hairpin intermediates can be induce

114 The rules for the palindrome-dependent pathway of gene amplification defin

115 re frequently than the 180-kb amplicon, is a palindrome derived from a region near the telomere of ch

116 ailed study of the extrusion of an imperfect palindrome, derived from the terminal regions of vaccini

117 amplification by array-CGH was enriched for palindromes detected by GAPF providing strong evidence f

118 stages, the 3'RR portion including the quasi-palindrome dictated antigen-dependent locus remodeling (

119 nts indicate that the G-rich regions and the palindrome do not interact directly.

120 equence, designated the HIP (highly iterated palindrome) element, occurs in approximately half of the

121 in the NeseNPV genome, each containing small palindromes embedded within direct repeats.

122 ts were compromised in melting the imperfect palindrome (EP) but normal in untwisting the AT-rich tra

123 equence was termed the endosperm specificity palindrome (ESP) element.

124 conic gene families, locate species-specific palindromes, examine the repetitive element content, and

125 r pathways are active in nearly all Y-linked palindromes, exposing an Achilles' heel in the mechanism

126 ly in the dA/dT(23) repeat, with evidence of palindrome extrusion in supercoiled plasmid.

127 Although palindrome extrusion was not detected in genomic DNA dur

128 contained two GC dyads in the center of the palindrome, flanked by a non-GC dyad.

129 YefM binds the long palindrome, followed sequentially by short palindrome re

130 In this study we address whether the linear palindromes form by an intermolecular reaction (that is,

131 Large DNA palindromes form sporadically in many eukaryotic and pro

132 ome profiling by the Genome-wide Analysis of Palindrome Formation (GAPF) assay with genome-wide copy-

133 Employing genome-wide analysis of palindrome formation (GAPF), we detected extensive palin

134 ral mechanisms have been proposed to explain palindrome formation but their relative contributions in

135 tion of the RAD52 gene significantly reduces palindrome formation by intermolecular recombination and

136 We induced palindrome formation by passaging cells lacking any form

137 es from model systems have demonstrated that palindrome formation can be an early step in DNA amplifi

138 Here we demonstrate that palindrome formation can occur in the absence of RAD50,

139 e of RAD50, YKU70, and LIG4, indicating that palindrome formation defines a new class of nonhomologou

140 rome formation (GAPF), we detected extensive palindrome formation in early TF and end-stage lymphomas

141 Here, we describe a molecular mechanism for palindrome formation in mammalian cells that is also con

142 We suggest that this model for long-palindrome formation in Streptomyces may represent a gen

143 Our results implicate palindrome formation in the amplification of regions wit

144 , did not make a significant contribution to palindrome formation induced by telomere losses.

145 Genome-wide analysis of palindrome formation is a new approach to identify struc

146 In addition, palindrome formation is dramatically reduced by a deleti

147 g of palindrome junctions, we show that long-palindrome formation occurs by unimolecular intra-strand

148 ved palindromic DNA (Genome-wide Analysis of Palindrome Formation) and whole genome sequencing (WGS).

149 ased approach called genome-wide analysis of palindrome formation, we show that palindromes occur fre

150 , as it apparently does in other examples of palindrome formation.

151 for DNA double-strand break repair genes in palindrome formation.

152 RAD51 and MRE11) have little or no effect on palindrome formation.

153 that dissimilar but comparably located TLC1 palindromes from other sensu stricto yeasts can function

154 By modification of palindrome-generating linear plasmids and development of

155 fficulties in their molecular analysis: long palindromes (>250 bp/arm) are highly unstable in Escheri

156 , we show that DNA molecules containing long palindromes (>900 bp/arm) can be transformed and stably

157 finity binding by EbfC to be the 4 bp broken palindrome GTnAC, where 'n' can be any nucleotide.

158 each plasmid mutated in only one arm of the palindrome had lost the site I mutation.

159 ssociated with mutagenesis of the large oriL palindrome have hindered comparisons of the functional r

160 three OBP binding sites are upstream of the palindrome in contrast to the sequence of the herpes sim

161 rmed at the site of a 246 bp interrupted DNA palindrome in the absence of the hairpin nuclease SbcCD

162 ion initiation sequence (DIS) is a conserved palindrome in the apical loop of a conserved hairpin mot

163 e processing of a 460 base pair (bp) perfect palindrome in the Escherichia coli chromosome with the s

164 We have previously demonstrated that a large palindrome in the mouse germ line derived from transgene

165 y to sequences containing an imperfect 20-bp palindrome in the terminal repeat (TR) of KSHV.

166 th high affinity for PurR is a 74-bp perfect palindrome in which weak PurBox2 and its flanking sequen

167 as been implicated in the formation of large palindromes in a variety of organisms.

168 The prevalence of large DNA palindromes in cancer is not known.

169 in yeast, appeared to decrease the number of palindromes in cells proliferating without telomeres.

170 otic process that constantly selects against palindromes in eukaryotic genomes.

171 igenesis and further support for the role of palindromes in gene amplification.

172 al basis for frequent translocations between palindromes in human meiosis and identify a conserved me

173 This indicates that the location of palindromes in the cancer genome can serve as a structur

174 d found that the selected variants contained palindromes in the DIS.

175 Massive palindromes in the human Y chromosome harbor mirror-imag

176 ors seem to have a nonrandom distribution of palindromes in their genomes, and a subset of palindromi

177 erted repeats (IRs) in the formation of long palindromes in yeast and Tetrahymena by a proposed mecha

178 h 6:2 or normal 4:4 segregation for the same palindrome, in the same cross, do manifest interference.

179 latory factors, and a complex arrangement of palindromes including a large inverted repeat of two tRN

180 sition that made the operator core a perfect palindrome increased repression by about 50% compared to

181 ll meiotic recombination events, most of the palindrome-induced breaks appear to be repaired by homol

182 ce 5'-TTAGGTTAGCCTAACCTAA-3', a perfect 9-bp palindrome interrupted by a single C.G base pair.

183 This GC-rich palindrome is completely different from the consensus p5

184 aLk change necessary to extrude an imperfect palindrome is considerably greater than that required fo

185 hat in Saccharomyces cerevisiae a linear DNA palindrome is efficiently formed from a single-copy circ

186 16 bp motif that consists of an interrupted palindrome is implicated in the DNA recognition by the m

187 These results suggest that the palindrome is required, not only for the attainment of t

188 The data suggest that the center of the palindrome is susceptible to double-strand breaks leadin

189 d activation by ORF50, but the presence of a palindrome itself is not absolutely required.

190 vel procedure that enables the sequencing of palindrome junctions, we show that long-palindrome forma

191 ication, convergent replication forks form a palindrome-like structural intermediate that requires nu

192 alindrome and most commonly a second related palindrome linked by a spacer region.

193 In addition to the loop within a 197-bp palindrome located in intron 40, four Alu elements locat

194 Instead, a palindrome located within the packaging signal (Psi) is

195 FabT was purified and bound to the DNA palindrome located within the promoter regions of the fa

196 FabR binding to a DNA palindrome located within the promoters of the fabB and

197 mbe as a model system, we show that a 160-bp palindrome (M-pal) is a meiotic recombination hotspot an

198 en linear and cruciform conformations of the palindromes may affect protein/DNA interactions and ther

199 Considering that DNA palindromes may constitute fragile genomic sites, our re

200 Our data lend support to the hypothesis that palindrome-mediated double-strand breaks in meiosis caus

201 The palindrome-mediated DSB formation depends on the primary

202 Palindrome-mediated genomic instability has been associa

203 utional t(11;22)s reside, implying a similar palindrome-mediated mechanism for generation of the t(17

204 ation of a previously unrecognized recurrent palindrome-mediated rearrangement, the t(8;22)(q24.13;q1

205 translocations occur in sperm suggests that palindrome-mediated translocation is a universal mechani

206 the 11q23 and 17q11 regions, has suggested a palindrome-mediated, stem-loop mechanism for the generat

207 in various tissues in animals, studying DNA palindrome metabolism in vivo, and understanding their p

208 Therefore, palindromes might be associated with gene amplicons in b

209 d by an oligonucleotide complementary to the palindrome; molecules lacking the palindrome could not d

210 Moreover, we identify a 10-bp perfect palindrome motif (CTGGCGCCAG) in the MKP2 promoter as a

211 response region contains a 30-bp tripartite palindrome motif.

212 The arms of these palindromes must have subsequently engaged in gene conve

213 Palindromes near chromosome ends are often triggered by

214 alysis of palindrome formation, we show that palindromes occur frequently and are widespread in human

215 report we focus on an N-terminal hydrophobic palindrome of PrP (112-AGAAAAGA-119) thought to feature

216 sted that specific separation of the central palindrome of the origin (site II) is an essential step

217 n 1 (NS1) binding site on the right terminal palindrome of the viral genome, which is composed of a m

218 cloned and sequenced the 5'- and 3'-terminal palindromes of MVC.

219 DNA palindromes often colocalize in cancer cells with chromo

220 mediated by double strand breaks in AT-rich palindromes on both chromosomes 11 and 22.

221 ogous crossing over between opposing arms of palindromes on sister chromatids.

222 nd from palindrome P5 to the proximal arm of palindrome P1, 1.5 Mb within AZFc.

223 ght to define AZFb were found to extend from palindrome P5 to the proximal arm of palindrome P1, 1.5

224 g region of RNA and contains a 10-nucleotide palindrome (pal; 5'-392-GGAGUGCUCC) located upstream of

225 g the roles that sequences downstream of the palindrome play in VZV oriS-dependent DNA replication.

226 DNA palindromes pose a threat to genome stability and have b

227 onstrate here that at least six of these MSY palindromes predate the divergence of the human and chim

228 this possibility, we coupled high-resolution palindrome profiling by the Genome-wide Analysis of Pali

229 on mechanism in which a break induced in the palindrome promotes homologous strand invasion and repai

230 trast to wild type (wt) PrP, PrP lacking the palindrome (PrPDelta112-119) neither converted to PrPSc

231 B harboring AT-rich microsatellite and quasi-palindrome (QP) sequences.

232 We have now characterized other palindrome rearrangements that arise from complex homolo

233 g palindrome, followed sequentially by short palindrome recognition.

234 Previous studies used palindromes, refractory to mismatch repair, as genetic m

235 The mutants also failed to melt the early palindrome region of the origin.

236 AIMIE detected repeated extragenic palindrome (REP) elements, CRISPR repeats, uptake signal

237 The DSB formation at the palindrome requires all of the gene products that are kn

238 Type IIS or interrupted palindrome restriction endonucleases, which result in si

239 is-regulatory portion of the LTRs, a complex palindrome-rich region acts as a hotspot of both siRNA m

240 Although the meeting was titled "DNA palindromes: roles, consequences, and implications of st

241 e of gene conversion within massive Y-linked palindromes runs counter to this hypothesis, most unique

242 Surprisingly, even in the absence of palindromes, SbcD affected the location of deletion endp

243 noic acid response elements termed Pal-17 (a palindrome separated by 17 bases) and DR-11 (a direct re

244 The natural operators are palindromes separated by variable length central spacers

245 ydrate response element (CHO-RE(FAS)) with a palindrome sequence (CATGTGn(5)GGCGTG) that is nearly id

246 Surprisingly, we find that deletion of the palindrome sequence affects neither the amyloidogenicity

247 Removal of a loosely conserved "putative" palindrome sequence in the PureA operator abrogated HPNi

248 ariant, Delta113-120 PrP23-144, in which the palindrome sequence is missing.

249 Indeed, analysis of MSY palindrome sequence variation in existing human populati

250 ment contains a highly conserved hydrophobic palindrome sequence, (113)AGAAAAGA(120), which has been

251 locking loops for hand-in-hand interactions, palindrome sequences for foot-to-foot interactions and a

252 crossovers accompanying 5:3 segregation of a palindrome show no conventional (i.e., positive) interfe

253 interchromosomal insertion at an extragenic palindrome site at Xq27.1 that completely cosegregates w

254 by 4 base pairs (DR-4) and with the inverted palindrome spaced by 6 base pairs (F2), but not with TRE

255 We propose two mechanisms for palindrome-stimulated deletion, SbcCD dependent and SbcC

256 asmids with mutations in only one arm of the palindrome supported origin-dependent DNA replication, w

257 300 short single-stranded DNA sequences with palindrome symmetry, leading to the selection of more th

258 ents, the Rep binding element (RBE), a small palindrome that comprises a single tip of an internal ha

259 ration-dependent interactions of a conserved palindrome that is initiated by separate G-rich stretche

260 ardation assay detected two sites within the palindrome that were important for protein binding.

261 differences in capture rates, focusing on 3' palindromes that are hypothesized to play a role in tran

262 qual sister chromatid-exchange events within palindromes that create unstable dicentric chromosomes,

263 hromosome instability and generate large DNA palindromes that facilitate gene amplification in human

264 a Y-shaped hairpin containing small internal palindromes that form the "ears" of the Y.

265 simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombina

266 We propose that upon extrusion of the palindrome the Rad50.Rad32 nuclease complex recognizes a

267 Within an H-palindrome, the H-DNA and canonical B-DNA are in a dynam

268 strand breaks may occur in the center of the palindrome, the tip of the putative hairpin, leading to

269 A complex of three palindromes, the largest spanning 3 Mb with 99.97% ident

270 ex is likely directly involved in processing palindromes through the homologous recombination pathway

271 Formation of long palindromes, through breakage-fusion-bridge cycles, is t

272 Insv homodimers preferentially bind CCAATTGG palindromes throughout the genome to mediate transcripti

273 are created when such unwinding induces the palindrome to reconfigure into a cruciform prior to fork

274 ters, which includes protection of the 16-bp palindrome to which Mcm1 dimers are known to bind as wel

275 Using small palindromes to monitor meiotic double-strand-break-repai

276 The protein binds to a DNA palindrome upstream of hetP and other genes.

277 HetR binds to a DNA palindrome upstream of the hetP gene.

278 differs significantly from the kissing loop palindromes utilized to initiate dimerization in primate

279 s also mapped and the predicted FadR-binding palindrome was found to span positions -19 to -35, upstr

280 effect when the NF-I binding element in the palindrome was mutated.

281 mutations on either arm or both arms of the palindrome were not impaired in protein synthesis and yi

282 th symmetrical mutations in both arms of the palindrome were replication incompetent.

283 Surprisingly, variants with GC-rich 4-nt palindromes were sustained throughout the selection peri

284 or 12-nt insertion/deletion loops; or 18-nt palindromes) were used to examine recognition of these m

285 se pairs (F2), but not with TREpal (unspaced palindrome), where homodimers appear to be simply two mo

286 romic Brachyury binding site and to the half-palindrome, whereas Brachyury does not bind to the TBX5

287 This contrasts with the interrupted palindrome, which forms a hairpin on the lagging-strand

288 The second component is an 18-bp AT palindrome, which is essential for ori-Lyt function.

289 d 22, resulting in deletions and loss of the palindrome, which then could stabilize the DNA structure

290 ment is configured as a direct tandem repeat palindrome with 80% homology to the p53 consensus bindin

291 A predicted 17-bp pseudo-palindrome with a consensus tTGTAATwwwATTACa was confirm

292 e most notable feature is that the full-site palindrome with coupling between quarter-sites one and f

293 lated promoter, we find that CviR binds to a palindrome with the ideal sequence CTGNCCNNNNGGNCAG.

294 ons, but notably they have revealed that DNA palindromes with an arm length of greater, similar 20 bp

295 ation events occurred in the vicinity of DNA palindromes with an arm length of greater, similar 20 bp

296 yefM-yoeB comprises adjacent long and short palindromes with core 5'-TGTACA-3' motifs.

297 Our data demonstrates that long palindromes with either no spacer (perfect) or a 2 bp sp

298 Both clusters contain palindromes with high sequence identity, presumably main

299 apo-IscR most likely recognizes an imperfect palindrome within the hya promoter.

300 A CGG palindrome within the promoter of glutamate synthase con