ライフサイエンスコーパス: Alu element

1 rmining the retropositional capability of an Alu element.

2 known with certainty to be the absence of an Alu element.

3 deletion (D allele) of a 287-base pair (bp) Alu element.

4 ster of nuclear receptor binding sites in an Alu element.

5 ith the locations of mobile elements such as Alu elements.

6 h we could not assess it as precisely as for Alu elements.

7 ose created during the retrotransposition of Alu elements.

8 me, we identified a total of 800 polymorphic Alu elements.

9 rs and ETS factors, to the highly repetitive Alu elements.

10 nds, and 58% map within the poly(A) tails of Alu elements.

11 our analyses on the 2318 human autosomal Ya Alu elements.

12 that allow analysis of individual Ya-lineage Alu elements.

13 een CpG and non-CpG substitutions within the Alu elements.

14 3-Lys9 by PCR using primer sets flanking the Alu elements.

15 built an atlas of 17,249 Pol III-transcribed Alu elements.

16 ) DNA, and three additional clones were near Alu elements.

17 ed of highly repetitive DNA sequences called Alu elements.

18 all human alternative exons are derived from Alu elements.

19 tes was found within sequences of repetitive Alu elements.

20 of the variation between recently integrated Alu elements.

21 t might influence expression from individual Alu elements.

22 gives them a selective advantage over other Alu elements.

23 rtion event involving at least two different Alu elements.

24 cluding many insertions of S and J subfamily Alu elements.

25 nactivation due to a rearrangement involving Alu elements.

26 positioning nucleosomes that is inherent to Alu elements.

27 ubfamilies, subfamilies of recently inserted Alu elements.

28 Sb family of Alu elements, a family of older Alu elements.

29 Pol III-dependent transcripts of individual Alu elements.

30 appreciated functions of non-coding RNAs and Alu elements.

31 tion of exons within introns in proximity to Alu elements.

32 man genes contain spliced exons derived from Alu elements.

33 ming events using recently integrated L1 and Alu elements.

34 genome reside within repeats, and 25% within Alu elements.

35 Alu elements, ~10% of the human genome, are the most com

36 exons when compared with exons derived from Alu elements, a class of primate-specific retrotransposo

37 e of nucleotide identity to the Sb family of Alu elements, a family of older Alu elements.

38 Alu elements, a major class of genomic repeats, had prev

39 g transcript, TARE-6, contained two adjacent Alu elements, a right monomer and a complete dimer, orie

40 Minor editing of highly active Alu elements abrogates the ability to activate both tran

41 itional class of demethylated loci mapped to Alu elements across the genome and accompanied repressio

42 However, very few Alu elements actively amplify.

43 -kb human fragment containing portions of an Alu element adjacent to the proviral 3'-LTR from an infe

44 atory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription

45 The distribution of both subfamilies of Alu elements along human chromosome 19 also appears to b

46 Finally, another family of SINEs, the human ALU element, also produces a self-cleaving RNA and is cl

47 hroughout the right half of selected genomic Alu elements altered Alu RNA steady-state levels in cult

48 erspersed nuclear element-1 (LINE-1) and the Alu element AluYb8 were determined in 380 placental samp

49 ity in the level of methylation for specific Alu elements among the members of 48 three-generation fa

50 ne (DAC), where we found a 1-16% decrease in Alu element and 18-60% LINE methylation within 3 days of

51 e acquired by recombination between this 16p Alu element and a closely related subtelomeric Alu eleme

52 intermolecular base-pairing between a 3' UTR Alu element and an Alu element within a long noncoding R

53 d in the reference sequence, localized to an Alu element and replaced the reference (AAAAG)(11) short

54 ce of a block of 1,284 bp comprised of three Alu elements and 328 bp of intervening unique-sequence D

55 ngle strand annealing (SSA) between proximal Alu elements and deletion of the intervening color marke

56 ific methylated genomic loci, including four Alu elements and eight promoters.

57 rsely correlated with the densities of older Alu elements and genes.

58 is performed with primers that bind genomic Alu elements and HIV-1 gag sequences, under conditions w

59 of multiple DNA repetitive elements, such as Alu elements and long interspersed nucleotide elements (

60 mammalian systems which are associated with Alu elements and SINEs (short interspersed elements) and

61 cularized exons, repetitive elements such as Alu elements and SINEs, competition score for forming ci

62 retrotransposition capability of individual Alu elements and successfully applied it to identify the

63 and derived CpG-methylation data from 31 178 Alu elements and their 5' flanking sequences, altogether

64 erates methylation profiles for thousands of Alu elements and their flanking sequences.

65 he sequence diversity of recently integrated Alu elements and to identify Alu elements that were pote

66 ading frames (uORFs) in the 5'UTR as well as Alu-elements and microRNA target sites in the 3'UTR have

67 p with SNPs and common repeats (particularly Alu elements) and guanine homopolymer content as paramet

68 , a SINE, appears to have originated from an Alu element, and hence is likely derived from 7SL RNA.

69 (STS) from the derived sequence outside the Alu element, and used a somatic cell hybrid mapping pane

70 uces the binding of p54(nrb) to the inverted Alu elements, and down-regulating synthesis of another p

71 d at human repetitive elements, particularly Alu elements, and may play a role in the suppression of

72 We submit that de novo transpositions of Alu elements, and saltatory appearances of Alu-mediated

73 e million copies of the approximately 300-bp Alu element are interspersed throughout the human genome

74 Alu elements are a class of non-autonomous retroposons b

75 Alu elements are a class of repetitive DNA sequences fou

76 Only a few Alu elements are able to retropose, and the factors dete

77 e role of A-tail length in determining which Alu elements are active.

78 It is generally thought that only a few Alu elements are capable of retrotransposition and that

79 Recently inserted Alu elements are closely related, suggesting that they a

80 Since Alu elements are confined to primates, it was unclear ho

81 The Alu elements are conserved approximately 300-nucleotide-

82 Most of these recently integrated Alu elements are contained with a series of discrete Alu

83 tors involved in transcriptional activity of Alu elements are discussed.

84 Alu elements are found exclusively in primate species an

85 i) polymorphic and fixed recently integrated Alu elements are found in genomic regions whose GC conte

86 PAX6 binding Alu elements are found primarily in old and intermediate

87 We show that functionally intact core Alu elements are highly abundant and far outnumber all o

88 Because Alu elements are highly repetitive, it has been difficul

89 istinguishable, and (ii) recently integrated Alu elements are inserted randomly, regardless of the GC

90 Alu elements are major contributors to lineage-specific

91 We show that Alu elements are more highly concentrated around houseke

92 t two-thirds of the CpG methylation sites in Alu elements are mutated, but of the remaining methylati

93 Alu elements are non-autonomous Short INterspersed Eleme

94 Alu elements are not distributed homogeneously throughou

95 We found that Alu elements are not preferentially degraded in GC-poor

96 ng evidence that recently integrated "young" Alu elements are not subject to positive or negative sel

97 Alu elements are one of the most successful families of

98 report that human mRNAs containing inverted Alu elements are present in the mammalian cytoplasm.

99 Alu elements are primate-specific members of the SINE (s

100 Alu elements are primate-specific retrotransposons that

101 A-T content, LINEs and MER repeats, whereas Alu elements are reduced.

102 Alu elements are retrotransposons that frequently form n

103 With over one million copies, Alu elements are the most abundant repetitive elements i

104 Alu elements are the most active and predominant type of

105 Alu elements are the most successful SINEs (Short INters

106 ts revealed that although the human-specific Alu elements are transcriptionally repressed, the older,

107 Alu elements are transposable elements that have reached

108 estral state (absence of the SINE) is known, Alu elements are useful genetic markers and have been ut

109 ived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and

110 to 40-nucleotide) inverted repeats, such as Alu elements, are sufficient to allow the intervening ex

111 Our data suggest that new Alu elements arise in unique, irreversible events, in a

112 iously thought, and support the potential of Alu elements as mutagenic factors in the human genome.

113 Breakpoints occurred inside Alu elements as well as in the 5' or 3' ends of them.

114 The nonautonomous Alu elements, as well as processed pseudogenes, are retr

115 0-fold increase in the number of polymorphic Alu elements associated with human phenotypes.

116 sms consisting of the presence/absence of an Alu element at a particular chromosomal location) offer

117 Alu elements at the junctions showed higher levels of di

118 Here, we present two Alu element-based alternative methods for the rapid iden

119 proximately 70% of lemur and 16% of marmoset Alu elements belong to lineage-specific subfamilies.

120 ilies, it is not known why all of the active Alu elements belong to the younger subfamilies.

121 isolated a transcriptionally active genomic Alu element belonging to the Ya5 subfamily.

122 Alu elements belonging to the previously identified "you

123 bited high levels of methylation at specific Alu elements came from families in which more than one m

124 Further, we show that inverted Alu elements can act in a similar fashion in their natur

125 Therefore, young Alu elements can be regarded as essentially neutral resi

126 t selective processes specifically targeting Alu elements can be ruled out as explanations for the ac

127 Alu elements cause gene disruptions by a process known a

128 tivity of L1 and related transposons such as Alu elements causes disease and contributes to speciatio

129 high sequence similarities between different Alu elements, combined with a potential recombinogenic r

130 Alu elements comprise >10% of the human genome.

131 n analysis of the mutation patterns for 5296 Alu elements comprising 20 subfamilies.

132 The human genome contains nearly 1.1 million Alu elements comprising roughly 11% of its total DNA con

133 random mutations within both subfamilies of Alu elements consistent with their recent evolutionary o

134 Alu elements constitute 10% of the human genome.

135 Our analysis of Alu elements containing one to four (Ya1-Ya4) of the Ya5

136 Sequence analysis of the loci with the Alu elements containing the longest A-tails (7 of the 19

137 sposon target-site duplications flanking the Alu element, containing potentially kinkable DNA sites.

138 inserted polymorphic (for presence/absence) Alu elements contribute to genome diversity among differ

139 poietic lineage, and that DNA methylation of Alu elements decreases with age, corresponding with a lo

140 In addition, this Alu element did not block the suppressive effect of co-i

141 er the rate of insertion and deletion inside Alu elements differed according to the base composition

142 flanked upstream by an potentially expressed Alu element, downstream by the H326 gene, and is located

143 The polymorphism is within an Alu element encoding four hexamer repeats recognized by

144 Interestingly, some Alu elements exhibited a strikingly tissue-specific patt

145 Sense and antisense Alu elements fold independently of one another into a se

146 nter is a database of taxon-specific primate Alu elements for use in phylogeny and population genetic

147 Three hundred forty-five recently integrated Alu elements from eight different Alu subfamilies were i

148 ion of the entire block containing the three Alu elements from one of the genes created the "short" i

149 There are nearly 900,000 old Alu elements from subfamilies S and J that appear to be

150 ication and retrieval of recently integrated Alu elements from the human genome.

151 The Alu element has been a major source of new exons during

152 Ancient Alu elements have been shown to be included in mature tr

153 Our data indicate that Alu elements have contributed to the acquisition of nove

154 ars to have evolved as a single lineage, and Alu elements have evolved into four currently active lin

155 Alu elements have inserted in primate genomes throughout

156 Alu elements have inserted in the human genome throughou

157 that only about 1000 of the over one million Alu elements have tails of 40 or more adenosine residues

158 Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-

159 rotransposons, in particular, LINE-1(L1) and Alu elements; however, no such assay exists for the youn

160 t in the 3' UTR of an SMD target and another Alu element in a cytoplasmic, polyadenylated long non-co

161 This motif was located within an Alu element in a region that was conserved in the murine

162 matches to the NF1 Alu repeat, three to the Alu element in BRCA2, and one to the Alu element in FGFR

163 the basis for the intron polymorphism is an Alu element in CE which is not present in the D gene.

164 to the Alu element in BRCA2, and one to the Alu element in FGFR2 (Apert syndrome).

165 fragment revealed that it is identical to an Alu element in intron 1 of the p53 gene.

166 verged from an Alu element in intron 6 to an Alu element in intron 1 through a heteroduplex fusion.

167 ead, the sequence gradually diverged from an Alu element in intron 6 to an Alu element in intron 1 th

168 t and involved the fusion of a portion of an Alu element in intron 6 with non-Alu sequence in intron

169 ng enzyme Dicer, and increased expression of Alu element in OIR.

170 Not all mRNAs that contain an Alu element in the 3' UTR are targeted for SMD even in t

171 formed by imperfect base-pairing between an Alu element in the 3' UTR of an SMD target and another A

172 In contrast, Alu elements in anthropoids show a skewed distribution s

173 out as explanations for the accumulation of Alu elements in GC-rich regions of the human genome.

174 ther, these results support a novel role for Alu elements in human gene regulation.

175 including, among hundreds of others, L1 and Alu elements in humans and Ty1 elements in yeast.

176 ates for the retrotransposition rate (RR) of Alu elements in humans of one new insertion every approx

177 BRCA1 gene breakpoints within or adjacent to Alu elements in intron 15; producing partial gene duplic

178 -like element in intron 2 and three types of Alu elements in intron 4 and 9, with varying copies of m

179 Moreover, we identified 44 of these Alu elements in linkage disequilibrium (r(2) > 0.7) with

180 the pattern of nucleosomal organization over Alu elements in native chromatin is specific and similar

181 ible explanation for the relative success of Alu elements in populating the human genome.

182 ns, phylogenies, and consensus sequences for Alu elements in primates including lemur, marmoset, maca

183 ong primates and suggest a potential role of Alu elements in the evolutionary diversity of proteins.

184 Of the approximately 1.3 million Alu elements in the human genome, only a tiny number are

185 ates, where the length increased in specific Alu elements in the human genome.

186 t but depletion of CpG dinucleotides and (v) Alu elements in the intronic regions or far from CpG isl

187 or independent parallel insertions of older Alu elements in the same genomic region.

188 messenger RNAs (mRNAs) that contain inverted Alu elements in their 3' untranslated region are ineffic

189 for researchers interested in characterizing Alu elements in their primate taxon of interest.

190 There are ~650,000 Alu elements in transcribed regions of the human genome.

191 hod to preferentially identify low-frequency Alu elements in various human DNA samples with different

192 is associated with scAlu RNA production from Alu elements in vivo.

193 ly inherited autosomal loci (1 LINE-1 and 39 Alu elements) in all of the caste and continental popula

194 Multicopy Alu elements include recently integrated subfamilies tha

195 Here, we report an analysis of Alu element-induced genomic instability through a novel

196 sible that long dsRNA structures formed from Alu elements influence gene expression.

197 Some Alu elements inserted in the genome so recently that the

198 Similar to the L1 retrotransposon family, Alu elements integrate primarily through an endonuclease

199 ould be due to a preferential degradation of Alu elements integrated in GC-poor regions by small inde

200 zably different from classical TPRT-mediated Alu element integration.

201 e for Alu replication, we introduced a human Alu element into mouse cells.

202 nvert either alternative or otherwise silent Alu elements into constitutive exons and this can lead t

203 When we classified Alu elements into major subfamilies, younger elements (A

204 , we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadeny

205 ny cells, mRNAs containing inverted repeated Alu elements (IRAlus) in their 3' untranslated regions (

206 a single exon that includes inverted repeat Alu elements (IRAlus).

207 The Alu element is bounded by 16-nucleotide direct repeats a

208 This Alu element is likely responsible for at least part of t

209 However, the activity of the Alu element is not correlated with its enhancer blocking

210 This Alu element is one component of the locus control region

211 ylome revealed that the methylation level of Alu elements is high in the intronic and intergenic regi

212 ropose that the differential distribution of Alu elements is likely to be due to a change in their pa

213 The amplification of most Alu elements is thought to occur through a limited numbe

214 A portion of Alu elements is transcribed by RNA Pol III, whereas the

215 a nucleosome centered over the 5 -end of the Alu element, is associated with repression of polymerase

216 r human DNA transposons nested within L1 and Alu elements known to be primate specific.

217 present work is a phylogenetic study of four Alu elements known to have gene regulatory functions in

218 bility) strongly correlate with densities of Alu elements; little evidence was found for the role of

219 197-bp palindrome located in intron 40, four Alu elements located in introns 1, 2, 3, and 50 were als

220 t interspersed transposable element (SINE or Alu elements), long terminal repeat (LTR), long interspe

221 We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease

222 criptionally repressed, the older, expressed Alu elements may be exapted by the human host to functio

223 esults suggest that transcriptionally active Alu elements may eliminate transcriptional interference

224 or understanding mechanisms by which certain Alu elements may evade chromatin-mediated transcriptiona

225 Therefore, these Alu elements may have been involved in the initial gene

226 Although Alu element-mediated homologous recombination events in

227 rs to be the first demonstration identifying Alu element-mediated recombination as a consistent mecha

228 Sequence data suggested that the Alu element might have previously been present in the ch

229 u element and a closely related subtelomeric Alu element of the Sx subfamily.

230 ce variation in the different sections of an Alu element on retrotransposition.

231 r supported by the presence of an incomplete Alu element on the upstream side of this insertion point

232 is whether selective pressures are affecting Alu elements on a large scale.

233 derscored a clear impact of primate-specific Alu elements on shaping the overall repertoire of human

234 omologous recombination between the flanking Alu elements on sister chromatids.

235 g new exons, but other impacts of intragenic Alu elements on their host RNA are largely unexplored.

236 The retrotransposition rate estimates for Alu elements, one in 40 births, is roughly half the rate

237 ne conversion events of pre-existing ancient Alu elements or independent parallel insertions of older

238 We conclude that Alu elements pose the largest transposon-based mutagenic

239 Finally, the intron length and abundance of Alu elements positively correlated with ABS event comple

240 An Alu element preceding the myeloperoxidase gene (MPO) con

241 own to have inserted into a fourth and older Alu element present in the "short" from of intron 1.

242 and a cercopithecoid monkey, with additional Alu elements present further upstream.

243 f repetitive genomic sequences (particularly Alu elements) present in these upstream regions.

244 etermined that genes (n = 456) with promoter Alu elements primarily related to transcription, apoptos

245 they are stable polymorphisms-newly inserted Alu elements rarely undergo deletion; third, the presenc

246 Alu elements represent the largest family of human mobil

247 undergo deletion; third, the presence of an Alu element represents identity by descent-the probabili

248 Analysis of the Yd Alu elements resulted in the recovery of two new Alu sub

249 Recombination between Alu elements results in genomic deletions associated wit

250 Evaluation of the 19 Alu elements retrieved from the draft sequence of the hu

251 We analyzed Alu elements retrieved from the GenBank database and ide

252 These results suggest that Alu elements retrotranspose at a faster rate in humans t

253 sis of the DNA sequences from the individual Alu elements revealed a low level of random mutations wi

254 DNA sequence analysis of the individual Alu elements revealed a low level of random mutations wi

255 ditionally, heterologous RNA species such as Alu element RNA and L1 transcripts with 3' extensions ar

256 o Alu RNA levels, suggesting that the master Alu element(s) have a multitude of individual difference

257 Each monomer of the dimeric Alu element shares sequence homology with the 7SL RNA co

258 Alu elements sharing sequence characteristics of the "ol

259 We found that in lemurs, Alu elements show a broader and more symmetric sequence

260 both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect m

261 peat polymorphisms (STRPs) and a polymorphic Alu element spanning a 22-kb region of the PLAT locus on

262 product has sustained a deletion between two Alu elements, such that the true breakpoint region is de

263 ased the level of H3-Lys9 methylation in the Alu elements, suggesting that H3-Lys9 methylation may be

264 tes a mixture of sequences from two distinct Alu elements, suggesting that the putative junction frag

265 The level of gene conversion between Alu elements suggests that it may have a significant inf

266 We analyzed one of these old subfamilies of Alu elements, Sx, for sequence conservation relative to

267 Second, most Alu elements tend to be coclustered with each other, but

268 ircRNAs had longer flanking introns and more Alu elements than other circRNAs in the same ABS event.

269 ci resulted in the recovery of a few "young" Alu elements that also resided at orthologous positions

270 ents explain disease-associated mutations in Alu elements that hamper hnRNP C binding.

271 The four Alu elements that impact differential gene expression we

272 complementarity with a specific site within Alu elements that is highly conserved within 3' untransl

273 nces in methylation were identified only for Alu elements that lie in sub-telomeric or sub-centromeri

274 is enriched with repeats, particularly fixed Alu elements that provide the homology required to maint

275 ntly integrated Alu elements and to identify Alu elements that were potentially retroposition compete

276 dditionally, we identified variable AluJ and AluS elements that likely arose due to non-retrotranspos

277 fically induce chromosomal translocations at Alu elements, the most numerous family of repetitive ele

278 ylation may be related to the suppression of Alu elements through DNA methylation.

279 With diverged Alu elements, translocation frequency was unaltered, yet

280 (DSBs) were introduced adjacent to identical Alu elements, translocations occurred at high frequency

281 Alu elements use a copy and paste retrotransposition mec

282 The block containing the three Alu elements was not found in intron 1 of the red or gre

283 classes of microsatellites with families of Alu elements was used to facilitate the development of g

284 sed on a phylogenetic tree of human-specific Alu elements, we estimate the sahAluY insertion time at

285 ne whether an analogous mechanism exists for Alu elements, we have analyzed three publicly available

286 e flanking unique sequences adjacent to each Alu element were used in polymerase chain reaction assay

287 Several hypomethylated Alu elements were identified and their hypomethylated st

288 s for several transcriptionally active human Alu elements were identified by cDNA cloning and used fo

289 About 22% (313/1452) of the Ya-lineage Alu elements were polymorphic for the insertion presence

290 ement, variable number of tandem repeat, and Alu) elements were identified, with the majority being s

291 t nucleosomes are consistently positioned at Alu elements where CPD hotspots form, but by 2 h post-ir

292 NA and a gorilla genomic clone, including an Alu element which is present in both species.

293 mately 30% of new STR mutations occur within Alu elements, which compose only 11% of the genome, but

294 tein is also responsible for the mobility of Alu elements, which constitute a further approximately 1

295 The polymorphic Alu elements will be useful tools for the study of human

296 exhibit greater methylation entropies; (iv) Alu elements with high methylation entropy are associate

297 -pairing between a 3' UTR Alu element and an Alu element within a long noncoding RNA (lncRNA) called

298 The results suggest that at least some Alu elements within human mRNAs serve as microRNA target

299 or the formation and remarkable expansion of Alu elements within the genome.

300 ty by descent-the probability that different Alu elements would independently insert into the exact s