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

6 ose created during the retrotransposition of Alu elements.

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

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

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

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

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

12 3-Lys9 by PCR using primer sets flanking the Alu elements.

13 Pol III-dependent transcripts of individual Alu elements.

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

15 ed of highly repetitive DNA sequences called Alu elements.

16 all human alternative exons are derived from Alu elements.

17 tes was found within sequences of repetitive Alu elements.

18 of the variation between recently integrated Alu elements.

19 t might influence expression from individual Alu elements.

20 gives them a selective advantage over other Alu elements.

21 rtion event involving at least two different Alu elements.

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

23 nactivation due to a rearrangement involving Alu elements.

24 positioning nucleosomes that is inherent to Alu elements.

25 ubfamilies, subfamilies of recently inserted Alu elements.

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

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

28 man genes contain spliced exons derived from Alu elements.

29 ming events using recently integrated L1 and Alu elements.

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

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

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

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

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

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

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

37 However, very few Alu elements actively amplify.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

65 Alu elements are a class of repetitive DNA sequences fou

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

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

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

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

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

71 The Alu elements are conserved approximately 300-nucleotide-

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

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

74 Alu elements are found exclusively in primate species an

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

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

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

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

79 Alu elements are major contributors to lineage-specific

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

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

82 Alu elements are not distributed homogeneously throughou

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

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

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

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

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

88 Alu elements are retrotransposons that frequently form n

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

90 Alu elements are the most active and predominant type of

91 Alu elements are the most successful SINEs (Short INters

92 Alu elements are transposable elements that have reached

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

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

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

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

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

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

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

100 0-fold increase in the number of polymorphic Alu elements associated with human phenotypes.

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

102 Alu elements at the junctions showed higher levels of di

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

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

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

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

107 Alu elements belonging to the previously identified "you

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

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

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

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

112 Alu elements cause gene disruptions by a process known a

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

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

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

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

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

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

119 Alu elements constitute 10% of the human genome.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

139 Alu elements have inserted in primate genomes throughout

140 Alu elements have inserted in the human genome throughou

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

176 Multicopy Alu elements include recently integrated subfamilies tha

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

200 197-bp palindrome located in intron 40, four Alu elements located in introns 1, 2, 3, and 50 were als

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

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

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

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

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

206 Although Alu element-mediated homologous recombination events in

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

223 Alu elements represent the largest family of human mobil

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

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

226 Recombination between Alu elements results in genomic deletions associated wit

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

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

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

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

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

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

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

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

235 Alu elements sharing sequence characteristics of the "ol

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

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

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

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

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

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

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

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

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

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

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

247 The four Alu elements that impact differential gene expression we

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

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

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

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

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

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

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

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

256 Alu elements use a copy and paste retrotransposition mec

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

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

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

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

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

262 Several hypomethylated Alu elements were identified and their hypomethylated st

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

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

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

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

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

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

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

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

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

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

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

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