ライフサイエンスコーパス: integration site

1 populations with identical genomic proviral integration sites).

2 errant cancer-related gene expression at the integration site.

3 nce of testing for rearrangements around the integration site.

4 thereby permitting precise assessment of the integration site.

5 flexible dinucleotides at the center of the integration site.

6 he sharp kink with RAG is 1 bp away from the integration site.

7 timing of incoming inputs at the axo-somatic integration site.

8 and microRNAs was activated surrounding the integration site.

9 RS revealed recurrent gaps and breaks at the integration site.

10 g of the nucleosomal DNA arm proximal to the integration site.

11 using DNA sequencing to identify the vector integration sites.

12 to allow rapid analysis of retroviral vector integration sites.

13 cHI1 plasmids or within multiple chromosomal integration sites.

14 ration sequencing data for retroviral vector integration sites.

15 ged/untagged molecules from distinct genomic integration sites.

16 ction, yielding a total of 1610 unique HIV-1 integration sites.

17 histones, BET protein-binding sites and MLV-integration sites.

18 repair in macrophages at HIV-1 proviral DNA integration sites.

19 e revealed a proportionally higher number of integration sites.

20 of four HCC patients and identified 255 HBV integration sites.

21 in all chromosomal (attB) and SCCmec (attS) integration sites.

22 ce for contamination during analysis of XMRV integration sites.

23 y enriched in flanking regions of 84% of the integration sites.

24 voir as shown by the duplication of proviral integration sites.

25 ents by high-throughput sequencing of vector-integration sites.

26 re integration near (<1.5 mum) their genomic integration sites.

27 ion of nuclear entry and alteration of viral integration sites.

28 ration sequencing data for retroviral vector integration sites.

29 -cell-specific Moloney murine leukemia virus integration site 1 (BMI1) is a component of the polycomb

30 The gene ectopic viral integration site 1 (EVI) and its variant myelodysplastic

31 Enhanced expression of ecotropic viral integration site 1 (EVI-1) occurs in approximately 10% o

32 Ecotropic viral integration site 1 (EVI1) is an oncogenic dual domain zi

33 Ecotropic viral integration site 1 (EVI1), a proto-oncogene and zinc fin

34 Ecotropic viral integration site 1 (EVI1), required for normal embryogen

35 Myeloid ecotropic viral integration site 1 (Meis1) forms a heterodimer with Pbx1

36 Myeloid ecotropic viral integration site 1 (MEIS1) is a transcription factor tha

37 Wingless-related MMTV integration site 1 (WNT1)/beta-catenin signaling plays a

38 ormation by competing with myeloid ecotropic integration site 1 for binding to the common heterodimer

39 factor 1) and MEIS1 (myeloid ecotropic viral integration site 1 homolog), and remain so until termina

40 the safe-harbor locus adeno-associated virus integration site 1 in human embryonic stem cells.

41 riptional signature of EVI1 (ecotropic viral integration site 1)-rearranged (EVI1-r) acute myeloid le

42 al repressor, ETS variant 6, ecotropic viral integration site 1, and homeobox A11.

43 Ecotropic viral integration site-1 (EVI1) is an oncogenic zinc finger tr

44 suppressor, whereas myeloid ecotropic viral integration site-1 (Meis1) is an oncogene.

45 The proto-oncogene EVI1 (ecotropic viral integration site-1), located on chromosome band 3q26, is

46 ess-related MMTV (mouse mammary tumor virus) integration site 3 (WNT3) by ingrowing axons from the th

47 ess-related MMTV (mouse mammary tumor virus) integration site 3 (WNT3).

48 Importantly, integration site analyses reveal a strong preference for

49 Both single-genome sequencing (SGS) and integration site analysis (ISA) provide useful informati

50 Integration site analysis confirmed the presence of larg

51 Inverse PCR strategy for integration site analysis demonstrated integration of at

52 Retroviral integration site analysis in 4 animals revealed a polycl

53 f HIV-1-infected cells using high-throughput integration site analysis in a hematopoietic stem cell-t

54 Viral integration site analysis indicated a reduction in clona

55 Lentiviral integration site analysis revealed that alternative hist

56 We developed VISA, a vector integration site analysis server, to analyze next-genera

57 Integration site analysis showed a positive safety profi

58 Integration site analysis showed polyclonality.

59 ion sequencing and corresponding chromosomal integration site analysis to selectively map the chromos

60 Here we present VISMapper, a vector integration site analysis web server, to analyze next-ge

61 Here we perform TCRB sequencing, integration site analysis, and single-cell RNA sequencin

62 eral blood liver and spleen and we performed integration site analysis.

63 Clones were confirmed by host-proviral integration site analysis.RESULTSHIV-1 genomic RNA with

64 In all seven lines the exact integration site and breakpoint sequences were identifie

65 line, this method can be used to analyse the integration site and configuration of any foreign DNA in

66 gene copy number is estimated, but the exact integration site and configuration of the foreign DNA re

67 either LexA or GAL4 are inserted at the same integration site and paired, the enhancer of one transge

68 Here, we used matched integration site and proviral sequencing (MIP-Seq), an e

69 brane proteins independent of the downstream integration site and that many membrane proteins can pro

70 emonstrate the ability to measure lentiviral integration sites and chromatin accessibility of host an

71 m which also provided a comprehensive map of integration sites and chromosomal hotspots for micro-org

72 ivating the search for localized clusters of integration sites and comparison of the clusters formed

73 en proven by the identification of transgene integration sites and flanking sequences in three CHO ce

74 ique in clonal cells with previously defined integration sites and further demonstrate the ability to

75 ne modifications) in +/-32 kb of these ERVs' integration sites and in control regions, and analyzed t

76 AS-regulated transgenes that differ in their integration sites and in the repetitive nature of the UA

77 taneously provide accurate prediction of HIV integration sites and mechanistic explanations of the de

78 poly(ADP-ribose) polymerase 2 (PARP2) to L1 integration sites and that PARP2 activation leads to the

79 To test this hypothesis, the HBV integration sites and the common mutations in the TERT p

80 dition, we performed studies to identify HPV integration sites and the relationship of integration to

81 hich required specific DNA sequences and was integration-site (and/or cell-line) specific.

82 ations in the unedited allele, indels at the integration site, and the addition of resistance genes t

83 quencing viruses, T cell receptor genes, HIV integration sites, and cellular transcriptomes.

84 oviruses with identical sequences, identical integration sites, and similar levels of RNA expression

85 tered out, and then unique retroviral vector integration sites are determined based on the alignment

86 nscription, nuclear import, and transport to integration sites are incompletely understood.

87 The vast majority (87%) of the integration sites are located within histone H3K4me1 isl

88 ase, we discover that at these larger scales integration sites are predominantly determined by chroma

89 Although MLV integration sites are significantly enriched at TSS, onl

90 ces of piggyBac by sequencing a large set of integration sites arising from transposition from two se

91 preference for the nucleotides flanking the integration site at the leader-repeat 1 boundary of the

92 athways, including the Wnt (wingless-related integration site)/beta-catenin pathway.

93 eted modulator of WNT (Wingless-related MMTV integration site)/beta-catenin signaling, is both necess

94 ces were detected in the distribution of HIV integration sites between cellular models of HIV latency

95 There were three, one and one consensus integration sites between the primary and metastatic tum

96 erences in the genomic distribution of HIV-1 integration sites between TN and TCM cells that accounte

97 us (PFV) retroviral intasome searches for an integration site by one-dimensional (1D) rotation-couple

98 Our findings show that HIV integration sites can play a critical role in expansion

99 Using a sensitive high-throughput integration site-capture technique and global expression

100 HIV integration site characteristics and genes were compared

101 We compared HIV integration site characteristics between four cellular m

102 on sites than expected in ACH-2 cells, their integration site characteristics consistently differed f

103 odels, there were significant differences in integration site characteristics, including orientation

104 Analysis of previously published HIV-1 integration site data showed that integration density in

105 Extensive tests on a high-density HIV integration site dataset showed that DeepHINT can outper

106 everal sets of experimentally determined HIV integration sites demonstrates the software.

107 w that paired sites buffer the enhancer from integration site-dependent effects on transcription in v

108 me1 occurs independently of each other in an integration site-dependent manner.

109 Tat-transactivating protein levels generate integration-site-dependent, stochastically-driven phenot

110 These findings show that integration site differences exist among the commonly us

111 ll lines generated with PhiC31 into a single integration site displayed nearly identical, enhancer-sp

112 CPSF6 complementation rescued HIV-1 integration site distribution in CPSF6 knockout cells, b

113 rounds of activation, analyzed the resulting integration site distribution.

114 also developed a multivariate model based on integration-site distributions and found that data from

115 liferation in CART19 therapy and how data on integration-site distributions can be linked to treatmen

116 Although integration site does not appear to be a key driver of c

117 Genes at integration sites enriched in responders were commonly f

118 blast growth factor (Fgf)-Wingless type MMTV integration site family (Wnt) genetic module in the ante

119 t activation of canonical Wingless-type MMTV integration site family (Wnt) signaling is pathognomonic

120 ngless-type MMTV (mouse mammary tumor virus) integration site family (WNT) signaling pathway in the r

121 The wingless-type MMTV integration site family (WNT)/beta-catenin/adenomatous p

122 Wingless-type MMTV integration site family (WNT)16 is a key regulator of bo

123 ed causative mutations in wingless-type MMTV integration site family 1 (WNT1).

124 e by wingless-type mouse mammary tumor virus integration site family member (WNT)/beta-catenin signal

125 SP7 transcription factor, wingless-type MMTV integration site family member 1 (WNT1), trimeric intrac

126 des the Wnt family member wingless-type MMTV integration site family member 16B (WNT16B).

127 rotein, which retains the Wingless-type MMTV integration site family member-ligand-binding domain, bu

128 ers to the wingless-type mammary tumor virus integration site family of proteins), that are regulated

129 WNT10A (Wingless-type MMTV integration site family, member 10A) plays a crucial rol

130 ymal Wingless-type Mouse Mammary Tumor Virus integration site family, member 10B (Wnt10b)/beta-cateni

131 The serine/threonine-specific proviral integration site for Moloney murine leukemia virus (PIM)

132 The provirus integration site for Moloney murine leukemia virus (Pim)

133 Proviral integration site for Moloney murine leukemia virus (Pim)

134 rnberg cells overexpress oncogenic (proviral integration site for Moloney murine leukemia virus (PIM)

135 ptosis (PUMA) and downregulation of proviral integration site for Moloney murine leukemia virus 1 kin

136 enic, serine-threonine kinase PIM1 (Proviral Integration site for Moloney murine leukemia virus 1) ha

137 on of the NFkappaB-dependent kinase proviral integration site for Moloney murine leukemia virus-1 (PI

138 expression of the oncogenic kinase proviral integration site for Moloney-murine leukemia 1 (PIM1) in

139 transport, the use of YidC as an additional integration site for multispanning membrane proteins may

140 his approach has applications for sequencing integration sites for gene therapy vectors, transposons,

141 Integration sites for infectious proviruses from those 4

142 The integration sites form approximately 60,000 tight cluste

143 r models of HIV latency and in comparison to integration sites found in patient samples.

144 a useful graphical interface to analyze the integration sites found in the genomic context.

145 ide integration map of more than one million integration sites from CD34(+) hematopoietic stem cells

146 thod for fast identification of viral vector integration sites from long read high-throughput sequenc

147 For the discovery of hepatitis B virus integration sites from probe capture data, the verified

148 The wingless and integration site growth factor-5a (Wnt5a) is a ligand of

149 integration machinery, the selection of HIV integration sites has also been shown to depend on the h

150 However, the corresponding integration sites have not been mapped.

151 al fragment (exons 8-11) 3' to the transgene integration site in R6/2.

152 1 locus is frequently found to be a proviral integration site in retrovirus-induced lymphomagenesis,

153 enic reporter clones and identified reporter integration sites in a massive and parallel manner.

154 technology have made it possible to analyze integration sites in cells from HIV-infected patients.

155 investigated the efficiency of gap repair at integration sites in different HIV-1 target cell types.

156 tions occur in the same intron as retroviral integration sites in gene therapy-induced T-ALL, suggest

157 The majority of integration sites in latently infected cells were in int

158 Analysis of integration sites in liver samples from six treated dogs

159 aches to reconstruct transgene structure and integration sites in models of Huntington's disease, rev

160 blood cells, and characterized the proviral integration sites in paired lymph node and blood samples

161 sites in the host genome; we identified 2410 integration sites in peripheral blood lymphocytes of fiv

162 sitivity and ability in identifying low-read integration sites in subpopulations of the tumor cells.

163 transgenes inserted at commonly used phiC31 integration sites in the Drosophila genome.

164 usSeq, for detecting known viruses and their integration sites in the human genome using next-generat

165 al proliferation of CD4(+) T cells and viral integration sites in the human genome.

166 ry and lateral line areas and vocal-acoustic integration sites in the preoptic area and ventral telen

167 gh-throughput sequencing to analyze proviral integration sites in these tumors.

168 HIV integration sites in Tpr-depleted cells are less associa

169 llection of genomic perturbations near viral integration sites, including direct gene disruption, vir

170 Our mutagenesis screen identified several integration sites, including oncogenes Gfi1, Myb, and Ra

171 anistic implications in the selection of HIV integration sites, including potential roles of several

172 A total of 181 integration sites, including the three found by WGS, wer

173 ng gene regulatory elements with the unique, integration site-independent ability to transfer the cha

174 n lysozyme locus (cLys-Cox-2), which directs integration site-independent, copy number-dependent tran

175 Their integration site influences genome stability and gene ex

176 ses were determined in the mouse genome, and integration site information was used to analyze the dis

177 under, suggesting that the UBC-GFP transgene integration site is closely linked to the MHC locus on c

178 both are significantly higher than when the integration site is moved near the terminus, consistent

179 oinjection of a Cre transgene construct, the integration site is random and in most cases not known.

180 Identifying retroviral vector integration sites is also important for retroviral mutag

181 High-throughput integration site (IS) analysis of wild-type adeno-associ

182 inistration of relational databases of viral integration site (IS) data.

183 A total of 534 HIV integration sites (IS) and 63 adjacent HIV env sequences

184 cription units, we sequenced 1 million HIV-1 integration sites isolated from cultured HEK293T cells.

185 stably marked at the clonal level by vector integration sites (ISs).

186 er mutations affecting WNT (wingless-related integration site), JAK-STAT (Janus kinase/signal transdu

187 The integration site known as AAVS1 is located in chromosome

188 fects: the regulatory environment of genomic integration sites leads to variation of expression patte

189 hed at TSS, only a small fraction of the MLV integration sites (<15%) occur in this region.

190 The distribution of integration sites mapped by Illumina sequencing confirms

191 tion of these microbial signatures and their integration sites may provide biomarkers for OCSCC/OPSCC

192 a homeobox (PBX) and myeloid ecotropic viral integration site (MEIS) proteins control cell fate decis

193 Through analysis of Steamer integration sites, mitochondrial DNA single-nucleotide p

194 Cancer SVs and viral integration sites must be discovered in a genome-wide sc

195 f genotoxicity, indicated by numerous common integration sites near proto-oncogenes and by increased

196 onment that dysregulate the wingless related integration site network, a central pathway maintaining

197 ent descending projections to vocal-acoustic integration sites, notably the hindbrain octavolateralis

198 subpopulations, and use this to identify the integration site nucleotide motifs of five retroviruses

199 ng, respectively, the R231E mutation altered integration site nucleotide preferences while K258E had

200 cell clones that differ only in the genomic integration site of an identical constitutively expresse

201 e TLA method to not only efficiently map the integration site of any transgene, but also provide addi

202 further identified MAPK ERK as one possible integration site of both signals, because its phosphoryl

203 ortance and urgency of mapping the transgene integration site of transgenic mouse strains used in bio

204 matin architecture is probed through mapping integration sites of exogenous lentiviruses.

205 Genes close to the integration sites of expanding clones may be associated

206 Integration sites of expressed viral transcripts frequen

207 version of VISDB contains a total of 77 632 integration sites of five DNA viruses and four RNA retro

208 number (often > 10(4)) of distinct proviral integration sites of HTLV-1 in each host that is greatly

209 It has been known for a number of years that integration sites of human immunodeficiency virus type 1

210 sensus sequence is not present in individual integration sites of human T-cell lymphotropic virus typ

211 Moreover, the integration sites of intact proviral sequences from elit

212 Therefore, the analysis of integration sites of retroviral vectors is a crucial ste

213 tide sequences are also found at the genomic integration sites of retroviruses(2-6) and other transpo

214 ransposases, where severe kinks occur at the integration sites of target DNA and thus prevent the rev

215 Integration sites of viral genes and oncogenes were dete

216 and insertion rates vary across species, and integration sites often cluster near genes related to an

217 Whole genome sequencing indicated a single integration site on mouse chromosome 8 (8qB2) with ~6 ge

218 nucleosomes in vitro and redistribute viral integration sites on the genomic scale.

219 we identified four transcriptionally active integration sites, one being in the TNFRSF6B gene.

220 ent and that the chromosomal location of the integration site or whether the transformed gene is enco

221 extensive efforts have focused on analyzing integration site populations from patient samples, but t

222 58, and NUP153 for infection and altered the integration site preference of HIV-1 without any discern

223 nents of nucleocytoplasmic trafficking alter integration site preference, not by altering the traffic

224 nown cofactors for nuclear entry, and alters integration site preference.

225 (MLV)-based vectors and the vector-specific integration site preferences played an important role in

226 xic, well below what was expected from their integration site preferences.

227 a command-line pipeline designed to map the integration sites produced by this assay and identify th

228 er, rapamycin did not significantly alter LV integration site profile or chromosomal distribution in

229 ancer Cell, Lau and colleagues report an HBV integration site recurrent in HCC that generates a chime

230 Tethering KAT7 to an ectopic alphoid DNA integration site removed heterochromatic H3K9me3 modific

231 he reporter gene from its unique chromosomal integration site resulted in no discernible genomic inst

232 uses are relatively promiscuous in choice of integration sites, retrotransposons can display marked i

233 Analysis of >12,000 SB integration sites revealed markedly different oncogene a

234 g sites analyzed using ChIP-Seq data and MLV-integration sites revealed significant positive correlat

235 Analysis of non-CRISPR integration sites revealed that Cas1 and Cas2 are direct

236 In contrast, nucleotide preferences at integration sites seem to be governed by the ability for

237 rtance of retroviral structural proteins for integration site selection and the avoidance of genomic

238 that indirect sequence recognition dictates integration site selection by favoring deformation of th

239 ublications advance our understanding of HIV integration site selection by focusing on the localizati

240 is available for integration, the process of integration site selection is not random.

241 We discuss approaches to alter integration site selection that could potentially improv

242 These findings link integration site selection to virulence and viral evolut

243 native splicing contributed significantly to integration site selection.

244 eciated physical contributions to retroviral integration site selection.

245 Analysis of the integration-site selection of these chimeric viruses sho

246 directly contact tDNA bases and affect local integration site sequence selection.

247 applicable algorithm to sort the individual integration site sequences into plus-strand and minus-st

248 c murine leukemia virus-related virus (XMRV) integration site sequences previously identified from hu

249 We describe here tagmentation-based tag integration site sequencing (TTISS), an efficient, scala

250 ty and T-cell repertoire, measured by vector integration site sequencing and T-cell receptor beta-cha

251 Analysis of integration sites showed that cancer genes were preferen

252 five parameters previously found to predict integration sites showed that intron density is the stro

253 omplexes and canonical Wnt (Wingless-related integration site) signal transduction.

254 li), thereby affecting Wnt (Wingless-related integration site) signaling and regulating smooth muscle

255 activator in canonical Wnt (wingless-related integration site) signaling.

256 pressor of canonical WNT (wingless-type MMTV integration site) signaling.

257 ugh SecYEG most likely constitutes the major integration site, small membrane proteins have been show

258 xts in which it is important to identify DNA integration sites, such as insertional mutagenesis scree

259 increased transcription of Wingless-related integration site target genes.

260 n HIV-1 infection, we analyzed virologic and integration site targeting properties of a CPSF6 variant

261 as reverse transcription, nuclear entry, and integration site targeting.

262 Despite a greater diversity of minority integration sites than expected in ACH-2 cells, their in

263 stem vocal-acoustic nuclei and other sensory integration sites that also differ, though less extensiv

264 Viral integration sites that contribute to oncogenesis are sel

265 associated DNA viruses and identifying viral integration sites that may unravel novel mechanisms of c

266 c transcription factor Ndt80 upstream of the integration site, thereby tightly linking its transcript

267 Moving the native bacterial integration site to different locations on the genome an

268 ed in serially transplanted mice, linked the integration sites to global hepatocyte gene expression,

269 er, until recently, there was no way to link integration sites to their cognate proviral sequences.

270 PFV and macaque simian foamy virus (SFVmac) integration sites toward centromeres, dampening the resu

271 This article presents the Genomic Integration Site Tracker (GeIST), a command-line pipelin

272 Many studies have reported viral integration sites (VISs) proximal to structural or funct

273 Remarkably a conserved integration site was found in over 50% of the cases.

274 A single transgene integration site was observed for five of the six founde

275 uence-independent preference for nucleosomal integration sites was observed, in distinction to the pr

276 nc-finger nuclease technology to engineer an integration site, we generated three transgenic P. falci

277 HIV-1 genomes and corresponding chromosomal integration sites, we show that the proviral reservoirs

278 Viral integration sites were also detected in expressed transc

279 HPV16 integration sites were broadly distributed in the genome

280 Cells were randomly cloned and integration sites were determined in individual clones.

281 As a result, a total of 332 viral integration sites were identified in the six tumors.

282 Twenty-six unique proviral integration sites were mapped between 46 and 3,552 nucle

283 Tol2 transposon integration sites were spread throughout both the macro-

284 Gene expression levels at HPV integration sites were statistically significantly highe

285 D locus, almost no signal was scored at this integration site when the transgene was inherited from t

286 erns were analyzed, revealing 127,386 unique integration sites which conformed to previously publishe

287 eletion of a prophage region that removed an integration site, which has been used for genome enginee

288 sequences define a set of unique lentiviral integration sites, which are compared to determine wheth

289 curately detects the known viruses and their integration sites with high sensitivity and specificity.

290 of two donors, we detected large clusters of integration sites with multiple breakpoints, implying cl

291 dentified 14 and 66 transcriptionally active integration sites with potentially activating integratio

292 nriched in the flanking regions of 84.5% the integration sites, with a median length of 7 bp.

293 by local treatment with a Wingless-type MMTV integration site (Wnt) antagonist, Dickkopf-1 (Dkk1).

294 1 but higher expression of wingless-related integration site (WNT) family pathway components charact

295 e protein for the canonical Wingless-related integration site (WNT) signaling receptors LRP5 and LRP6

296 (FST), ecodysplasin (EDA), wingless-related integration site (Wnt), and beta-carotene oxygenase 2 (B

297 oblast growth factor (FGF), wingless-related integration site (WNT), and bone morphogenetic protein (

298 The vital role of Wingless-type MMTV integration site (Wnt)/beta-catenin signaling in the mod

299 Wingless-related integration site (WNT)/beta-catenin signaling regulates

300 erging to dysregulate the Wingless-type MMTV integration site (Wnt)/beta-catenin signaling, a key reg