ライフサイエンスコーパス: cistrome

1 slocations result in reprogramming of the AR cistrome.

2 ity dynamics are also predictive of the ESR1 cistrome.

3 tion potential by disrupting over 65% of its cistrome.

4 4) as a potential key regulator of the SCC25 cistrome.

5 ecific differences in the prostate cancer AR cistrome.

6 romatin remodeling and evolution of the Sox2 cistrome.

7 ps with the estradiol (E2)-dependent ERalpha cistrome.

8 epressor functions across the AML1-ETO/RUNX1 cistrome.

9 s: MARGE-potential, MARGE-express, and MARGE-cistrome.

10 ion factor binding sites has been termed the cistrome.

11 U.1 and did not contribute to the basal IRF8 cistrome.

12 ceptor (AR) and glucocorticoid receptor (GR) cistromes.

13 l approach for predicting cell-type specific cistromes.

14 AR-dependent gene expression profiles and AR cistromes.

15 ng data sets, including a large number of TF cistromes.

16 de the first comparison of the ETS1 and ETS2 cistromes.

17 creases, but not reprograms, GATA2 and FOXA1 cistromes.

18 MARGE-cistrome adopts a novel semisupervised learning approach

19 cantly repressed genes associated with NCOR1 cistrome, again, with the GO terms acetylation and ETS b

20 scriptional program by repartitioning the ER cistrome, altering the balance of its associated transcr

21 Transcriptome and cistrome analyses identified several glaucoma- and extra

22 Integrated transcriptome and cistrome analyses identify pre-B cell receptor and cell

23 AR cistrome analyses in CRPC cells have identified a large

24 Transcriptome and BRD4 cistrome analyses reveal enhanced expression of the GTPa

25 Transcriptome and cistrome analyses revealed that FOXA2 broadly controls g

26 Here, we first used transcriptome and cistrome analyses to establish the list of T3/TR direct

27 Computational cistrome analysis identified MYC as a regulator of the l

28 Computational cistrome analysis predicted several transcription factor

29 Cistrome analysis revealed the dynamic activities of a v

30 sulted in recruitment of EZH2 across the ERG-cistrome and a genome-wide loss of ERG-mediated transcri

31 Cistrome and chromatin analyses revealed that HNF4G is a

32 in mouse liver, we reveal a high-confidence cistrome and define direct target genes.

33 Comparison to cistrome and epicistrome datasets identifies association

34 Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidati

35 able low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we devel

36 LncRNA promoter analyses, global cistrome and gain-of-function analyses confirm that incr

37 periments to provide information on both the cistrome and interactome for a given protein.

38 grative analysis of the N-Myc transcriptome, cistrome and interactome using in vivo, in vitro and ex

39 interactions with the AP-1 change the HOXB13 cistrome and interactome.

40 a broad distribution of affinities on the GR cistrome and interactome.

41 ativity and equilibrium with FOXA1 define AR cistrome and reveal a previously unknown function of FOX

42 cted lability within the adipocyte PPARgamma cistrome and show that, even in terminally differentiate

43 hanisms by which GATA2 and FOXA1 regulate AR cistrome and suggest that FOXA1 acts upstream of GATA2 a

44 Exploring the AP-1 cistrome and the AP-1-regulated transcriptome, we obtain

45 variant 1 (ETV1) positively regulated the AR cistrome and transcriptional output in ETV1-translocated

46 We have determined the cistrome and transcriptome for the nuclear receptor live

47 udies and first-in-field mapping of the CRY1 cistrome and transcriptome reveal that CRY1 regulates DN

48 hromatin regions and activate an alternative cistrome and transcriptome.

49 e examine if the effect of bexarotene on RXR cistrome and transcriptomes depend on APOE isoform and A

50 teoblast progeny (OB), characterized the two cistromes and assessed their relationship to changes in

51 , Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identi

52 We find that AR and GR cistromes and transcription programs exhibit significant

53 Integrative profiling of E2F8 cistromes and transcriptomes in AR-negative CRPC cells r

54 matically catalog all of the genes bound by (cistromes) and transcriptionally activated by (regulomes

55 ies for transcriptome, enhancer histone mark cistrome, and chromatin conformation pattern mapping.

56 me to "ignite" an otherwise fully dissipated cistrome, and drive it to criticality; (iii) how couplin

57 substantial rewiring of human and mouse REST cistromes, and that REST may have human-specific roles i

58 reover, global DNA methylation and the N-Myc cistrome are redirected following Rb1 loss.

59 Transcription factor cistromes are highly cell-type specific.

60 of the BMAL1, REV-ERB-alpha and REV-ERB-beta cistromes are highly enriched for both clock and metabol

61 the EGF-induced ERalpha genomic targets, its cistromes, are distinct from those induced by estrogen i

62 pied promoters and the subset of the ERalpha cistrome associated with coactivation.

63 chanism of LXR action in skin, we mapped its cistrome by identifying LXRbeta-RXRalpha binding sites u

64 aled that FOXA1 reprograms both AR and GATA2 cistrome by preferably recruiting them to FKHD-containin

65 Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs.

66 ional profiling and determined BRD2 and BRD4 cistromes by identifying their global chromatin binding

67 MARGE-cistrome can predict the binding sites of silenced trans

68 Here, we analyze the perturbations to the AR cistrome caused by a minor groove binding molecule that

69 roach to discover genome-wide changes in RXR cistrome (ChIP-Seq) and gene expression profile (RNA-Seq

70 To define the pS118-ER cistrome, chromatin immunoprecipitation sequencing was p

71 has unique activities, and whether the AR-V7 cistrome contains unique binding sites have yielded conf

72 ression changes induced by SPA together with cistrome data and protein-interactomes.

73 ), CCCTC binding factor (CTCF), AR and FoxA1 cistrome data as well as androgen-regulated gene express

74 The Cistrome Data Browser (DB) is a resource of human and mo

75 Integrated with the Cistrome Data Browser database which contains thousands

76 Assessment on 129 ATAC-seq datasets from the Cistrome Data Browser demonstrates CEMIG's exceptional p

77 The Cistrome Data Browser is a resource of ChIP-seq, ATAC-se

78 analysis of expression profiling, Brd2/Brd4 cistrome data, and changes in chromatin accessibility, w

79 To overcome this challenge, we built the Cistrome database, a collection of ChIP-seq and chromati

80 Currently, the Cistrome DB contains approximately 47,000 human and mous

81 Furthermore, the Cistrome DB has a new Toolkit module with several featur

82 The Cistrome DB is a user-friendly, up-to-date, and well mai

83 Second, the Cistrome DB Toolkit facilitates searches for factor bind

84 Cistrome DB v3.0 contains approximately 45 000 human and

85 Cistrome DB v3.0 expands the display of quality control

86 Cistrome DB v3.0 is available at

87 The Cistrome DB v3.0 user interface is implemented as a sing

88 Epigenomic analyses of PAX8-dependent cistrome demonstrate that PAX8 largely occupies active e

89 The PR cistrome displayed a bimodal distribution.

90 Pdx1 and Slc2a2, and has a mature beta-cell cistrome distinct from that of pancreatic endocrine prog

91 However, cistrome dynamics in plants remain largely underexplored

92 Integrative cistrome, epigenome and transcriptome analysis identifie

93 ecule MYC inhibitor, MYCi975, on the MYC/MAX cistromes, epigenome, transcriptome, and tumorigenesis.

94 e response in which repressive and inductive cistromes establish a dynamic balance between macrophage

95 s over these transcription regulators' tumor cistromes, exemplified at the 8q24 locus harboring both

96 Mechanistically, RB loss led to E2F1 cistrome expansion and different binding specificity, al

97 Human REST cistrome expansion involves additional peaks in genes ta

98 omic remodeling, LPS-activated NF-kappaB-p65 cistrome expansion, and increased enhancer activity.

99 MARGE-cistrome exploits information from H3K27ac signal at DNa

100 Cistrome Explorer and its source code are available at a

101 of ChIP-seq, DNase-seq and ATAC-seq samples, Cistrome Explorer enables the discovery of patterns of C

102 We developed Cistrome Explorer, a web-based interactive visual analyt

103 Using ChIP-seq, we demonstrate that the cistrome for the AP-1 transcription factor c-Jun is comp

104 tive analysis of the forkhead box A2 (FOXA2) cistrome for the human endometrium.

105 Cistrome-GO has two working modes: solo mode for ChIP-se

106 Here, we provide Cistrome-GO, a website implementation of this method wit

107 The macrophage RXR cistrome has 5200 genomic binding sites, which are not i

108 transcription factor's mutant phenotype and cistrome hence reveals the continued and distinct requir

109 How FOXA1 controls the AR cistrome, however, is incompletely understood.

110 Analysis of the PGRB cistrome identified binding events at genes encoding pro

111 Defining the GR-cistrome identified Gc regulation of motility genes.

112 AD heritability was enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network

113 In this study, we examined the AR cistrome in a PCa cell line-derived CRPC model using int

114 nclusion, expression of the AIB1 4-selective cistrome in a small subpopulation of cells triggers an "

115 onducted a genome-wide analysis of the RUNX2 cistrome in both pre-osteoblastic MC3T3-E1 cells (POB) a

116 , in the maintenance of the luminal-specific cistrome in breast cancer cells.

117 Unexpectedly, the REST cistrome in differentiated neurons exhibited unique feat

118 plied ChIP-seq analysis to identify the REST cistrome in human CD4+ T cells and compared it with publ

119 We defined the KN1 cistrome in maize inflorescences and found that KN1 bind

120 set of the estrogen receptor alpha (ERalpha) cistrome in MCF7 breast cancer cells provides specificit

121 tion of the IRF3-dependent transcriptome and cistrome in mouse hepatocytes identifies Ppp2r1b as a di

122 in patterns consistent with the oncogenic AR cistrome in PCa samples and drove tumor formation in the

123 the first unbiased profiling of the E2A-PBX1 cistrome in pre-B ALL cells and reveals a previously una

124 Here we defined the BCL6 cistrome in primary human germinal center Tfh cells to a

125 s parameter, dependent on the details of the cistrome in question; (ii) the ability of an active cist

126 Through the analysis of the ER cistrome in tamoxifen-resistant breast cancer cells, we

127 e approach was used here to define the FOXA2 cistrome in the human endometrium.

128 e approach was used here to define the FOXA2 cistrome in the murine uterus.

129 While ERG was able to reprogram the AR cistrome in the process of prostate carcinogenesis, ERG

130 Motif analysis of the HDAC3 cistrome in the testes identified SOX30, which has a sim

131 d that CBFA2T3 targets the RARalpha/RXRalpha cistrome in U937 AML cells, predominantly at myeloid-spe

132 s systematically identified the SNP-enriched cistrome in vascular endothelium subjected to well-defin

133 Here, we characterize the KLF15 cistrome in vivo in skeletal muscle and find that the ma

134 To characterize the TRbeta1 cistrome in vivo, we expressed a biotinylated TRbeta1 in

135 ng (ChIP-seq), we demonstrate that PPARgamma cistromes in mouse adipocytes and macrophages are predom

136 y genome-wide mapping of the c-Fos and c-Jun cistromes in NHEKs, demonstrating that 77% of all the LX

137 dea was confirmed through discovery that VDR cistromes in POBs and OBs were also strikingly different

138 bution of genome-wide VDR-binding sites (VDR cistrome) in HSCs and facilitates VDR binding at SMAD3 p

139 genomic analyses reveal that most of the SHP cistrome, including lipogenic genes repressed by FGF19,

140 f AR in ER-positive BC xenografts reprograms cistromes, inhibits oncogenic pathways, and promotes cel

141 lyses, we found that the Bcl-6 and NF-kappaB cistromes intersect, within nucleosomal distance, at nea

142 We believe CR Cistrome is a valuable resource for the epigenetics comm

143 ted transcriptome, and that 90% of the Bcl-6 cistrome is collapsed following Tlr4 activation.

144 Significantly, we found that the AR cistrome is largely retained in the CRPC stage.

145 In prostate cancer, the AR cistrome is reprogrammed relative to normal prostate epi

146 The cistrome is the complete set of transcription factor (TF

147 cycle, but their targeting to stage-specific cistromes is poorly described(1,2).

148 Functional studies, CBP/p300 cistrome mapping, and transcriptome in CRPC revealed tha

149 y differentiated cells, PU.1 can remodel the cistrome of another master regulator.

150 While the cistrome of ER is well established, surprisingly little

151 ed PIAS1 as corepressor, and reprogramed the cistrome of IRF3, a key transcription factor of the IFN-

152 direct gene targets of KLF5, we defined the cistrome of KLF5 using ChIP-seq in both Calu-3 and 16HBE

153 Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drough

154 ics approach to profile and characterize the cistrome of TRbeta, map changes in chromatin accessibili

155 cer risk-associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of histone

156 We found that the cistromes of ligand-activated RARalpha and VDR largely o

157 inherited risk variants, SNVs accumulate in cistromes of master transcription regulators required fo

158 tumors as opposed to adjacent normal tissue cistromes of master transcription regulators, including

159 3 and TP63 bind to overlapping, but distinct cistromes of sites through utilization of distinctive co

160 Comparative analysis of the cistromes of TFEB/TFE3 and REV-ERBalpha showed an extens

161 riptional role that dissects the overlapping cistromes of the two most common ETS gene fusions in PC:

162 such as ChIP-Seq have described the entire "cistrome" of transcription factors involved in specific

163 termined the genome-wide cis-acting targets (cistromes) of both REV-ERB isoforms in murine liver, whi

164 e-specific transformation by altering the AR cistrome, priming the prostate epithelium to respond to

165 new study mapping the human pancreatic islet cistrome provides a roadmap for exploring the effects of

166 Analysis of the uterine FOXA2 cistrome provides novel insights into mechanisms governi

167 Sustained AR activation results in cistrome rearrangement toward transcription factor PROP

168 AR cistromes regulated by steroidal androgens and SARMs wer

169 und that approximately half of the PPARgamma cistrome represents direct DNA binding; both half sites

170 ionally linking these specific factors to AR cistrome reprogramming.

171 1 in adipocytes modifies the adipocyte PPARg cistrome resulting in impaired glucose tolerance and ins

172 By integrating the cistrome results into a TF network analysis, we mapped a

173 Thus, the hematopoietic stem/progenitor cell cistrome revealed a mediator of a signaling pathway that

174 Bioinformatics analysis of the cistrome revealed an enrichment of AP1 cis-regulatory mo

175 Analysis of the PU.1 cistrome revealed that two-thirds of PU.1 binding occurs

176 In addition, the MCF7 RNA polymerase II cistrome reveals preferential occupancy of E2-regulated

177 Partitioning the genome according to cistromes reveals the enrichment of somatic SNVs in pros

178 Notably, this cistrome shift was associated with a unique AR transcrip

179 Bioinformatic analysis of the PLZF cistrome shows that PLZF negatively regulates multiple p

180 The EGF-induced ERalpha cistrome specifically regulates genes found overexpresse

181 Functional and cistrome studies of YY1 uncover its roles in promoting p

182 motif GRHL2 in the breast cancer-specific ER cistrome suggests that it may play a role in the differe

183 ponsive transcription factors and define the cistrome that regulates vascular and hematopoietic devel

184 on of S305 by IKKbeta establishes an ERalpha cistrome that substantially overlaps with the estradiol

185 zalutamide treatment to a non-canonical EZH2 cistrome that triggers the transcriptional activation of

186 y on a global scale the components of the TF cistromes that function to orchestrate circadian gene ex

187 ell and animal models, the E2A-PBX1-enforced cistrome, the E2A-PBX1 interactome, and related mechanis

188 can indirectly activate a portion of the AR cistrome through epigenetic activation of GR.

189 e in question; (ii) the ability of an active cistrome to "ignite" an otherwise fully dissipated cistr

190 of XBP1 (XBP1s) binds to the hepatic 12-hour cistrome to directly regulate the 12-hour clock, with a

191 lized prostate cell line reprogrammed the AR cistrome to resemble that of a prostate tumor, functiona

192 gue 2 (EZH2) co-occupies the reprogrammed AR cistrome to transcriptionally modulate stem cell and neu

193 drive it to criticality; (iii) how coupling cistromes together can reduce their critical branching p

194 These approaches integrated cistrome, transcriptome and drug sensitivity relationshi

195 U.1 motifs, predicting occupancy in the PU.1 cistrome under binding site restriction.

196 Here we show that the androgen receptor (AR) cistrome undergoes extensive reprogramming during prosta

197 nal mechanisms, we generated the first KLF15 cistromes using newly engineered Klf15(3xFLAG) mice.

198 R) in prostate cancer and to regulate the AR cistrome via demethylation of its pioneer factor FOXA1.

199 The residual VDR cistrome was composed of 4617 sites, which was increased

200 The cistrome was integrated with transcription data to obtai

201 Upon CHD1 loss, the AR cistrome was redistributed in patterns consistent with t

202 ion with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fas

203 de scale, revealed that TRalpha1 and TRbeta1 cistromes were also different.

204 We found that REST cistromes were distinct among cell types, with REST bind

205 in gene expression, the normal and tumor ER cistromes were distinct and sufficient to segregate norm

206 quencing (ChIP-seq), we define the NF-kappaB cistrome, which is comprised of 31,070 cis-acting bindin

207 ChIP-Seq defined the RARgamma cistrome, which was significantly enriched at active enh

208 To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for

209 Integration of the WAT NR1D1 cistrome with differential gene expression reveals broad

210 fully annotated 12 SNPs present in the c-Myc cistrome with properties consistent with modulating c-My

211 The isoforms displayed remarkably different cistromes with numerous differential binding sites.