Dynamic Chromatin Modification Sustains Epithelial-Mesenchymal Transition following Inducible Expression of Snail-1
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Ben Wittner
PROVIDER: E-GEOD-52593 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Epithelial-Mesenchymal Transition (EMT) is thought to contribute to cancer metastasis, but its underlying mechanisms are not well understood. To define early steps in this cellular transformation, we analyzed human mammary epithelial cells with tightly regulated expression of Snail-1, a master regulator of EMT. Following Snail-1 induction, epithelial markers were repressed within 6 hours and mesenchymal genes induced at 24 hours. Snail-1 binding to its target promoters was transient (6-48 hours) despite continued protein expression and it was followed by both transient and long-lasting chromatin changes. To generate a potent reversible EMT-inducing stimulus, we created a Snail-1 retroviral expression construct, using a fused estrogen receptor (ER) response element to mediate regulation by exogenous 4-hydroxy-tamoxifen (4-OHT). Since Snail-1 protein stability and nuclear localization are suppressed by GSK3-beta-mediated phosphorylation, we substituted the six targeted amino acids (ER-Snail-1(6SA)), thus conferring constitutive activity to the induced protein (Zhou et al., 2004, Pubmed ID 15448698). Infection of non-transformed, immortalized human mammary epithelial MCF10A cells with ER-Snail-1(6SA), followed by treatment with 4-OHT, triggered morphological and biomarker characteristics of EMT. At 0, 6, 48 and 120 hours after beginning exposure to 4-OHT in ethanol (or, for controls, ethanol only) we ChIPed Snail-1 and 6 histone marks. We perfomed two replicates of each, except we only had one replicate of H3K27Me3 at 6 hours.
2013-12-18 | E-GEOD-52591 | biostudies-arrayexpress
Project description:Epithelial-Mesenchymal Transition (EMT) is thought to contribute to cancer metastasis, but its underlying mechanisms are not well understood. To define early steps in this cellular transformation, we analyzed human mammary epithelial cells with tightly regulated expression of Snail-1, a master regulator of EMT. Following Snail-1 induction, epithelial markers were repressed within 6 hours and mesenchymal genes induced at 24 hours. Snail-1 binding to its target promoters was transient (6-48 hours) despite continued protein expression and it was followed by both transient and long-lasting chromatin changes. To generate a potent reversible EMT-inducing stimulus, we created a Snail-1 retroviral expression construct, using a fused estrogen receptor (ER) response element to mediate regulation by exogenous 4-hydroxy-tamoxifen (4-OHT). Since Snail-1 protein stability and nuclear localization are suppressed by GSK3-beta-mediated phosphorylation, we substituted the six targeted amino acids (ER-Snail-1(6SA)), thus conferring constitutive activity to the induced protein (Zhou et al., 2004, Pubmed ID 15448698). Infection of non-transformed, immortalized human mammary epithelial MCF10A cells with ER-Snail-1(6SA), followed by treatment with 4-OHT, triggered morphological and biomarker characteristics of EMT. At 3, 6, 12, 24, 72 and 120 hours after beginning exposure to 4-OHT in ethanol (or, for controls, ethanol only) we extracted RNA and did gene expression analysis using microarrays. We perfomed three replicates of each.
2013-12-18 | E-GEOD-52592 | biostudies-arrayexpress
Project description:DNA methylation profiles of primary human leukocyte subsets. Complementary MeDIP-seq data for the same samples have been deposited in ArrayExpress under accession number E-ERAD-179 (https://www.ebi.ac.uk/arrayexpress/experiments/E-ERAD-179/) .
2013-12-09 | E-MTAB-2145 | biostudies-arrayexpress
Project description:Illumina 450k DNA methylation microarray analysis of seminoma-like TCam-2 cells xenografted in nude mice. 2120EP embryonal carcinoma cells served as control. TCam-2 cells acquire pluripotency and become epigenetically reprogrammed to an embryonal carcinoma-like state during in vivo growth. This analysis is part of the article 'BMP inhibition in seminomas initiates acquisition of pluripotency via NODAL signaling resulting in reprogramming to an embryonal carcinoma' by Nettersheim et al., 2015. PLoS Genetics Genomic DNA was isolated from tumors of TCam-2 and 2102EP cells xenografted for 1, 2, 4 and 6 weeks as well as 4 and 8 weeks, respectively. In vivo samples of TCam-2 cells were analyzed in biological duplicates. In vitro cultivated TCam-2 / 2102EP cells as well as 2102EP xenografted for 4 and 8 weeks were analyzed once.
2015-08-01 | E-GEOD-60787 | biostudies-arrayexpress
Project description:Illumina cDNA expression microarray analysis of seminoma-like TCam-2 cells xenografted in nude mice. 2120EP embryonal carcinoma cells served as control. TCam-2 cells acquire pluripotency and become epigenetically reprogrammed to an embryonal carcinoma-like state during in vivo growth. This analysis is part of the article 'BMP inhibition in seminomas initiates acquisition of pluripotency via NODAL signaling resulting in reprogramming to an embryonal carcinoma' by Nettersheim et al., 2015. PLoS Genetics Total RNA was isolated from tumors of TCam-2 and 2102EP cells xenografted for 1, 2, 4 and 6 weeks as well as 4 and 8 weeks, respectively. 1x10^7 cells were xenografted. In vivo samples of TCam-2 cells were analyzed in biological duplicates. In vitro cultivated TCam-2 / 2102EP cells as well as 2102EP xenografted for 4 and 8 weeks were analyzed once.
2015-08-01 | E-GEOD-60698 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-04-18 | E-GEOD-46162 | biostudies-arrayexpress
Project description:The centromere is defined by the presence of a centromere-specific histone H3 variant, CENH3. Establishment and maintenance of the centromeric chromatin (CEN chromatin) is determined by poorly understood epigenetic mechanisms. Interestingly, CEN chromatin in several eukaryotes showed euchromatic characteristics although being embedded within pericentromeric heterochromatin. Specifically, H3K4me2 appeared to be a unique histone modification mark associated with animal centromeres. We developed a genomic tiling array for four fully sequenced rice centromeres. A ChIP-chip approach was used to study the patterns of several euchromatic histone modification marks, including H3K4me2, H3K4me3, H3K36me3, and H3K4K9a, associated with rice centromeres. We demonstrate that the CENH3 subdomains within the four centromeres are depleted with the four histone H3 marks. The vast majority of the four histone marks were associated with the genes located in the H3 subdomains within the centromeric cores. Genes in the centromeres showed similar histone modification patterns as those located outside of the centromeres. Thus, the euchromatic characteristics of rice CEN chromatin are trademarks of the transcribed sequences embedded in the H3 subdomains of the centromeres. We propose that the constitutively expressed genes located in rice centromeres may provide a barrier for loading of CENH3 into the H3 subdomains. The separation of CENH3 into the H3 subdomains is favorable for the three dimensional structure and its associated function of rice centromeres. We developed a genomic tiling array that covers four rice centromeres (Cen4, Cen5, Cen7, and Cen8) using the NimbleGen 3x720K array based on the NimbleGen HD2 platform. We used four antibodies (H3K4me3, H3K4me2, H3K36me3, H3K4K9ac) to perform ChIP-chip experiments. ChIP was conducted using leaf tissue from two-week old rice seedlings. We have 3 biological replicates for each antibody and 6 technological replicates of hybridization with position exchange on the array. Thus, each histone modification included 18 hybridization experiments.
2011-11-09 | E-GEOD-29597 | biostudies-arrayexpress
Project description:In this study, we combined a subsystem-based comparative genomic approach with experimental validation to reconstruct the metabolic and regulatory networks of carbohydrate utilization in 11 complete genomes from the Thermotogales order. Exression profiling studies were performed using total RNA isolated from mid log phase cultures of T. maritima grown on minimal media with distinct carbon sources.
2013-08-02 | E-GEOD-47615 | biostudies-arrayexpress
Project description:The NCI-60 cancer cell lines have been used for studying cancer pathogenesis and for drug discovery. This dataset adds to the growing number of datasets on various genomic platforms that have been made public on Cellminer (http://discover.nci.nih.gov/cellminer/) 61 cell lines (including PR:DU145 and its drug resistant derivative PR:RC01) were arrayed. Of these, 56 were done one time, four cell lines were done with either two or three replicates, and one cell line (LC:A549) was done with three replicates and two dye flips. Two color arrays were used, with Cy3 mostly used for sample and Cy5 for the reference pool of 6 normal male samples.
2011-10-23 | E-GEOD-30291 | biostudies-arrayexpress
Project description:In this study, a GFP-tagged version of the protein HCF-1 was immuno-precipitated from C. elegans lysates of the strain IU171 and co-purifying proteins were identified by LC-MS/MS. As a negative control, the same immuno-precipitation was conducted from wild-type (strain N2) worms that did not carry a HCF-1::GFP transgene.
2024-01-29 | PXD047509 | Pride