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Transcription profiling by array of human MCF7 breast cancer cells with FOXP3 target gene expression with and without MOF knockdown

ABSTRACT: As we clarified before, FOXP3 gene is an X-linked tumor suppressor for both human and mouse. And we also clarified direct target genes of FOXP3 in human cancer cells. Recently we identified that MOF, a histone acetyltransferase, can be a FOXP3's molecular partner to regulate target gene expression. We conducted a microarray analysis using MCF7 cell, a human breast cancer cell line, with FOXP3-tet-off system with and without MOF knock down before and after FOXP3 overexpression. After 48 hrs of RNAi treatments in MCF7 cells, FOXP3 was overexpressed and those cells were cultured for additional 48 hrs. Total RNA were extracted using Qiagen's RNeasy column and were applied to Affymetrix Human U133 Plus 2.0 array according to the manufacture's protocol.

ORGANISM(S): Homo sapiens

SUBMITTER: Katoh Hiroto

PROVIDER: S-ECPF-MTAB-688 | biostudies-other |

REPOSITORIES: biostudies-other

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Project description:Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor alpha (ERalpha) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERalpha binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5' and 3' ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERalpha binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERalpha-positive from ERalpha-negative breast tumors. The expression dynamics of the genes adjacent to ERalpha binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERalpha appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERalpha target genes. Unexpectedly, we found that only 22%-24% of the bona fide human ERalpha binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERalpha binding and gene regulation. Experiment Overall Design: We used oligonucleotide expression microarrays (Affymetrix GeneChip U133 Plus 2.0) to identify estradiol (E2)-responsive genes in the estrogen-receptor positive breast cancer cell line, MCF7. MCF7 cells were grown to 30-50% confluency and exposed to 10 nM E2 (or vehicle only) at 12, 24, and 48 hours. Each timepoint was performed in triplicate (ie, biological replicates). Total RNA was isolated from cells using the Qiagen RNeasy kit, and 5 micrograms of total RNA was amplified, labeled and hybridized to the array according to the manufacturer’s protocols.

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Transcription profiling by array of human MCF7 breast cancer cells with FOXP3 target gene expression with and without MOF knockdown

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