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Luminal lncRNAs Regulation by ERα-controlled Enhancers in a Ligand-independent Manner in Breast Cancer Cells

ABSTRACT: Estrogen receptor-α (ERα) is a ligand-inducible protein which mediates estrogenic hormones signaling and defines the luminal breast cancer phenotype. Recently, we demonstrated that ERα binds chromatin in absence of ligand (apoERα) regulating transcription of protein-coding genes and several lncRNAs. Noteworthy, apoERα-regulated lncRNAs marginally overlap estrogen-induced transcripts representing a signature of luminal breast cancer genes. DSCAM-AS1 is a paradigmatic example of apoERα activity since its expression is largely unaffected by estrogenic treatment despite an E2-induced increment of ERα binding on its promoter. Analysing H3K27ac ChIP-Seq performed in hormone-deprived MCF-7, we identified a set of Super Enhancers (SEs) occupied by apoERα including one mapped in proximity of DSCAM-AS1. Using ChIP-qPCR, we validated ChIP-Seq signal of apoERα, p300 and CTCF at both DSCAM-AS1 TSS and at its associated SE. Furthermore, analysing MCF-7 ChIA-PET data and performing a 3C experiment, we confirmed a long range chromatin interaction between the SE and the DSCAM-AS1 TSS. Interestingly, CTCF binding downstream to DSCAM-AS1 shows an enrichment in hormone-depleted medium as compared to other experimental conditions, indicating that CTCF demarcates enhancer actions at DSCAM-AS1 locus. The analysis of this lncRNA provides a paradigm of transcriptional regulation of a luminal specific apoERα regulated lncRNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE108693 | GEO | 2018/02/06

REPOSITORIES: GEO

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