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Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ATAC-Seq]

ABSTRACT: Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ATAC-Seq]

PROVIDER: PRJNA605355 | ENA |

REPOSITORIES: ENA

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Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ATAC-Seq]

Project description:Breast cancer is one of the most prevalent cancers in women worldwide. Through the regulation of many coding and non-coding target genes, estrogen (E2 or 17b-estradiol) and its nuclear receptor ERα play important roles in breast cancer development and progression. Despite intensive studies on estrogen-regulated coding genes over the past decades, molecular mechanisms underlying estrogen-regulated non-coding RNAs in breast cancer remain to be elucidated. Here, we performed extensive epigenomic studies including GRO-seq and ATAC-seq, and identified genome-wide estrogen-regulated long non-coding RNAs (lncRNAs). Similar to the coding targets of ERα, the transcription of estrogen-regulated lncRNAs correlates with the activation status of ERα-bound enhancers, measured by eRNA production, chromatin accessibility, and the occupancy of the enhancer regulatory components including P300, MED1, and ARID1B. Our 3D chromatin architecture analyses suggest that lncRNAs and their neighboring E2-resonsive coding genes, exemplified by LINC00160 and RUNX1, might be regulated as a 3D structural unit resulted from enhancer-promoter interactions. Finally, we evaluated the expression levels of LINC00160 and RUNX1 in various types of breast cancer and found that their expression positively correlated with the survival rate in ER+ breast cancer patients, implying that the estrogen-regulated LINC00160 and its neighboring RUNX1 might represent potential biomarkers for ER+ breast cancers.

2020-09-30 | GSE144925 | GEO

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Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer

Project description:Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer

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Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ChIP-Seq]

Project description:Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ChIP-Seq]

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Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer.

Project description: Not available

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Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-09-30 | GSE144927 | GEO

Estrogen-independent genomic ER binding analysis

Project description:Hormone-independent breast cancer cells (MCF-7/LTED and HCC-1428/LTED) were analyzed by ChIP-seq for estrogen receptor a to identify ER-DNA binding events that occur in the absence of estrogens.

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ChIP-Seq of human MCF-7 cells with ER-alpha and ER-beta anitbodies following estrogen treatment

Project description:We performed chromatin immunoprecipitation (ChIP) with overnight with antibodies against the C-terminus (HC-20, from Santa Cruz Biotechnology, Europe) or the N-terminus (anti-Estrogen Receptor 18-32, from SigmaAldrich, Italy) of human ER-alpha with or without estrogen treatment for 45 minutes on TAP-ER-beta cells, and the immunoprecipitated DNA was sequenced with the Illumina/Solexa Genome Analyzer. (Note: Raw data files not provided by submitter)

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Estrogen-regulated genes predict survival in estrogen receptor and/or progesterone receptor-positive breast cancers

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