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Series GSE144925 Query DataSets for GSE144925
Status Public on Sep 30, 2020
Title Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer [ATAC-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design Assay for Transposase-Accessible Chromatin followed by high throughput sequencing (ATAC-seq)
Contributor(s) Zhao Z, Zhijie L
Citation(s) 32506995
Submission date Feb 07, 2020
Last update date Dec 30, 2020
Contact name Zhijie Jason Liu
Organization name Universality of Texas Health Science Center at San Antonio
Department Department of Molecular Medicine
Lab Liu lab
Street address 7703 Floyd Curl Drive
City San Antonio
State/province TEXAS
ZIP/Postal code 78229
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (2)
GSM4301065 MCF7_Veh_ATACseq
GSM4301066 MCF7_E2_ATACseq
This SubSeries is part of SuperSeries:
GSE144927 Epigenomics-Based Identification of Estrogen-regulated Long Noncoding RNAs in ER+ Breast Cancer
BioProject PRJNA605355
SRA SRP247628

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Supplementary file Size Download File type/resource
GSE144925_RAW.tar 391.2 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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