GEO DataSets

(Submitter supplied) The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNA (ncRNA) transcripts in mammalian cells, bidirectional ncRNAs referred to as eRNAs are present on enhancers. However, it has remained unclear whether these eRNAs are functional, or merely a reflection of enhancer activation. Here, we report that 17 β-estradiol (E2)-bound estrogen receptor alpha (ERα) on enhancers causes a global increase in eRNA transcription on enhancers adjacent to E2 upregulated coding genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

11 Samples

Download data: BIGWIG

(Submitter supplied) Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

20 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21290

4 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21290

2 Samples

Download data: BW

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21290

2 Samples

Download data: BW

(Submitter supplied) In order to identity enhancer RNA across human cell and tissue types, histone modifications and RNA-Seq data were used to calculate candidate enhancers and classify enhancer RNA

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis

Download data: XLS

(Submitter supplied) To study the effects of BCAS2, an eRNA-interacting protein, depletion on estrogen receptor alpha binding upon estrogen treatment.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: BW

(Submitter supplied) To study the effects of BCAS2, an eRNA-interacting protein, depletion on estrogen-responsive genes.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

46 Samples

Download data

(Submitter supplied) To annotate estrogen-regulated eRNAs in MCF-7 breast cancer cells, we used RNA-sequencing of polyA-depleted and polyA-enriched RNA fractions to assemble the gene bodies of eRNAs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

6 Samples

Download data: BW

(Submitter supplied) To annotate estrogen-regulated eRNAs in MCF-7 breast cancer cells, we used precision nuclear run-on and sequencing of capped RNA (PRO-cap) to determine the transcription start sites of eRNAs.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

8 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

14 Samples

Download data: BED

(Submitter supplied) In this study, we used Global Run-On sequencing (GRO-seq), a method that assays the genome-wide location and orientation of all active RNA polymerases. We generated a global profile of active transcription at ERα binding sites in MCF-7 human breast cancer cells in response to short time course of E2 treatment. This method enabled us to detect active transcription at enhancers and define a class of primary transcripts transcribed uni- or bidirectionally from the ERα binding sites. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

6 Samples

Download data: BED

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

47 Samples

Download data: BIGWIG

(Submitter supplied) An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-?-estradiol-induced preferential recruitment to oestrogen receptor ? (ER-?)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-? distinct from classic cofactors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BIGWIG

(Submitter supplied) An emerging theme of gene regulation is the involvement of architectural chromosomal molecules in transcription control. Condensins are critical regulators of mitotic chromosomes, but their interphase chromatin localization and functions remain poorly understood. Here we report that both the condensin I and condensin II complexes exhibit an unexpected, dramatic 17-β-estradiol-induced preferential recruitment to oestrogen receptor α (ER-α)-bound active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-α distinct from classic cofactors. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

39 Samples

Download data: BIGWIG

(Submitter supplied) We used genome-wide sequencing methods to study stimulus-dependent enhancer function in neurons. We identified ~12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL9318

48 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Selective transcriptional activation and repression of genes throughout signaling cascades and development are poorly understood. Transcription factors (TF) orchestrate patterns and magnitude of transcriptional response, but TF action, or inaction, is highly dependent upon TF kinetics, distance from genes, chromatin architecture, and the local occupancy of other TFs. We integrated genomic transcription, chromosome looping, TF binding, and chromatin structure data to analyze the molecular cascade that results from estradiol-induced (E2) signaling in human MCF-7 breast cancer cells and addressed the context-specific nature of gene regulation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: BIGWIG

(Submitter supplied) In mammals, argonaute (AGO) proteins have been characterized for their roles in small RNA-mediated post-transcriptional and also in transcriptional gene silencing. We report here a different role for AGO1 in estradiol-triggered transcriptional activation in human cells. We show that in MCF-7 mammary gland cells AGO1 associates to transcriptional enhancers of estrogen receptor alpha (ERα) and that this association is upregulated by treating the cells with estrogen (E2), displaying a positive correlation with the activation of these enhancers.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

8 Samples

Download data: BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21290

24 Samples

Download data: BW