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CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

ABSTRACT: CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

PROVIDER: PRJNA336182 | ENA |

REPOSITORIES: ENA

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CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions [RNA-seq]

Project description:In our work we used high-throughput sequencing methods to get insight in the role of CTCF in ER-mediated gene regulation in luminal breast cancer cells. After assessing genome-wide binding of CTCF, ER, FOXA1 and Lamin B in MCF7 cells treated with estrogen for different time points, we could correlate the interaction to the chromatin with estrogen-induced de novo transcription (from GRO-seq data) and loop formation (from ChIA-PET, Fullwood et al., 2009). We observed that CTCF binding correlates with ER-mediated transcription and its depletion can affect ER-ER loop formation and subsequently gene expression.

2016-12-10 | GSE85088 | GEO

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions [ChIP-seq]

2016-12-10 | GSE85106 | GEO

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions.

Project description: Not available

| S-EPMC5159541 | biostudies-literature

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

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

2016-12-10 | GSE85108 | GEO

ChIP-Seq of human breast cancer cell lines treated with estrogen and tamoxifen to investigate CTCF binding

Project description:CCCTC-binding factor (CTCF) is a conserved zinc finger transcription factor involved in chromatin looping. Recent evidence has shown a role for CTCF in ER biology. This experiment maps CTCF binding genome-wide in breast cancer cells and shows that CTCF binding does not change with estrogen or tamoxifen treatment. We find a small but reproducible proportion of CTCF binding events that overlap with both the nuclear receptor estrogen receptor and the forkhead protein FoxA1. These overlapping binding events are likely to be functional as they are biased towards estrogen-regulated genes. In addition, we identify cell-line specific CTCF binding events. These cell-line specific CTCF binding events are more likely to be associated with cell-line specific ER vinding events and are also more likely to be adjacent to genes that are expressed in that particular cell line. These data suggest a positive, pro-transcriptional role for CTCF in ER-mediated gene expression in breast cancer cells.

2011-12-07 | E-MTAB-740 | biostudies-arrayexpress

Estrogen signaling modulates the colon microenvironment during obesity

Project description:Estrogen signaling modulates the colon microenvironment during obesity

| PRJNA630214 | ENA

Exploring the interaction between the SWI/SNF chromatin remodeling complex and the zinc finger factor CTCF

Project description:The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships between many CTCF-mediated activities involve direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases and BRG1 further support the interplay between master regulators of mammalian genome folding. Here we report a comprehensive LC-MS/MS mapping of the components of the SWI/SNF chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4-8 of CTCF, thus suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin-remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome.

2021-09-09 | PXD022037 | Pride

The insulator protein SU(HW) modulates nuclear lamina interactions of the Drosophila genome: DamID

Project description:Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that of these five proteins, only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens LAD – NL interactions by a local antagonistic effect. Our results provide insights into the evolution of LAD organization and reveal a role for SU(HW) in the regulation of genome – NL interactions. DamID experiments for Lamin, CTCF, SU(HW), GAF, DWG, and BEAF-32, and for Lamin after overexpression and after knockdown of SU(HW), were performed in Drosophila cell cultures. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation. The supplementary file 'GSE20311_DamID_norm_mean.txt' contains the mean log2(Dam-fusion/Dam-only) values of two replicates.

2011-01-24 | E-GEOD-20311 | biostudies-arrayexpress

Nuclear Estrogen Receptor alpha (ERα) interactome following estrogen and antiestrogen treatment.

Project description:The Estrogen Receptor alpha (ERα) controls key cellular functions in hormone responsive breast cancer by assembling in large functional multiprotein complexes. ERα ligands are classified as agonists and antagonist, according to the response they elicit, thus the molecular characterization of the of ERα nuclear iteractome composition following estrogen and antiestrogen stimulation whose is needed to understand their effects on estrogen target tissues, in particular breast cancer. To this aim interaction proteomics coupled to mass spectrometry (MS) was applied to map the ERα nuclear interacting partners in MCF7 breast cancer cell nuclei following estrogen and antiestrogen stimuli.

2020-09-02 | PXD018709 | Pride

SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites

Project description:SATB1, a nuclear matrix-associated protein, has long been proposed to function as a global chromatin loop organizer in T cells. However, the precise roles of SATB1 in chromatin organization remain elusive. Here we show that the depletion of SATB1 in immortalized T cells led to pronounced changes in gene expression, particularly for genes involved in cell proliferation and T cell activation, as well as 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased association among the SATB1/CTCF co-occupied sites, as well as increased chromatin contacts across these sites, thereby altering the genome-wide chromatin loop landscape. SATB1 does not regulate genome architecture by modulating CTCF occupancy. Rather, the topological effects imposed by SATB1 may be attributed to SATB1-dependent anchoring of CTCF to the salt extraction-resistant nuclear matrix. Together, our findings suggest that the functional interplay between nuclear matrix and CTCF plays a critical role in orchestrating 3D genome organization.

2023-03-05 | GSE199007 | GEO

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