Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming [ChIP-seq]

ABSTRACT: The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization and subsequent gene expression in cancer remain poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of H3K27Ac-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-Seq, STAG2 ChIP-Seq and H3K27Ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may contribute to malignant phenotype in STAG2-mutant cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE156771 | GEO | 2022/02/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming [RNA-seq]

Project description:The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization and subsequent gene expression in cancer remain poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of H3K27Ac-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-Seq, STAG2 ChIP-Seq and H3K27Ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may contribute to malignant phenotype in STAG2-mutant cancer.

2022-02-20 | GSE156770 | GEO

Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming [HiChIP]

2022-02-20 | GSE156772 | GEO

Cohesin protein STAG2 regulates expression of IRF9 and interferon signaling in melanoma via enhancer loop reprogramming [Hi-C]

2022-02-20 | GSE186055 | GEO

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin-STAG1 from WAPL

Project description:The human genome folds to create thousands of loops connecting sites that are bound by the insulator protein CTCF and the ring-shaped cohesin complex. It is thought that most of these loops emerge through a process whereby cohesin extrudes chromatin, forming an initially small loop that grows larger and larger until the loop’s expansion is arrested by CTCF. Cohesin rings comprise four proteins: SMC1, SMC3, SCC1, and, in higher eukaryotes, either STAG1 or STAG2. We explore differential roles of especially STAG1, STAG2 and ESCO1 proteins in chromatin organization.

2020-02-27 | GSE138405 | GEO

STAG2 mutations and 3D genome organization, chromatin loops, and polycomb signaling in glioblastoma multiforme

Project description:Inactivating mutations of genes encoding the cohesin complex are common in a wide range of human cancers. STAG2 is the most commonly mutated subunit. Here we report the impact of stable correction of endogenous, naturally occurring STAG2 mutations on gene expression, 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme. Correction of mutant STAG2 significantly altered the expression of ~10% of all expressed genes. The genes most highly regulated by STAG2 (e.g. FGF7, c-KIT, MAGE tumor antigens) were virtually all upregulated in STAG2-mutant cells. Hi-C revealed that ~3% of A/B compartments switched after STAG2 correction, and confirmed prior findings that STAG2 is dispensable for maintenance of Topologically Associating Domains (TADs). The size and strength of thousands of chromatin loops were altered by STAG2 correction, a subset of which controlled the expression of adjacent genes. Loops specific to STAG2-mutant cells and tumors were very large, supporting prior findings that STAG1-containing cohesin complexes have greater loop extrusion processivity than STAG2-containing cohesin complexes, and suggesting that long loops may be a generalizable feature of STAG2-mutant cancers. Finally, STAG2-regulated chromatin loops were enriched for the H3K27me3 Polycomb epigenetic mark, revealing that inactivation of STAG2 can activate Polycomb signaling in GBM. Together these findings illuminate the landscape of STAG2-regulated genes, A/B compartments, chromatin loops, and pathways in GBM, providing important clues into the still mysterious mechanism of STAG2 tumor suppression in human cancer.

2024-05-07 | GSE240343 | GEO

Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcription control (ChiP-Seq 2)

Project description:Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A and RAD21, cohesin contains in somatic cells one of two orthologous STAG subunits, STAG1 or STAG2. How these variable subunits affect the function of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either STAG1 or STAG2. Following rapid depletion of either subunit, we perform high resolution Hi-C, RNA-sequencing and sequential ChIP studies to show that STAG1 and STAG2 do not co-occupy individual binding sites and have distinct ways how they affect looping and gene expression. These findings are supported at the single cell level by single-molecule localizations via dSTORM super-resolution imaging. Since somatic and congenital mutations of the STAG subunits are associated with cancer (STAG2) and intellectual disability syndromes with congenital abnormalities (STAG1 and STAG2), we verified STAG1-/STAG2-dependencies using human neural stem cells, hence highlighting their importance for understanding particular disease contexts.

2020-03-06 | GSE140751 | GEO

Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cells [RNA-seq]

Project description:Purpose: Cohesin is a ring-shaped complex that is critical to genome organization and is an important regulator of gene expression. How cohesin accessory proteins contribute to cohesin function remain unclear. The purpose of this study is to assess the roles of cohesin accessory proteins, STAG1 and STAG2, in cohesin localization and gene expression. Method: The role of STAG1 and STAG2 in gene regulation was assessed by performing RNA-seq in wildtype and CRISPR-Cas9 genome edited STAG knockout mouse embryonic stem cells (mESCs). The redundancy of the STAGs was addressed by using siRNA against STAG1 in a STAG2-knockout background.

2020-08-10 | GSE144115 | GEO

Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [Hi-C]

Project description:Cohesin mediates sister chromatid cohesion and organizes the genome through the formation of chromatin loops. Two versions of the complex carrying either STAG1 or STAG2 show overlapping and specific functions and both are required to fulfill embryonic development. Cohesin-STAG1 displays longer residence time on chromatin that depends on CTCF and ESCO1 and establishes longer, long-lived chromatin loops together with CTCF. Cohesin-STAG2 shows a preferential interaction with WAPL and mediates shorter loops involved in tissue-specific transcription independently of CTCF. Here we show that the two variants respond in opposite ways to knock down of NIPBL, the putative cohesin loader that is also essential for loop extrusion. Cohesin-STAG1 levels increase on chromatin under this condition and the complex accumulates further at CTCF positions while cohesin-STAG2 is diminished genome-wide. Our data support a model in which NIPBL is not required for association of cohesin with chromatin but it is for loop extrusion, which in turn facilitates stabilization of cohesin-STAG2 at CTCF positions after being loaded elsewhere. In contrast, cohesin-STAG1 is preferentially loaded at CTCF sites independently of NIPBL. Nevertheless, loop formation by these chromatin-bound complexes is impaired and gene expression is severely affected, resembling alterations in Cornelia de Lange patients

2023-01-30 | GSE207115 | GEO

Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [ChIP-Seq]

2023-01-30 | GSE207113 | GEO

Response of cohesin STAG1 and STAG2 to reduction of NIPBL levels [RNA-Seq]

2023-01-30 | GSE207110 | GEO