Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic and epigenomic analysis of WSTF knockdown in colorectal cancer cells [ChIP-Seq]

ABSTRACT: This study investigates the role of Williams syndrome transcription factor (WSTF/BAZ1B) in colorectal cancer (CRC) progression through multi-omics approaches. WSTF was knocked down in SW620 colorectal cancer cells using siRNA to assess its impact on gene expression and metabolism. Additionally, WSTF overexpression was performed followed by ChIP-seq to identify genome-wide binding sites and direct transcriptional targets. The study aims to elucidate WSTF-mediated regulatory mechanisms and identify potential downstream effectors including GLYCTK in CRC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE328335 | GEO | 2026/04/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [mRNA-seq]

Project description:Loss of the chromatin remodeler WSTF (BAZ1B), a gene deleted in Williams syndrome, causes reproducible, genome-scale reprogramming of chromatin states and transcript processing that links altered chromatin composition to misprocessed transcripts and aberrant signaling. Using engineered HCT116-WSTFKO cells and patient-derived Williams syndrome cell lines, we combine transcriptome profiling, microscopy, chromatin CUT&RUN, and histone post-translational modification (HPTM)-defined chromatin state modeling to show that WSTF localizes to promoters and gene bodies of actively transcribed loci together with ASH2L and CBP. Loss of WSTF causes depletion of ASH2L/CBP, selective loss of H3K4me2 and multiple acetylation marks, and gain of Polycomb components. This loss results in systematic conversion from a multi-mark active promoter/enhancer chromatin landscape to a hypoacetylated, H3K4me2-depleted, PRC-enriched landscape. These chromatin changes coincide with widespread isoform switching and splicing alterations in genes encoding chromatin regulators and signaling pathways. This WSTF deficiency produces Wnt/β-catenin hyperactivation. A locus-specific example at TCF7L2 demonstrates how gene body loss of active marks drives isoform switching that alters DNA binding domains and decouples stabilized nuclear β-catenin from canonical target engagement. Our results link signaling dysregulation to developmental pathway misregulation consistent with Williams syndrome phenotypes.

2025-12-24 | GSE314625 | GEO

WSTF deficiency reprograms regulatory networks by linking locus‑specific chromatin remodeling to altered isoform expression and misdirected signaling [CUT&Run]

2025-12-24 | GSE314624 | GEO

Changes in gene expression in BAZ1B knockout and heterozygous targeted clones

Project description:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the maintenance of heterochromatin, including at the human inactive X chromosome (Xi). WSTF is encoded by BAZ1B, and is one of twenty-eight genes that are hemizygously deleted in the genetic disorder Williams-Beuren syndrome (WBS). To explore the function of WSTF, we performed zinc finger nuclease-assisted targeting of the BAZ1B gene and isolated several independent knockout clones in human cells. Our results show that, while heterochromatin at the Xi is unaltered, new inappropriate areas of heterochromatin spontaneously form and resolve throughout the nucleus. In three independent mutants, the expression of a large number of genes were impacted, both up and down, by WSTF loss. In addition, we found that cells lacking WSTF responded appropriately to vitamin D treatment, a process we expected to be disrupted. Given the inappropriate appearance of regions of heterochromatin in BAZ1B knockout cells, it is evident that WSTF performs a critical role in maintaining chromatin and transcriptional states. Clearly, further exploration is necessary to fully understand the role of WSTF in maintenance of the epigenome and how WSTF haploinsufficiency contributes to the wide array of symptoms exhibited in WBS patients.

2014-05-21 | GSE47390 | GEO

Changes in gene expression in BAZ1B knockout and heterozygous targeted clones

2014-05-21 | E-GEOD-47390 | biostudies-arrayexpress

RNA-seq of human iPSCs derived neural crest stem cells (NCSCs) upon knock-down of BAZ1B (WSTF), including 3 williams beuren syndrome lines, 1 atypical deletion line, and 3 individuals with 7q11.23 duplication syndrome. Each line has been infected with a scramble, or at least one of two short-hairpins (as described in the coupled paper).

Project description:In order to dissect the role of BAZ1B in the paradigmatic craniofacial dysmorphisms that characterize Williams Beuren Syndrome and the simmetrical genetically opposite 7q11.23 duplication syndrome(7dupASD), we selected a large cohort of NCSCs lines (4 from WBS patients, 3 from 7dupASD patients and 4 from control individuals) to perform transcriptomic profiling. These lines show a clear cranial identity signatures which is crucial to pinpoint the disease pathogenesis, We then knocked-down (KD) BAZ1B via RNA interference in all lines across the three genetic conditions, including also NCSCs derived from a particularly informative atypical WBS patient (atWBS) bearing a partial deletion of the region that spares BAZ1B and six additional genes (see paper). In order to establish a high-resolution gradient of BAZ1B dosages, we selected two distinct shRNA against BAZ1B (i.e., sh1 and sh2) along with a scrambled shRNA sequence (hereafter scr) as negative control, for a total of 32 NCSC lines. KD efficiency was evaluated both at the RNA level by quantitative PCR (qPCR), confirming the attainment of the desired gradient with an overall reduction of about 40% for sh1 and 70% for sh2, as well as reduction at the protein level, as detected by Western blot (see the coupled paper).

2020-02-29 | E-MTAB-8455 | biostudies-arrayexpress

RNA-seq of HRasV12-induced senescence with WSTF overexpression

Project description:We discovered that WSTF is downregulated in senescent cells by autophagy degradation. Forced expression of WSTF inhibits senescence-associated secretory phenotype, via inhibition of chromatin accesibility over inflammatory genes.

2022-10-05 | GSE214409 | GEO

ATAC-seq of HRasV12-induced senescence with WSTF overexpression

2022-10-05 | GSE214408 | GEO

Haploinsufficiency of BAZ1B contributes to Williams syndrome through transcriptional dysregulation of neurodevelopmental pathways

Project description:Williams syndrome (WS) is a neurodevelopmental disorder caused by a genomic deletion of ~28 genes that results in a cognitive and behavioral profile marked by overall intellectual impairment with relative strength in expressive language and hypersocial behavior. Advancements in protocols for neuron differentiation from induced pluripotent stem cells allowed us to elucidate the molecular circuitry underpinning the ontogeny of Williams syndrome. In patient-derived stem cells and neurons, we determined the expression profile of the Williams-Beuren Syndrome Critical Region deleted genes and the genome-wide transcriptional consequences of the hemizygous genomic microdeletion at 7q11.23. Derived neurons displayed disease-relevant hallmarks and indicated novel aberrant pathways in WS neurons including over-activated Wnt signaling accompanying an incomplete neurogenic commitment. We show that haploinsufficiency of the ATP-dependent chromatin remodeler, BAZ1B, which is deleted in WS, significantly contributes to this differentiation defect. Chromatin-immunoprecipitation (ChIP-seq) revealed BAZ1B target gene functions are enriched for neurogenesis, neuron differentiation, and disease-relevant phenotypes. BAZ1B haploinsufficiency caused widespread gene expression changes in neural progenitor cells, and together with BAZ1B ChIP-seq target genes, explained 42% of the transcriptional dysregulation in WS neurons. BAZ1B contributes to regulating the balance between neural precursor self-renewal and differentiation and the differentiation defect caused by BAZ1B haploinsufficiency can be rescued by mitigating over-active Wnt signaling in neural stem cells. Altogether, these results reveal a pivotal role for BAZ1B in neurodevelopment and implicate its haploinsufficiency as a likely contributor to the neurological phenotypes in WS.

2016-01-19 | GSE71664 | GEO

Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer

Project description:Metastasis is the main cause of cancer-related deaths in patients with solid tumors, including colorectal cancer (CRC). Circulating tumor cells (CTCs) and epigenetic alterations are involved in the development of metastasis. It is important to characterize the DNA methylation pattern of metastasis-competent CTCs to better understand the metastatic process and obtain new clinical applications for cancer patients. Therefore, the aim of this study was to investigate the DNA methylation landscape of metastasis-competent CTCs in CRC. The DNA methylome of the human colorectal cancer-derived cell line CTC-MCC-41 was compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells using a genome-wide methylation analysis.

2023-09-20 | GSE220096 | GEO

mRNA expression profile of control and senescent human colorectal cancer cell line SW620

Project description:To reveal the difference in mRNA expression profile between non-senescent cancer cells and senescent cancer cells in colorectal cancer, CRC cell line SW620 was treated with hydrogen peroxide to induce senescent.

2023-03-14 | GSE226998 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data