COCA-seq: genome-wide mapping of O-GlcNAc-associated open chromatin
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1248474 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33047235_1.fastq.gz | Fastqsanger.gz | |||
| SRR33047235_2.fastq.gz | Fastqsanger.gz | |||
| SRR33047236_1.fastq.gz | Fastqsanger.gz | |||
| SRR33047236_2.fastq.gz | Fastqsanger.gz | |||
| SRR33047237_1.fastq.gz | Fastqsanger.gz |
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Project description:O-GlcNAcylation, a prevalent reversible post-translational modification, intricately alters non-histone proteins, influencing the organization of gene transcriptional regulation within the accessible chromatin environment. This nucleoplasmic landscape, characterized by histone-free regions, fundamentally enables O-GlcNAc-mediated modulation through dynamic accessibility. However, unraveling the O-GlcNAc-open chromatin interplay that governs sophisticated transcriptional regulatory networks remains constrained by current techniques, which lack the resolution to probe this spatiotemporal crosstalk. Here, we reported a general strategy to systematically and chemoselectively profile O-GlcNAc-associated chromatin accessibility on a genome-wide scale (COCA-seq). Through comprehensive validation across low- and high-throughput levels, we demonstrated COCA-seq's dual fidelity in both O-GlcNAc chemoselectivity and open chromatin specificity. We employed it to delve into doxorubicin resistance for breast cancer, scrutinizing pivotal regulatory genes and transcription factors implicated in this complex biological event, such as NRF1 and XBP1. By integrating bulk RNA-seq with COCA-seq, we offered a multiomics perspective, shedding light on related biological processes and pathways like drug efflux and stress homeostasis, thereby uncovering potential mechanisms by which O-GlcNAc-associated open chromatin orchestrates tumor drug resistance. COCA-seq emerges as a general and versatile tool across various biological contexts, poised to reveal the landscape of O-GlcNAc-associated open chromatin regions across the genome and decipher the significance of glycosylation behind it.
2025-04-14 | GSE294152 | GEO
Project description:O-GlcNAcylation, a prevalent reversible post-translational modification, intricately alters non-histone proteins, influencing the organization of gene transcriptional regulation within the accessible chromatin environment. This nucleoplasmic landscape, characterized by histone-free regions, fundamentally enables O-GlcNAc-mediated modulation through dynamic accessibility. However, unraveling the O-GlcNAc-open chromatin interplay that governs sophisticated transcriptional regulatory networks remains constrained by current techniques, which lack the resolution to probe this spatiotemporal crosstalk. Here, we reported a general strategy to systematically and chemoselectively profile O-GlcNAc-associated chromatin accessibility on a genome-wide scale (COCA-seq). Through comprehensive validation across low- and high-throughput levels, we demonstrated COCA-seq's dual fidelity in both O-GlcNAc chemoselectivity and open chromatin specificity. We employed it to delve into doxorubicin resistance for breast cancer, scrutinizing pivotal regulatory genes and transcription factors implicated in this complex biological event, such as NRF1 and XBP1. By integrating bulk RNA-seq with COCA-seq, we offered a multiomics perspective, shedding light on related biological processes and pathways like drug efflux and stress homeostasis, thereby uncovering potential mechanisms by which O-GlcNAc-associated open chromatin orchestrates tumor drug resistance. COCA-seq emerges as a general and versatile tool across various biological contexts, poised to reveal the landscape of O-GlcNAc-associated open chromatin regions across the genome and decipher the significance of glycosylation behind it.
2025-04-14 | GSE294153 | GEO
Project description:COCA-seq: genome-wide mapping of O-GlcNAc-associated open chromatin [RNA-Seq]
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Project description:Mapping open chromatin in mouse nephron progenitor cells
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Project description:O-linked N-acetylglucosamine (O-GlcNAc) is a necessary protein modification installed onto hundreds of nucleocytoplasmic proteins by O-GlcNAc transferase (OGT). Recently, we developed an antibody-free metabolic feeding approach that enables unbiased mapping of O-GlcNAcylated proteins in a genome-wide manner, providing insight into the regulation of genes by O-GlcNAcylated proteins within Drosophila. Here we apply this O-GlcNAc chemical mapping strategy to a time course (TC) feeding experiment within Drosophila larvae, generated the first ever TC ChIP-seq experiment performed on both a protein modification and within a living organism. TC metabolic labeling experiments were performed in wild-type and O-GlcNAc hydrolase (OGA) deficient Drosophila. Analysis of the resulting sequencing data revealed that a loss of OGA causes a global increase in the retention of O-GlcNAc modification on proteins bound to the genome, suggesting most nuclear proteins are sensitive to effects of O-GlcNAc cycling. Interestingly, some loci are more sensitive to the impacts of a loss of OGA compared to others. This study will present an improved understanding of the regulation of gene expression by O-GlcNAc while providing the broader community with experimental methods for time-resolved analysis of genome-wide binding by proteins.
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Project description:Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected. One mild digestion and one extensive digestion was applied to the mESC cells, followed by sequencing.
2013-10-01 | E-GEOD-50706 | biostudies-arrayexpress
Project description:O-linked β-N-acetylglucosamine (O-GlcNAc) modification, a posttranslational modification (PTM) enriched in the nucleus and cytoplasm, is acknowledged to substantially contribute to the regulation of chromatin assembly and gene expression. studies have indicated that O-GlcNAc modification plays an important role in the process of cellular senescence. To integratively illustrate the regulatory role of O-GlcNAc modification in the oncogene-induced senescence (OIS) process, we employed a chemical reporter-based multi-omics strategy for a time-series proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins (OCPs) in human primary fibroblasts
2025-04-20 | PXD063140 |
Project description:Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected.
2013-10-01 | GSE50706 | GEO
Project description:Mapping open chromatin in iPSCs derived from beta-cells
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Project description:We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin interactions. By integrating FAIRE-seq and Hi-C, OCEAN-C detects open chromatin interactions enriched by active cis-regulatory elements. We identify more than 10,000 hubs of open chromatin interactions (HOCIs) in human cells, which are mainly active promoters and enhancers bound by many DNA-binding proteins and form interaction networks crucial for gene transcription. In addition to identifying large-scale topological structures including topologically associated domains and A/B compartments, OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers and broad H3K4me3 domains.
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