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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

ABSTRACT: We performed cleavage under targets and release using nuclease (CUT&RUN) sequencing to characterize ATAC peaks identified by snATAC-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213150 | GEO | 2023/04/28

REPOSITORIES: GEO

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The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [multi-omics]

Project description:We performed single nucleus RNA sequencing (snRNA-seq) and assay for transposase-accessible chromatin with sequencing (snATAC-seq) to map the epigenetic and gene expression signatures of human kidney organoids during the organoid differentiation time course.

2023-04-28 | GSE213151 | GEO

CUT&RUN of TAF4b and H3K4me3 in E16.5 prospermatogonia

Project description:Taf4b-deficient male mice are initially sub-fertile and become infertile due to a depletion of the spermatogonial stem cell (SSC) reserve. During embryonic time points, significantly reduced numbers of germ cells have been observed in the Taf4b-deficient male gonad and previous research has shown that Taf4b mRNA expression peaks at E15.5. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates cell cycle and SSC gene programs. However, the direct targets of TAF4b have not been thoroughly explored. Therefore, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in E16.5 mouse prospermatogonia.

2023-10-04 | GSE188701 | GEO

Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN

Project description:Endosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. Profiling the endosperm epigenetic landscape on a genome-wide scale is challenging due to its small size, mode of development, and close association with maternal tissue. Here, we applied a low input chromatin profiling method, CUT&RUN (cleavage under targets and release using nuclease), to profile parental-specific chromatin modifications using low numbers of Arabidopsis endosperm nuclei. We demonstrate that CUT&RUN generates genome-wide H3K27me3 landscapes with high sensitivity, specificity and reproducibility using around 20,000 endosperm nuclei purified by flow cytometry and fluorescence-activated cell sorting. H3K27me3 peaks identified by CUT&RUN and previous ChIP (chromatin immunoprecipitation) approaches were largely overlapping, with some distinctions in heterochromatin. The versatility and simplicity of CUT&RUN makes it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable the study of tissue or even cell-type specific epigenomes in Arabidopsis and other plant species.

2019-02-22 | GSE123602 | GEO

The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

Project description:The gene regulatory landscape of kidney organoid differentiation revealed by single nucleus multiomic analyses [CUT&RUN]

| PRJNA879346 | ENA

CUT&RUN (H3K27Ac3) in MGE, CGE, LGE and cortical regions from mouse embryonic forebrain

Project description:While comparative genetic analysis has been performed between distinct regions of the embryonic forebrain, a comprehensive characterization of differential epigenomic organization has not been performed. We collected single-cell chromatin accessibility profiles from four distinct neurogenic regions of the embryonic mouse forebrain using single nuclei ATAC-Seq (snATAC-Seq). We identified thousands of differentially accessible peaks, many restricted to distinct progenitor cell types or brain regions. We integrated snATAC-Seq and single cell transcriptome data to characterize changes of chromatin accessibility at enhancers and promoters that were tightly coupled to transcript abundance. Multi-modal integration of histone modifications (CUT&Tag and CUT&RUN), promoter-enhancer interactions (Capture-C) and high-order chromatin structure (Hi-C) extended these initial observations. This dataset reveals a diverse chromatin landscape with region-specific regulatory mechanisms and genomic interactions in distinct neurogenic regions of the embryonic mouse brain and represents an extensive public resource of a ‘ground truth’ epigenomic landscape at this critical stage of neurogenesis.

2022-07-01 | GSE201400 | GEO

Chromatin conformation and histone modification profiling across human kidney anatomic regions [CUT&RUN]

Project description:Here, we leveraged our recently described high-yield nuclei extraction method and performed Hi-C and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing of histone modifications (H3K4me3 and H3K27me3) in parallel on the kidney cortex, medulla and papilla samples dissected from the same donor. This site describes the CUT&RUN data.

2024-06-20 | GSE253630 | GEO

A streamlined protocol and analysis pipeline for CUT&RUN chromatin profiling

Project description:Over the past two decades, the dominant technology for chromatin profiling has been chromatin immunoprecipitation (ChIP), in which cellular components are solubilized to fragment chromatin, and an antibody is added to precipitate a DNA/protein complex of interest. We previously described a novel alternative to ChIP, Cleavage Under Targets & Release Using Nuclease (CUT&RUN), in which the antibody is added to permeabilized cells followed by binding of a Protein A-Micrococcal Nuclease (pA/MNase) fusion protein to the antibody (PMID 29651053). Upon activation of tethered MNase, the bound complex is excised and released into the supernatant for DNA extraction and sequencing. Here we introduce four extensions to CUT&RUN: 1) a hybrid Protein A-Protein G-MNase construct that allows simplified purification using a commercial kit; 2) a modified digestion protocol that prevents release of the enzyme and so minimizes artifactual cleavage of accessible DNA; 3) a calibration strategy based on carryover of E. coli DNA introduced with the fusion protein; and 4) a novel peak-calling strategy that is customized for the low-background profiles obtained using CUT&RUN. These new features, coupled with the previously described low-cost, high efficiency, high reproducibility and high-throughput capability of CUT&RUN make it the method of choice for routine epigenomic profiling.

2019-06-24 | GSE126612 | GEO

CUT&RUN of TAF4b and H3K4me3 in E16.5 oocytes

Project description:Research has shown that Taf4b-deficient female mice display excessive perinatal germ cell death, delayed germ cell cyst breakdown, and increased chromosome asynapsis. Therefore, we hypothesized that TAF4b, as part of TFIID, regulates oogenesis and meiotic gene programs. However, the direct targets of TAF4b have not been thoroughly explored. Therefore, we performed Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in E16.5 mouse oocytes.

2022-01-25 | GSE186991 | GEO

Cut&Run in Drosophila melanogaster control, mutant and knockdown ovaries

Project description:H3K27me3 profiles using Cleavage under targets and Release using nuclease (Cut&Run) in control and KD Drosophila melanogaster ovaries. We examined the impact on chromatin profiles in Drosophila melanogaster ovaries in which the lid, the Sin3a, the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissue-specific shRNA expression. We additionally explored H3K27me3 and H3K9me3 in control and dhd mutant ovaries either carrying or not a transgene.

2021-12-10 | GSE174250 | GEO

Deciphering the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression with single-nucleus CUT&RUN [single-nucleus CUT&RUN]

Project description:Single-cell RNA sequencing (scRNA-seq) has proven to be an invaluable tool for the study of tumor evolution. However, interrogating regulatory epigenetic alterations during cancer progression at the resolution of single-cells has remained a major challenge due to the lack of sensitivity of current assays. Here, we developed the highly-sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived cell lines. We find that the epigenome can employ diverse modes to contribute towards cancer progression. Notably, we demonstrate that gene expression changes during cancer progression are co-modulated by alterations in both copy number and chromatin activity to drive epigenetic rewiring of cell-states. Furthermore, intratumor epigenetic heterogeneity may predispose sub-clonal populations within the primary tumor to acquire malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to existing toolkit of single-cell assays to dissect the function of the epigenome during cancer progression.

2024-11-18 | GSE212249 | GEO

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