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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE253630 | GEO | 2024/06/20

REPOSITORIES: GEO

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Chromatin conformation and histone modification profiling across human kidney anatomic regions [Hi-C]

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 Hi-C data.

2024-06-20 | GSE253632 | GEO

Genome-wide profiling of transcription factor-DNA binding interactions in Candida albicans: a comprehensive CUT&RUN method and data analysis workflow

Project description:Regulatory transcription factors control many important biological processes including cellular differentiation, responses to environmental perturbations and stresses, and host-pathogen interactions. Determining the genome-wide binding of regulatory transcription factors to DNA is essential to understanding the function of transcription factors in these often complex biological processes. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a modern method for genome-wide mapping of in vivo protein-DNA binding interactions that is an attractive alternative to the traditional and widely used chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. CUT&RUN is amenable to a higher throughput experimental setup and has a substantially higher dynamic range with lower per-sample sequencing costs compared to ChIP-seq. Here, we describe a comprehensive CUT&RUN protocol and accompanying data analysis workflow that is tailored for genome-wide analysis of transcription factor-DNA binding interactions in the human fungal pathogen Candida albicans. This detailed protocol describes all necessary experimental procedures, from epitope tagging of transcription factor coding genes, to library preparation for sequencing; additionally, it includes our customized computational workflow for CUT&RUN data analysis.

2022-07-15 | GSE193803 | GEO

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

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

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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.

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

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

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The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis [CUT&RUN]

Project description:The purpose of this study was to decipher the molecular function of ARID3A. We leveraged gene expression (RNA-Seq) and chromatin profiling (ATAC-Seq and CUT&RUN) to evaluate gene expression changes upon restoring Arid3a expression in the context of the Gata1s mutation and miR-125b overexpression

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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

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.

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Targeted in situ genome-wide profiling with high efficiency for low cell numbers

Project description:Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely- used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and has been used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT&RUN requires less than a day at the lab bench and requires no special skills.

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