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

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

PROVIDER: PRJNA509360 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8310960_1.fastq.gz	Fastqsanger.gz
	SRR8310960_2.fastq.gz	Fastqsanger.gz
	SRR8310961_1.fastq.gz	Fastqsanger.gz
	SRR8310961_2.fastq.gz	Fastqsanger.gz
	SRR8310952_1.fastq.gz	Fastqsanger.gz

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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 female mouse primordial germ cells at E11.5 and E12.5 days of gestation for H3K27me3

Project description:To evaluate the impacts of X-chromosome reactivation on repressive H3K27me3 chromatin marks, allele-specific low input CUT&Run experiments were conducted starting from genomic DNA obtained from FACS-sorted primordial germ cells.

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CUT&RUN-seq of H3K4me3, H3K27me3 and H3K27ac in mll2wt and mll2[Y2602A] mESC

Project description:CUT&RUN-seq of H3K4me3, H3K27me3 and H3K27ac in mouse ESCs carrying a homozygous point mutation in the catalytic domain of mll2[Y2602A]. CUT&RUN was performed according to Skene & Henikoff, 2017 and purified DNA was using for library preparation with NEBNext DNA Ultra II kit (NEB E7645S; input: 5 ng of DNA). Libraries were multiplexed and sequenced on a NextSeq500 (Paired-End; read length 40). Each sample is present in 3 biological replicates.

2023-11-15 | E-MTAB-13466 | biostudies-arrayexpress

Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells [CUT&RUN, ChIP-Seq]

Project description:Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells [CUT&RUN, ChIP-Seq]

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Integrative Low-input Transcriptomic and Cistromic Analyses Identify CREB Target Genes in Cystic Epithelial Cells [CUT&RUN, ChIP-Seq]

Project description:Transcription factors (TFs) play crucial roles in kidney development and disease by recognizing specific DNA sequences to control gene expression programs. The kidney’s cellular heterogeneity poses substantial challenges to identifying the genomic binding sites and direct target genes of TFs in vivo. We apply the CUT&RUN (cleavage under targets and release using nuclease) technique, together with transcriptomic analysis, to identify cAMP-response element-binding protein (CREB) target genes in cystic epithelial cells of autosomal dominant polycystic kidney disease (ADPKD). Our results reveal that CREB binds to and activates ribosomal biogenesis genes, and that inhibition of CREB retards cyst growth in ADPKD mouse models. Our findings demonstrate that CUT&RUN is a powerful method for genome-scale profiling and identifying direct targets of TFs from small numbers of specific kidney cells.

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Bulk Cut&run and Cut&tag

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Cut-and-Run in situ factor profiling maps DNA binding and 3D contact sites at high resolution

Project description:Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, Cut-and-Run is performed in situ, allowing for both high-resolution chromatin mapping and probing of the local chromatin environment. When applied to yeast and human nuclei, Cut-and-Run yielded precise transcription factor profiles while avoiding cross-linking and solubilization issues. Cut-and-Run is simple to perform and at low temperatures is inherently robust, with extremely low backgrounds that make it especially cost-effective for transcription factor and chromatin profiling. When used in conjunction with native ChIP-seq and applied to human CTCF, Cut-and-Run mapped high-resolution 3D directional interactions. We conclude that Cut- and-Run is a suitable complement or replacement for ChIP-seq that can also provide 3D mapping information.

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A tissue dissociation method optimized for ATAC-seq and CUT&RUN in Drosophila pupal tissues [CUT&RUN]

Project description:Chromatin accessibility, histone modifications and transcription factor binding are highly dynamic during Drosophila metamorphosis and drive global changes in gene expression as larval tissues differentiate into adult structures. Unfortunately, the presence of pupa cuticle on many Drosophila tissues during metamorphosis prevents enzyme access to cells and has limited the use of enzymatic in situ methods for assessing chromatin accessibility and histone modifications. Here, we present a dissociation method for cuticle-bound pupal tissues that is optimized for use with ATAC-Seq and CUT&RUN to interrogate chromatin accessibility and histone modifications. We show this method provides comparable chromatin accessibility data to the non-enzymatic approach FAIRE-seq, with only a fraction of the amount of input tissue required. This approach is also compatible with CUT&RUN, which allows genome-wide mapping of histone modifications with less than 1/10th of the tissue input required for more conventional approaches such as Chromatin Immunoprecipitation Sequencing (ChIP-seq). Our protocol makes it possible to use newer, more sensitive enzymatic in situ approaches to interrogate gene regulatory networks during Drosophila metamorphosis.

2022-08-14 | GSE211043 | GEO

Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag

Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.

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