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CUT&Tag sequencing analyses target genes directly bound by transcription factors

ABSTRACT: CUT&Tag sequencing analyses target genes directly bound by transcription factors

PROVIDER: PRJNA1093037 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28490622_1.fastq.gz	Fastqsanger.gz
	SRR28490622_2.fastq.gz	Fastqsanger.gz
	SRR28490623_1.fastq.gz	Fastqsanger.gz
	SRR28490623_2.fastq.gz	Fastqsanger.gz
	SRR28490624_1.fastq.gz	Fastqsanger.gz

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CUT&Tag sequencing analyses target genes directly bound by transcription factors

Project description:TF occupancy within or near a gene promoter or enhancer region is often assumed to be sufficient evidence for the gene to be classified as a direct TF target. We identified the TF ATF3 and ONECUT2 occupancy sites and direct target candidate genes using the CUT&Tag in hepatocyte organoids.

2025-04-08 | GSE262703 | GEO

Chromatin-bound Mtf2 Restricts Extraembryonic Competence in Naïve Pluripotency [Cut & Tag]

Project description:Chromatin-bound Mtf2 Restricts Extraembryonic Competence in Naïve Pluripotency [Cut & Tag]

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CUT&Tag analysis uncovered Pou4f1-bound DNA elements in E16.5 retinas

Project description:CUT&Tag analysis uncovered Pou4f1-bound DNA elements in E16.5 retinas

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Low-cost high-resolution chromatin profiling with CUT&Tag

Project description:We recently introduced CUT&Tag, an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei, and then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds DNA sequencing adapters (“tagmentation”) for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses exposure artifacts to ensure high-fidelity mapping of the antibody-targeted protein and improves signal-to-noise over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube from cells to amplified libraries, providing low-cost high-resolution genome-wide chromatin maps. By simplifying library preparation, CUT&Tag requires less than a day at the bench from live cells to sequencing-ready barcoded libraries. Because of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for ~$25 per sample, enabling routine genome-wide profiling of chromatin proteins and modifications that requires no special skills or equipment.

2020-07-15 | GSE145187 | GEO

CUT&Tag analysis of H3K9la in Cal27 and HN30 cells

Project description:To identify the genes directly regulated by H3K9la on a genome-wide scale, we performed CUT&Tag assays using a H3K9la specific antibody in CAL27 and HN30 with or without the lactic acid treatment, and performed CUT&Tag assays using a H3K9la specific antibody in HN30 under hypoxia condition.

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KAS-CUT&Tag for direct mapping of transcription bubbles

Project description:We introduce KAS-CUT&Tag, a method that combines N3-kethoxal labeling of exposed guanines with CUT&Tag to directly map Pol II at transcription bubbles. Pol II-induced bubbles are enriched at many highly-expressed genes, but the highest enrichment is at canonical histone genes in all phases of the cell cycle.

2026-07-21 | GSE317877 | GEO

Histone succinylation directly inhibits Jumonji domain demethylases and stabilizes repressive chromatin states [CUT&Tag]

Project description:Histone succinylation directly inhibits Jumonji domain demethylases and stabilizes repressive chromatin states [CUT&Tag]

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Comparative analyses of ChIP-seq, CUT&RUN and CUT&Tag for Polycomb chromatin profiling

Project description:Chromatin profiling methods such as ChIP-seq, CUT&RUN, and CUT&Tag differ substantially in background structure, signal distribution, and resolution, complicating direct quantitative comparison across platforms. In this study, we systematically compared conventional and double-crosslink ChIP-seq, CUT&RUN, and CUT&Tag by profiling the Polycomb-associated histone modification H3K27me3 in human cardiomyocytes and the PRC2 catalytic subunit EZH2 in pluripotent stem cells. To enable cross-assay comparison, we developed a biologically informed normalization strategy based on stable Polycomb reference loci, allowing harmonization of signal scales while preserving assay-intrinsic signal architecture. This approach revealed that CUT&RUN preferentially captures broad H3K27me3 domains, whereas CUT&Tag provides sharper and more localized enrichment for both H3K27me3 and EZH2. Together, our results establish a practical framework for cross-platform epigenomic comparison and guide the selection of chromatin profiling strategies. This GEO submission includes only datasets newly generated in this study. Additional publicly available datasets analyzed for comparison are cited in the associated manuscript and were not re-submitted here.

2026-05-12 | GSE314247 | GEO

CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays [CUT&Tag]

Project description:Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow for in situ investigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag. Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods. This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to limitations of ChIP-Seq. We also demonstrate that newer in situ chromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons.

2025-08-11 | GSE288759 | GEO

HCT116_SMARCA4 CUT&Tag

Project description:HCT116_SMARCA4 CUT&Tag

| PRJNA875063 | ENA