Project description:It remains a challenge to decipher the complex relationship between DNA methylation, histone modification, and the underlying DNA sequence with limited input material. Here, we developed an efficient, low-input, and low-cost method for simultaneous profiling of genomic binding sites of histone modification and methylation status of the underlying DNA at single-base resolution from the same cells in a single experiment by integrating CUT&Tag with tagmentation-based bisulfite sequencing (CUT&Tag-BS). We demonstrated the validity of our method for both active and repressive histone modifications using 250,000 mouse ESCs. CUT&Tag-BS showed similar enrichment patterns of histone modification to those observed in non-bisulfite-treated control; it further revealed that H3K4me1-marked regions are mostly CpG-poor, lack of methylation concordance, and exhibit prevalent DNA methylation heterogeneity among the cells. We anticipate that CUT&Tag-BS will be widely applied to directly address the genomic relationship between DNA methylation and histone modification, especially in low-input scenario with precious biological samples.
Project description:We performed CUT&Tag-Seq against histone H3K27me3 in mouse small intestinal TCRβ+CD8αα+ intraepithelial lymphocytes (IELs) of wild-type mice to analyze epigenetic modifications.
Project description:To investigate the relationship between KDM1A and ZMYM3, we conducted CUT&Tag-seq experiments to detect the KDM1A-mediated histone de-methylation in HCC cells with ZMYM3 downregulation.
Project description:We report the application of cut&tag technology for high-throughput profiling of histone modifications Raji Epstein–Barr viral genome in reponse to bryostatin treatment. Dual- and tri-methylation of lysine 4 on histone H3 protein indicate genes that are actively expressed/regulated. Tri-methylation of lysine 27 on histone H3 protein marks genes that are negatively regulated or suppressed for expression.
Project description:Chromatin-protein interactions are fundamental for the regulation of gene transcription. While ChIP-seq has long been the standard method for mapping these interactions, emerging techniques such as CUT&RUN and CUT&Tag, which offer advantages including low input requirements and high signal-to-noise ratios, have garnered attention. However, these enzyme-based tagmentation approaches may introduce potential biases, and comparative assessment with ChIP-seq remain absent. This study aims to systematically evaluate and compare the performance of ChIP-seq, CUT&Tag, and CUT&RUN for profiling genome-wide transcription factors and histone modifications binding. This study provides a comprehensive evaluation of ChIP-seq, CUT&Tag, and CUT&RUN for detecting active and repressive histone modifications as well as transcription factor binding. Our results show that all three methods reliably detect histone modifications and transcription factor enrichment, with CUT&Tag demonstrating a relatively higher signal-to-noise ratio. Rigorous peak comparison analysis identified differential enrichment sites detected by the three methods. Additionally, we observed a notable correlation between CUT&Tag signal intensity and chromatin accessibility, suggesting the potential for CUT&Tag to detect regions of active chromatin.
Project description:We profiled medullary thymic epithelial cells and intestinal epithelial cells by CUT&Tag to investigate mechanisms of T-cell tolerance.
Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.
Project description:This experiment employed CUT&Tag-seq (Cleavage Under Targets and Tagmentation with sequencing) to explore the mechanism of how different concentrations of VFAs regulate ruminal epithelial histone modifications under the Grain-diet and Hay-diet patterns in both am and pm. Cells from Grain-am, Grain-pm, Hay-am, and Hay-pm treatment groups were havest for CUT&Tag-seq experiments, n=3 pooled biological replicates per library. The primary histones used for CUT&Tag were Acetyl-Histone H3 (Lys27) Rabbit mAb (H3K27ac, 8173S, CST), Acetyl-Histone H3 (Lys9) (C5B11) Rabbit mAb (H3K9ac, 9649S, CST), and Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb (H3K4me3, 9751S, CST).
