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ABSTRACT: C2C12 H3K9la cut&tag

PROVIDER: PRJNA885248 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21763637_1.fastq.gz	Fastqsanger.gz
	SRR21763637_2.fastq.gz	Fastqsanger.gz
	SRR21763638_1.fastq.gz	Fastqsanger.gz
	SRR21763638_2.fastq.gz	Fastqsanger.gz
	SRR21763639_1.fastq.gz	Fastqsanger.gz

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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.

2024-08-09 | GSE273524 | GEO

CUT - Tag detection results for H3K9la, H4K8la, and H4K16la in tenocyte

Project description:We found that lactate and lactylation were significantly elevated in rotator cuff tears, and lactylation primarily regulates histones in tenocytes. Therefore, we screened for histone lactylation and identified that H3K9, H4K8, and H4K16 had the most prominent increases. Subsequently, we conducted CUT - Tag assays on them. The results indicated that H3K9la was enriched at the promoters of ENO3 and COL1, while H4K16la was enriched at the promoter of TNMD, which induced the transcriptional expression of these genes. Moreover, as a glycolytic enzyme, ENO3 is further involved in the H3K9la–Eno3–lactate–H3K9la positive feedback loop to maintain a high lactate level. This feedback loop continuously drives the H3K9 - COL1 and H4K16 - TNMD regulatory axes, ultimately promoting the repair of rotator cuff tear injuries.

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CUT&Tag analysis of H3K9la in Cal27 and HN30 cells

Project description:CUT&Tag analysis of H3K9la in Cal27 and HN30 cells

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HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription

Project description:Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. Interestingly, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on TSSs and the regulated Kla can facilitate in signaling pathways and progress of tumorigenesis. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.

2024-01-16 | GSE239656 | GEO

CUT - Tag detection results for H3K9la, H4K8la, and H4K16la in tenocyte

Project description:CUT - Tag detection results for H3K9la, H4K8la, and H4K16la in tenocyte

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CUT&Tag for DUX recruitment,domain-influenced chormatin modifications, and a potential binding partner with a member of the SWI/SNF complex

Project description:In order to determine that CUT&Tag is similar to known DUX ChIP-seq, we performed CUT&Tag with a mCherry-tagged DUX (with the mCherry antibody). Once confirmed, we pewrformed CUT&Tag for other DUX derivatives with their mCherry tag Then, we performed CUT&Tag for H3K9ac, which is known to globally increase in 2-cell-like cells, which occurs after DUX expression, and CUT&Tag for SMARCC1, a subunit of the SWI/SNF complex

2023-08-07 | GSE224297 | GEO

scNanoSeq-CUT&Tag: a long-read single-cell CUT&Tag sequencing method for efficient chromatin modification profiling within individual cells

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.

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A protocol for high-throughput microplate-based CUT&Tag

Project description:Cleavage Under Targets & Tagmentation (CUT&Tag) is a versatile method for measuring genomic occupancy of chromatin-associated proteins with high sensitivity and specificity. CUT&Tag has low sequencing requirements and is therefore suitable for highly multiplexed experiments, but methods to process samples at throughput without specialized equipment are lacking. Here we present a method for simultaneous parallel processing of 96 CUT&Tag samples in a standard microplate. Plate-CUT&Tag can be carried out in a similar time frame to benchtop CUT&Tag and yields data of comparable quality. We present data from cell culture and patient leukemia samples processed with Plate-CUT&Tag to illustrate its utility in large-scale preclinical and translational studies.

2025-09-18 | GSE308505 | GEO

CUT&Tag and BioCUT&Tag enables investigation of the AT-rich epigenome of Plasmodium falciparum from low input samples

Project description:This study aimed to adapt CUT&Tag to Plasmodium falciparum samples as an efficient and sensitive alternative to classical ChIP-sequencing. We compare H3K9me3 and HP1 CUT&Tag with ChIP-seq datasets, showing successful establishment of CUT&Tag in P. falciparum. Next we aimed to scale down required input material for our CUT&Tag reactions and generated high-quality HP1 tracks with as little as 10.000 nuclei. To minimise potential sample loss we tested feasibility of utilising (frozen) saponin parasite isolates as input material instead of nuclei, which proved to be viable. Lastly, we deployed our new technique Dimerisation-induced Biotinylation-CUT&Tag (DiBioCUT&Tag) to catch transient interactions by biotinylation of strongly associated proteins such as histones. We tested this technique on HP1 and compared standart CUT&Tag with DiBioCUT&Tag. Furthermore, we explored interactions of the transcription factor BDP5, which we were previously unable to succesfully ChIP.

2024-06-27 | GSE270104 | GEO

Benchmark of chromatin-protein interaction methods in haploid round spermatids

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.

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