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Chromatin assessibility detection in the absence of Fzd5 gene in intestinal epithelium [Cut & Tag]

ABSTRACT: Chromatin assessibility detection in the absence of Fzd5 gene in intestinal epithelium [Cut & Tag]

PROVIDER: PRJNA914278 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22828238_1.fastq.gz	Fastqsanger.gz
	SRR22828238_2.fastq.gz	Fastqsanger.gz
	SRR22828239_1.fastq.gz	Fastqsanger.gz
	SRR22828239_2.fastq.gz	Fastqsanger.gz
	SRR22828240_1.fastq.gz	Fastqsanger.gz

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Chromatin assessibility detection in the absence of Fzd5 gene in intestinal epithelium [Cut & Tag]

Project description:Using CUT&TAG to assess Fzd5 knockdown effect on epithelial chromatin assessiblity change, using anitbodies targeting PoII2, H3K4trime3, and Beta-catenin.

2024-08-31 | GSE221414 | GEO

FZD5 is an essential regulator of intestinal crypt homeostasis and surrogate Wnt agonist response

Project description:The rapid regeneration of the small intestinal epithelium is sustained by crypt intestinal stem cells (ISCs). Wnt/b-catenin signaling is essential for intestinal crypt homeostasis and maintenance of Lgr5+ ISC, and yet no single or combinatorial knockout of Frizzled (FZD) genes, representing Wnt receptors, has phenocopied the severe intestinal epithelial effects of Wnt signaling blockade. The elusive identification of specific Frizzled (Fzd) receptor(s) underlying homeostatic proliferation and ISC function would greatly inform therapeutic mucosal repair strategies. In prior pharmacologic studies, bioengineered antagonists that block Wnt binding to both FZD5 and FZD8 receptors induced lethal crypt and villus loss, implicating FZD5 and/or FZD8 as essential for ISCs maintenance. Here, the potential function of Fzd5 in during intestinal homeostasis was examined by epithelial-specific Fzd5 ko, which rapidly elicited lethal pan-intestinal crypt and villus loss, and by Lgr5-specific Fzd5 cKO, which strongly reduced Lgr5+ ISC while inducing their premature differentiation. In parallel, Fzd5 cKO potently repressed Wnt target gene expression, with phenotypic rescue by constitutive activation of b-catenin in vivo and confirmation upon in vitro organoid culture. Fzd5 cKO but not Fzd8 cKO in organoids ablated responsiveness to dual specificity bioengineered FZD5/FZD8-selective Wnt surrogate agonists, which reversed DSS-induced colitis phenotypes in both wild-type and Fzd8 cKO mice. Overall, our results implicate the FZD5 receptor as an essential regulator of crypt homeostasis, Lgr5+ ISCs and intestinal response to bioengineered Wnt surrogate agonists.

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HCT116_SMARCA4 CUT&Tag

Project description:HCT116_SMARCA4 CUT&Tag

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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.

2024-09-06 | GSE249799 | GEO

Frizzled5 Maintains Homeostasis of Adult Intestinal Epithelium Through Organization of Chromatin Accessibility

Project description:Analyze the gene profiles and chromatin accessibility change upon Fzd5 knockout in mouse intestinal epithelium

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CUT&Tag and BioCUT&Tag enables investigation of the AT-rich and dynamic 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.

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H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (CUT&Tag I)

Project description:H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (CUT&Tag I)

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H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (CUT&Tag III)

Project description:H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (CUT&Tag III)

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H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (CUT&Tag II)

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CUT&TAG of OE19 cell line

Project description:To map the chromatin binding sites for SMC1 in OE19 cells, we performed CUT&TAG.