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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

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

PROVIDER: PRJNA1125002 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29442569_1.fastq.gz	Fastqsanger.gz
	SRR29442569_2.fastq.gz	Fastqsanger.gz
	SRR29442570_1.fastq.gz	Fastqsanger.gz
	SRR29442570_2.fastq.gz	Fastqsanger.gz
	SRR29442571_1.fastq.gz	Fastqsanger.gz

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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.

2024-06-27 | GSE270104 | GEO

A chromatin integration labeling method enables lower-input epigenomic profiling

Project description:A chromatin integration labeling method enables lower-input epigenomic profiling

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A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation

Project description:A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation

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CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins

Project description:Identification of in vivo direct RNA targets for RNA binding proteins (RBP) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) using antibodies against endogenous RNA binding proteins. However, in many cases it is desirable to profile targets of an RNA binding protein for which an immunoprecipitation-grade antibody is lacking. Here we describe a scalable method for using CRISPR/Cas9-mediated homologous recombination to insert a peptide tag into the endogenous RNA binding protein locus. Further, we show that TAG-eCLIP performed using tag-specific antibodies can yield the same robust binding profiles after proper control normalization as eCLIP with antibodies against endogenous proteins. Finally, we note that antibodies against commonly used tags can immunoprecipitate significant amounts of antibody-specific RNA, emphasizing the need for paired controls alongside each experiment for normalization. TAG-eCLIP enables eCLIP profiling of new native proteins where no suitable antibody exists, expanding the RBP-RNA landscape.

2017-08-22 | GSE88722 | GEO

A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [RNA-Seq]

Project description:A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [RNA-Seq]

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A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [ChIP-seq]

Project description:A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [ChIP-seq]

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A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [scRNA-seq]

Project description:A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [scRNA-seq]

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Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [Cut&Tag]

Project description:Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [Cut&Tag]

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Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples

Project description:Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples

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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

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