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CUT&Tag analysis genome-wide maps of chromatin state in hCD34+ cells with X-RARG fusion genes overexpression.

ABSTRACT: CUT&Tag analysis genome-wide maps of chromatin state in hCD34+ cells with X-RARG fusion genes overexpression.

PROVIDER: PRJNA1018455 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26099136_1.fastq.gz	Fastqsanger.gz
	SRR26099136_2.fastq.gz	Fastqsanger.gz
	SRR26099137_1.fastq.gz	Fastqsanger.gz
	SRR26099137_2.fastq.gz	Fastqsanger.gz
	SRR26099138_1.fastq.gz	Fastqsanger.gz

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CUT&Tag analysis genome-wide maps of chromatin state in hCD34+ cells with X-RARG fusion genes overexpression.

Project description:CUT&Tag technology were used for high-throughput profiling of RARG fusion genes or PML-RARA with core promoters of its target genes in hCD34+ cells with RARG fusion genes or PML-RARA overexpression. We first expressed HA-tagged X-RARG fusions or HA-tagged PML-RARA in hCD34+ cells and then performed CUT&Tag with antibody to RARG fusion genes or PML-RARA and analyzed the binding of RARG fusion genes or PML-RARA with core promoters of its target genes. Common peaks for the binding sites of RARG fusions and PML-RARA and unique peaks for specific targets of RARG fusions that are not targets of PML-RARA were identified.

2024-10-15 | GSE243414 | GEO

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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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The effect RARG fusion genes or PML-RARA overexpression in human CD34+ cells on the gene expression.

Project description:Currently, AML with RARG rearrangements (RARG AML), including NUP98-RARG, PML-RARG, CPSF6-RARG, NPM1-RARG, and HNRNPC-RARG, has been identified as a novel entity of AML. Overexpression of RARG fusions in human CD34+ cells promoted the expansion of immature myeloid cells, reduced the percentage of mature granulocytes, inhibited the differentiation of myeloid cells, and self-renewal abilities of hCD34+ cells. To understand how RARG fusion proteins regulate their target genes in the hematopoietic system, we first expressed HA-tagged X-RARG fusions or HA-tagged PML-RARA in hCD34+ cells. We then analyzed the differential genes expression in hCD34+ cells with or without RARG fusion genes or PML-RARA overexpression through RNA-seq.

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