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Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [ATAC-seq]

ABSTRACT: Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [ATAC-seq]

PROVIDER: PRJNA939173 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23633036_1.fastq.gz	Fastqsanger.gz
	SRR23633036_2.fastq.gz	Fastqsanger.gz
	SRR23633037_1.fastq.gz	Fastqsanger.gz
	SRR23633037_2.fastq.gz	Fastqsanger.gz
	SRR23633038_1.fastq.gz	Fastqsanger.gz

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Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma

Project description:Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma

| PRJNA939172 | ENA

Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [Hi-C]

Project description:Liver cancer, particularly hepatocellular carcinoma (HCC), poses a significant global threat to human lives. To advance the development of innovative diagnostic and treatment approaches, it is essential to examine the hidden features of HCC, particularly its 3D genome architecture, which is not well understood. In this study, we investigated the 3D genome organization of four HCC cell lines—Hep3B, Huh1, Huh7, and SNU449—using in situ Hi-C and ATAC-seq. Our findings revealed that HCCs had elevated long-range interactions compared to HMECs, both intra- and interchromosomal. Unexpectedly, they displayed cell line-specific compartmental modifications at the Mb scale, which could aid in determining HCC subtypes. At the sub-Mb scale, we observed a decrease in intra-TAD interactions and chromatin loops in HCCs compared to HMECs. Lastly, we discovered a correlation between gene expression and 3D chromatin architecture in SLC8A1, which encodes the sodium-calcium antiporter known to induce apoptosis. Our findings suggest that HCCs have a distinct 3D genome organization that is different from normal and other cancer cells. Overall, we take this as evidence that genome organization plays a crucial role in cancer phenotype determination. Further exploration of epigenetics in HCC will lead us to a better understanding of specific gene regulation mechanisms and uncover novel targets for cancer treatments.

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Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [ATAC-seq]

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Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [Hi-C]

Project description:Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [Hi-C]

| PRJNA939175 | ENA

Cell line-specific features of 3D chromatin organization in hepatocellular carcinoma.

Project description:Liver cancer, particularly hepatocellular carcinoma (HCC), poses a significant global threat to human lives. To advance the development of innovative diagnostic and treatment approaches, it is essential to examine the hidden features of HCC, particularly its 3D genome architecture, which is not well understood. In this study, we investigated the 3D genome organization of four HCC cell lines-Hep3B, Huh1, Huh7, and SNU449-using in situ Hi-C and assay for transposase-accessible chromatin sequencing. Our findings revealed that HCC cell lines had more long-range interactions, both intra-and interchromosomal, compared to human mammary epithelial cells (HMECs). Unexpectedly, HCC cell lines displayed cell line-specific compartmental modifications at the megabase (Mb) scale, which could potentially be leveraged in determining HCC subtypes. At the sub-Mb scale, we observed decreases in intra-TAD (topologically associated domain) interactions and chromatin loops in HCC cell lines compared to HMECs. Lastly, we discovered a correlation between gene expression and the 3D chromatin architecture of SLC8A1, which encodes a sodium-calcium antiporter whose modulation is known to induce apoptosis by comparison between HCC cell lines and HMECs. Our findings suggest that HCC cell lines have a distinct 3D genome organization that is different from those of normal and other cancer cells based on the analysis of compartments, TADs, and chromatin loops. Overall, we take this as evidence that genome organization plays a crucial role in cancer phenotype determination. Further exploration of epigenetics in HCC will help us to better understand specific gene regulation mechanisms and uncover novel targets for cancer treatment.

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Changes in 3D genome organization of hepatocellular carcinoma (HCC) cells induced by lipid overload

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3D organization profiling of human hepatocellular carcinoma cell line PLC/PRF/5 in comparison with normal human liver cell line L02 by in situ Hi-C

Project description:Genetic and epigenetic alterations accumulate in the process of hepatocellular carcinogenesis, but the role of genomic spatial organization in HCC is still unknown.

2022-09-11 | GSE212943 | GEO

Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-06-22 | GSE226217 | GEO

Changes in 3D genome organization of hepatocellular carcinoma (HCC) cells induced by lipid overload

Project description:We analyzed the 3D genome organization via the High-throughput/resolution chromosome conformation capture (Hi-C) data generated from lipid overload-induced HCC cells.

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Project description:The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

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