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Transcriptional Profile and Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Danio rerio

PROVIDER: GSE178803 | GEO | 2022/05/24

REPOSITORIES: GEO

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Transcriptional profile and chromatin accessibility in zebrafish melanocytes and melanoma tumors.

Project description:Transcriptional and epigenetic characterization of melanocytes and melanoma cells isolated from their in vivo context promises to unveil key differences between these developmentally related normal and cancer cell populations. We therefore engineered an enhanced Danio rerio (zebrafish) melanoma model with fluorescently labeled melanocytes to allow for isolation of normal (wild type) and premalignant (BRAFV600E-mutant) populations for comparison to fully transformed BRAFV600E-mutant, p53 loss-of-function melanoma cells. Using fluorescence-activated cell sorting to isolate these populations, we performed high-quality RNA- and ATAC-seq on sorted zebrafish melanocytes vs. melanoma cells, which we provide as a resource here. Melanocytes had consistent transcriptional and accessibility profiles, as did melanoma cells. Comparing melanocytes and melanoma, we note 4128 differentially expressed genes and 56,936 differentially accessible regions with overall gene expression profiles analogous to human melanocytes and the pigmentation melanoma subtype. Combining the RNA- and ATAC-seq data surprisingly revealed that increased chromatin accessibility did not always correspond with increased gene expression, suggesting that though there is widespread dysregulation in chromatin accessibility in melanoma, there is a potentially more refined gene expression program driving cancerous melanoma. These data serve as a resource to identify candidate regulators of the normal vs. diseased states in a genetically controlled in vivo context.

| S-EPMC8727958 | biostudies-literature

Transcriptional Profile and Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors

Project description:Transcriptional Profile and Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors

| PRJNA741103 | ENA

Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors [ATAC-seq]

Project description:With high genetic heterogeneity in melanoma, understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes, pathways, and epigenetic regions influencing melanoma development. We performed RNA-seq and ATAC-seq on fluorescently-isolated melanocytes and melanoma cells from a zebrafish melanoma model.

2022-05-24 | GSE178802 | GEO

Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA-seq]

2022-05-24 | GSE178801 | GEO

Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors [ATAC-seq]

Project description:Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors [ATAC-seq]

| PRJNA741110 | ENA

Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA-seq]

Project description:Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA-seq]

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Transcriptome profile and Genome-wide chromatin accessibility profile of zebrafish cardiomyocytes throughout heart development

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

2019-01-10 | GSE120238 | GEO

Chromatin Accessibility Impacts Transcriptional Reprogramming in Oocytes.

Project description:Oocytes have a remarkable ability to reactivate silenced genes in somatic cells. However, it is not clear how the chromatin architecture of somatic cells affects this transcriptional reprogramming. Here, we investigated the relationship between the chromatin opening and transcriptional activation. We reveal changes in chromatin accessibility and their relevance to transcriptional reprogramming after transplantation of somatic nuclei into Xenopus oocytes. Genes that are silenced, but have pre-existing open transcription start sites in donor cells, are prone to be activated after nuclear transfer, suggesting that the chromatin signature of somatic nuclei influences transcriptional reprogramming. There are also activated genes associated with new open chromatin sites, and transcription factors in oocytes play an important role in transcriptional reprogramming from such genes. Finally, we show that genes resistant to reprogramming are associated with closed chromatin configurations. We conclude that chromatin accessibility is a central factor for successful transcriptional reprogramming in oocytes.

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Melan-a melanocytes and B16 melanoma cells

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

2008-07-31 | GSE11588 | GEO

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis.

Project description:Human erythropoiesis serves as a paradigm of physiologic cellular differentiation. This process is also of considerable interest for better understanding anemias and identifying new therapies. Here, we apply deep transcriptomic and accessible chromatin profiling to characterize a faithful ex vivo human erythroid differentiation system from hematopoietic stem and progenitor cells. We reveal stage-specific transcriptional states and chromatin accessibility during various stages of erythropoiesis, including 14,260 differentially expressed genes and 63,659 variably accessible chromatin peaks. Our analysis suggests differentiation stage-predominant roles for specific master regulators, including GATA1 and KLF1. We integrate chromatin profiles with common and rare genetic variants associated with erythroid cell traits and diseases, finding that variants regulating different erythroid phenotypes likely act at variable points during differentiation. In addition, we identify a regulator of terminal erythropoiesis, TMCC2, more broadly illustrating the value of this comprehensive analysis to improve our understanding of erythropoiesis in health and disease.

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