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Microarray analysis of genes impacted by 5 day knockdown of SLC24A5 in normal human melanocytes.

ABSTRACT: A major development in pigmentation research was the discovery of the involvement of SLC24A5 in natural variation in skin colour. This study used Agilent whole-genome microarrays to examine the impact of SLC24A5 knockdown on the transcriptome of normal human melanocytes derived from lightly and darkly pigmented donors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE21565 | GEO | 2012/04/26

SECONDARY ACCESSION(S): PRJNA126191

REPOSITORIES: GEO

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Microarray analysis of genes impacted by 5 day knockdown of SLC24A5 in normal human melanocytes.

Project description:A major development in pigmentation research was the discovery of the involvement of SLC24A5 in natural variation in skin colour. This study used Agilent whole-genome microarrays to examine the impact of SLC24A5 knockdown on the transcriptome of normal human melanocytes derived from lightly and darkly pigmented donors. 2 melanocyte cell lines were treated for 6h, with 2 separate siRNA duplexes to target SLC24A5. Treatment of the cells with a non-targeting siRNA control duplex, lipofectamine transfection reagent alone and unchallenged cells, cultured alongside the cellular treatments comprised the controls for the experiment. All treatments and controls were conducted in triplicate, in both cell lines.

2012-04-25 | E-GEOD-21565 | biostudies-arrayexpress

A genome-wide genetic screen uncovers novel determinants of human pigmentation

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A genome-wide genetic screen uncovers novel determinants of human pigmentation

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Comparison of the Transcriptional Profiles of Melanocytes from Dark and Light Skinned Individuals under Basal Conditions and Following Ultraviolet-B Irradiation

Project description:We analysed the whole-genome transcriptional profile of 6 cell lines of dark melanocytes (DM) and 6 of light melanocytes (LM) at basal conditions and after UVB at different time points (6, 12 and 24h) to investigate the mechanisms by which melanocytes protect human skin from the damaging effects of ultraviolet-B radiation (UVB). Further, we assessed the effect of different keratinocyte-conditioned media (KCM+ and KCM-) on melanocytes. We analysed six lines of melanocytes isolated from lightly pigmented neonatal foreskin (LM), and six lines from darkly pigmented neonatal foreskin (DM), at 0, 6, 12 and 24 hours post UV irradiation. We also assessed the effect of different keratinocyte-conditioned media (KCM+ or KCM-)

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Integrative functional genomic analyses identify novel genetic variants influencing skin pigmentation in indigenous Africans [Cut&Run, ATAC-seq]

Project description:Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation. To identify candidate enhancers and regulatory regions in skin pigmentation, we performed CUT&RUN and ATAC assays in two melanocytic cell lines (MNT-1 and WM88). We used the darkly pigmented MNT-1 cell line because it is widely used for studying skin pigmentation and it has a transcription pattern similar to normal melanocytes. We used the WM88 cell line because the cells are lightly pigmented and may have a different trans-environment (e.g., different levels of transcription factors and open chromatin regions) compared with MNT-1 cells. To identify regulatory regions in MNT-1 cells, we conducted CUT&RUN assays using antibodies against H3K4me3, H3K27ac, MITF and SOX10. We further performed ATAC-seq in both MNT-1 and WM88 cells to identify open chromatin regions.

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Expression data from non-pigmented and pigmented mouse melanocytes

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Genome-wide analysis of gene expression in human pluripotent stem cell-derived melanocyte progenitors, mature melanocytes, and disease-specific melanocytes

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2013-06-01 | E-GEOD-45226 | biostudies-arrayexpress

Comparison of gene expression signatures in human melanocytes after indirect cold physical plasma treatment and direct UV-irradiation

Project description:Cold atmospheric plasma is assembled out of various components such as UV-radiation, electrons, ions and an electromagnetic field at low temperature. In recent years cold atmospheric plasma gains interest as a medical tool used for improved healing of chronic wounds. In order to examine the impact of cold atmospheric plasma on the melanogenesis in human skin, the gene expression signature of differently treated lightly pigmented primary human melanocytes was analysed. Melanocytes were either treated in vitro indirectly by cold atmospheric plasma or irradiated by UV-radiation. After 2 h incubation the microarray analysis was performed.

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Genome-wide analysis of gene expression in human pluripotent stem cell-derived melanocyte progenitors, mature melanocytes, and disease-specific melanocytes

2013-06-01 | GSE45226 | GEO

Integrative functional genomic analyses identify novel genetic variants influencing skin pigmentation in indigenous Africans [RNA-seq]

Project description:Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. We identified 1,157 candidate variants influencing skin pigmentation in indigenous Africans by genome-wide association studies and scans of natural selection based on differentiation in allele frequencies between lightly pigmented southern African Khoesan populations and other darkly pigmented African populations. We applied massively parallel reporter and chromosome conformation capture assays to identify novel regulatory variants and their target genes related to skin pigmentation in melanocytic cells. We identified 165 SNPs showing strong differential regulatory activities between alleles. Combining CRISPR-mediated genome editing, transcriptome profiling and melanin assays, we identified causal regulatory variants impacting pigmentation near MFSD12/HMG20B, MITF, OCA2, and DDB1/CYB561A3/TMEM138. We identified CYB561A3 as a novel gene regulating pigmentation by impacting genes involved in oxidative phosphorylation and melanogenesis. Our results broaden our understanding of the genetic basis of human skin color diversity and human adaptation. To test the role of candidate enhancers and variants in skin pigmentation, we performed CRISPR inhibition or knockout of enhancers containing the functional variants identified by MPRA in melanocytic cells. Then, we performed gene expression profiling analysis using data obtained from RNA-seq of these CRISPR-edited cells. We also performed RNA-seq using CYB561A3-koncout MNT1 cells or CYB561A3-overexpressing MNT1 cells

2022-09-15 | GSE213142 | GEO

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