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Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans

ABSTRACT: Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans

PROVIDER: PRJNA1004653 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21529731_1.fastq.gz	Fastqsanger.gz
	SRR21529731_2.fastq.gz	Fastqsanger.gz
	SRR21529732_1.fastq.gz	Fastqsanger.gz
	SRR21529732_2.fastq.gz	Fastqsanger.gz
	SRR21529733_1.fastq.gz	Fastqsanger.gz

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Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans

Project description:Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.

2023-08-11 | GSE240717 | 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

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Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans [HiChIP & Hi-C]

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 decipher the target genes of the MFVs, we performed Hi-C and H3K27ac HiChIP assays in MNT1 cells. Hi-C is a high-throughput method for detecting chromatin interactions at whole genome scale and is often used to identify topologically associating domains (TADs) in the nucleus. H3K27ac HiChIP can identify chromatin interactions enriched for H3K27ac, a histone modification associated with active promoters and enhancers. We performed bridge linker mediated Hi-C and H3K27ac HiChIP using double (Hae3_Alu1) as well as single (Hae3) enzyme digestion in MNT-1 cells.

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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.

2023-08-31 | GSE240716 | GEO

Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans [HiChIP & Hi-C]

Project description:Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans [HiChIP & Hi-C]

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

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

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

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

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NHLBI TOPMed: Integrative Genomic Studies of Heart and Blood Related Traits in Africans (Africa6K)

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NHLBI TOPMed: Integrative Genomic Studies of Heart and Blood Related Traits in Africans (Africa6K)

Project description:NHLBI TOPMed: Integrative Genomic Studies of Heart and Blood Related Traits in Africans (Africa6K)

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Comparative transcriptome profiles of Lindian chicken eyelids identify melanin genes controlling eyelid pigmentation

Project description:During the long history of chicken domestication, eyelid color, like skin color and shank color, has been one of the unique physical traits of Chinese indigenous chickens that influence consumer behavior. In China, the Lindian chicken, which has colored feathers, is renowned for the appetizing flavor of its meat and eggs, and its eyelid colors varies from deep to light shades, including black, gray, red, and light yellow. To identify the genes controlling eyelid pigmentation, the expression profiles of black and light-yellow eyelids of Lindian chickens were analyzed with transcriptome sequencing. We detected 13,466 genes expressed in the eyelids, among which 14 were differentially expressed. A KEGG pathway analysis showed that tyrosine metabolism and melanogenesis genes were significantly enriched among these DEGs (corrected P < 0.05). Therefore, we infer that melanin metabolism is one of main factors affecting Lindian chicken eyelid pigmentation. In summary, we have identified the melanin genes responsible for eyelid pigmentation of the Lindian chicken, and also provide a valuable resource for the future study of the physical traits of chickens.

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