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

Adaptation strategies of Pseudothermotoga species to hydrostatic pressure by transcriptional analyses

Project description:Pseudothermotoga elfii strain DSM9442 and P. elfii subsp. lettingae strain TMOT are hyperthermophilic bacteria. P. elfii is a moderate piezophile, isolated from an oil-producing well in Africa at a depth of more than 1600 m. P. lettingae is piezotolerant, isolated from a thermophilic bioreactor fed with methanol as the sole carbon and energy source. In this study, we analysed these bacteria at the genomic and transcriptomic levels. According to the hydrostatic pressure growth conditions the transcriptomic analyses revealed differentially expressed genes emphasizing amino acid and sugars metabolism and transport as the major hydrostatic pressure responding processes. Notably, this work highlights the central role of the amino acid aspartate as key intermediate of the pressure adaptation mechanisms of the deep strain P. elfii DSM 9442. In addition, several differentially expressed genes involved in the membrane and cell wall biosynthesis pathways may be linked to the chain formation morphotype previously described at high pressure for strain P. elfii DSM9442.

2023-03-30 | GSE226101 | GEO

Integrative tissue analyses of men with prostate cancer

Project description:Integrative tissue analyses of men with prostate cancer

| PRJNA758910 | ENA

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

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

| PRJNA1004653 | ENA

Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

Project description:Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes

| PRJNA922597 | ENA

Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors

Project description:Integrative genomic analyses identify lncRNA regulatory networks across pediatric leukemias and solid tumors

| PRJNA998073 | ENA

INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA

Project description:This SuperSeries is composed of the following subset Series: GSE35082: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (expression) GSE35329: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data) GSE35367: INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (CGH) Refer to individual Series

2012-07-31 | E-GEOD-35383 | biostudies-arrayexpress

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