Genome-wide transcriptome analysis of human epidermal melanocytes

• The transcriptome of human melanocytes was determined using RNA sequencing.
• We compared melanocytes with different pigmentation levels from different skin types.
• Our analysis focused on cell signaling genes like receptors and ion channels.
• Pigmentation genes specific to melanocytes were expressed at very high levels.
• Our study found 15 novel genes differentially expressed in light vs. dark human melanocytes.

Because human epidermal melanocytes (HEMs) provide critical protection against skin cancer, sunburn, and photoaging, a genome-wide perspective of gene expression in these cells is vital to understanding human skin physiology. In this study we performed high throughput sequencing of HEMs to obtain a complete data set of transcript sizes, abundances, and splicing. As expected, we found that melanocyte specific genes that function in pigmentation were among the highest expressed genes. We analyzed receptor, ion channel and transcription factor gene families to get a better understanding of the cell signaling pathways used by melanocytes. We also performed a comparative transcriptomic analysis of lightly versus darkly pigmented HEMs and found 16 genes differentially expressed in the two pigmentation phenotypes; of those, only one putative melanosomal transporter (SLC45A2) has known function in pigmentation. In addition, we found 166 transcript isoforms expressed exclusively in one pigmentation phenotype, 17 of which are genes involved in signal transduction. Our melanocyte transcriptome study provides a comprehensive view and may help identify novel pigmentation genes and potential pharmacological targets.