Cornell- Common Fund Data Supplement Regulation of the Melanocyte Lineage by the AP2 Transcription Factor Family

摘要

Abstract This application is being submitted in response to NOT-RM-19-009. We will use Common Fund resources from available databases to broaden our understanding of the genes and regulatory interactions underlying melanocyte biology. The focus of our parent grant is the melanocyte stem cell (MSC), which is a tractable model of other adult stem cells. Specifically, we are interested in how the transcription factors MITF and AP-2 interact to regulate melanocyte development, and in this supplement proposal we will utilize phenotype information from KOMP project, HiC data from the 4Dnucleome, and SNP/gene expression association data from the GTex project to gain greater understanding of the gene regulatory networks (GRNs) responsible for melanocyte generation and maintenance. Mutations in TFAP2A, the gene encoding AP-2a, cause Branchio- Oculo-Facial syndrome (BOFS), a congenital defect which includes premature hair graying. We have previously shown that AP-2 proteins are required early in neural crest development for melanocyte formation. Further, AP-2 proteins can interact genetically with MITF, considered the master regulator of the melanocyte lineage. However, the relative positions of AP-2 and MITF within this GRN, how they function at the level of the genome to control expression, and the numbers and types of genes present within this network remain unclear. We have recently determined that a combination of AP-2a and AP-2b are required for the GRN governing the balance between proliferation, differentiation, and survival in MSCs and that different combinations of mutant alleles leads to different pigmentation phenotypes, including premature graying as seen in BOFS patients. We are now examining how these changes occur by performing scRNAseq and scATACseq experiments to reveal alterations in gene expression and cis-regulatory circuitry compared with controls. Further, we have carried out CUT&RUN, an improvement over ChIP-seq, to identify the genome- wide binding sites of MITF and TFAP2A in wild-type, MITF-deleted, and TFAP2A-deleted melanoma cell lines, subsequently performing RNA-seq on each cell line. These new data provide an outstanding platform to interrogate Common Fund datasets for a systems biology understanding of the components and structure of the GRN governing MSC behavior. In brief, we will integrate the phenotype and genomic data described above with: KOMP data on mice with pigmentation defects: HiC data from two melanoma cell lines revealing relevant TFAP2 enhancer-promoter connections; and GTex data to link specific SNPs with gene expression levels. The expected outcome of the proposed one-year project is a deeper understanding of the GRN controlling the balance of MSC growth and differentiation. An understanding of the mechanisms whereby MITF and TFAP2 contribute to MSC maintenance, alongside how these factors are regulated, will have a broad impact regarding the mechanisms of aging and the initiation and progression of melanoma, as well as revealing the utility of these public datasets for systems level analysis.