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

康奈尔大学共同基金数据补充 AP2 转录因子家族对黑素细胞谱系的调节

• 批准号: 9985505
• 负责人: Robert Aaron Cornell
• 金额: $ 25.45万
• 依托单位: UNIVERSITY OF IOWA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-08-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9985505
• 关键词: ATAC-seq; Address; Affect; Aging; Alleles; Binding; Binding Sites; Biology; Birth; Branchio-Oculo-Facial Syndromes; Cell Line; Cell Lineage; Cell Maintenance; Cell physiology; Cells; Cessation of life; ChIP-seq; Chromatin; Color; Communities; Congenital Abnormality; Data; Data Set; Databases; Defect; Development; Developmental Process; Differentiation and Growth; Disease; Embryo; Enhancers; Epidermis; Equilibrium; Family; Funding; Gene Expression; Gene Structure; Generations; Genes; Genome; Genotype-Tissue Expression Project; Glean; Growth; Hair; Hair shaft structure; Health; Human; Improve Access; In Vitro; Knowledge; Link; Literature; MEL Gene; Maintenance; Malignant Neoplasms; Mediating; Melanoma Cell; Modeling; Mus; Mutant Strains Mice; Mutation; Natural regeneration; Neural Crest; Outcome; Parents; Patients; Pattern; Phenotype; Pigmentation physiologic function; Pigments; Positioning Attribute; Proliferating; Proteins; Publications; Regulation; Regulator Genes; Regulatory Element; Resolution; Resources; Role; Site; Skin; Stem cells; Structural Genes; Study models; System; Systems Biology; TFAP2A gene; TFAP2B gene; TFAP2C gene; Testing; Tissues; Transcription Coactivator; Transcription Factor AP-2 Alpha; Zebrafish; adult stem cell; cell behavior; enhancer-binding protein AP-2; experimental study; genome-wide; genomic data; interest; meetings; melanocyte; melanoma; member; mutant; paralogous gene; parent grant; phenotypic data; pluripotency; premature; promoter; regenerative; response; transcription factor; transcriptome sequencing

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.

抽象的 本申请是为了回应 NOT-RM-19-009 而提交的。我们将使用共同基金资源 从可用的数据库中扩大我们对基因和调控相互作用的理解 黑素细胞生物学。我们家长资助的重点是黑素细胞干细胞 (MSC)，这是一种易于处理的细胞 其他成体干细胞的模型。具体来说，我们感兴趣的是转录因子 MITF 和 AP-2 如何 相互作用来调节黑素细胞的发育，在这个补充提案中，我们将利用表型 来自 KOMP 项目的信息、来自 4D 核组的 HiC 数据以及 SNP/基因表达关联数据 来自 GTex 项目，以更好地了解负责的基因调控网络 (GRN) 黑素细胞的生成和维持。 TFAP2A（编码 AP-2a 的基因）的突变会导致 Branchio- 眼面部综合征 (BOFS)，一种先天性缺陷，包括头发过早变白。我们有 先前表明，AP-2 蛋白是神经嵴发育早期黑素细胞形成所必需的。 此外，AP-2 蛋白可以与 MITF 发生遗传相互作用，MITF 被认为是黑素细胞的主要调节因子 血统。然而，AP-2 和 MITF 在这个 GRN 中的相对位置，以及它们如何在以下层面发挥作用： 控制表达的基因组，以及该网络中存在的基因的数量和类型仍然存在 不清楚。我们最近确定 GRN 需要 AP-2a 和 AP-2b 的组合 控制 MSC 增殖、分化和存活之间的平衡 突变等位基因的组合会导致不同的色素沉着表型，包括过早变白 见于 BOFS 患者。我们现在正在通过执行 scRNAseq 和 scATACseq 实验揭示了与 控制。此外，我们还进行了 CUT&RUN，这是对 ChIP-seq 的改进，以识别基因组- MITF 和 TFAP2A 在野生型、MITF 缺失和 TFAP2A 缺失黑色素瘤细胞系中的广泛结合位点， 随后对每个细胞系进行 RNA-seq。这些新数据提供了一个出色的平台 询问共同基金数据集，以了解系统生物学的组成部分和结构 GRN 管理 MSC 行为。简而言之，我们将整合所描述的表型和基因组数据 上面是：关于色素沉着缺陷小鼠的 KOMP 数据：来自两种黑色素瘤细胞系的 HiC 数据揭示 相关的 TFAP2 增强子-启动子连接；和 GTex 数据将特定 SNP 与基因表达联系起来 水平。拟议的为期一年的项目的预期成果是对 GRN 有更深入的了解 控制MSC生长和分化的平衡。了解 MITF 的机制 和 TFAP2 对 MSC 维护的贡献，以及这些因素的调节方式，将具有广泛的影响 对衰老机制和黑色素瘤的发生和进展的影响，以及 揭示这些公共数据集用于系统级分析的效用。