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 该申请是针对NOT-RM-19-009提交的。我们将使用共同的基金资源 从可用数据库扩大我们对基因和监管相互作用的理解 黑素细胞生物学。我们父母赠款的重点是黑素细胞干细胞（MSC） 其他成年干细胞的模型。具体而言，我们对转录因子MITF和AP-2如何感兴趣 相互作用以调节黑素细胞的发育，在此补充建议中，我们将利用表型 来自KOMP项目的信息，4Dnucleome的HIC数据和SNP/基因表达关联数据 从GTEX项目中获得对负责基因调节网络（GRN）的更多了解 黑素细胞的产生和维护。 TFAP2A的突变，编码AP-2a的基因，引起分支 - Oculo-Facial综合征（BOFS），一种先天性缺陷，包括过早的头发灰色。我们有 先前的表明，在神经rest发育中需要AP-2蛋白以形成黑素细胞。 此外，AP-2蛋白可以与MITF遗传相互作用，该蛋白被认为是黑色素细胞的主要调节剂 血统。但是，AP-2和MITF在此GRN中的相对位置，它们如何在 控制表达的基因组，并且该网络中存在的基因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 管理MSC中的增殖，分化和生存之间的平衡和不同 突变等位基因的组合导致不同的色素沉着表型，包括过早的灰色 在BOFS患者中看到。我们现在正在研究这些变化是如何通过执行scrnaseq和 SCATACSEQ实验揭示了基因表达和顺式调节电路的改变， 控件。此外，我们进行了切割和运行，这比Chip-seq进行了改进，以确定基因组 - MITF和TFAP2A的宽结合位点，野生型，MITF删除和TFAP2A骨骼黑色素瘤细胞系， 随后在每个细胞系上执行RNA-Seq。这些新数据为 询问通用基金数据集，以了解系统生物学对组件和结构的理解 管理MSC行为的GRN。简而言之，我们将整合描述的表型和基因组数据 上面的：具有色素沉着缺陷的小鼠的KOMP数据：来自两个黑色素瘤细胞系的HIC数据揭示了 相关的TFAP2增强器促销连接；和GTEX数据将特定SNP与基因表达联系起来 水平。拟议的一年项目的预期结果是对GRN的更深入了解 控制MSC增长和分化的平衡。了解MITF的机制 TFAP2有助于MSC维护，以及如何调节这些因素，将具有广泛的 对衰老机制以及黑色素瘤的启动和进展的影响以及 揭示这些公共数据集的实用性用于系统级别分析。