Evolution of new regulatory networks via genetic arms races between KRAB zinc finger proteins and retrotransposons

通过 KRAB 锌指蛋白和反转录转座子之间的基因军备竞赛，新的调控网络的进化

• 批准号: 10088455
• 负责人: Sofie Reda Salama
• 金额: $ 68.54万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-02-12 至 2023-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10088455
• 关键词: Amino Acid Sequence; Amino Acids; Binding; Binding Proteins; Biological; Biological Assay; Cell Differentiation process; Cell Maintenance; Cells; ChIP-seq; Clustered Regularly Interspaced Short Palindromic Repeats; DNA; DNA Binding; DNA Insertion Elements; Data; Data Aggregation; Data Collection; Development; Elements; Embryonic Development; Enhancers; Ensure; Epiblast; Event; Evolution; Family; Gene Cluster; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Gene Proteins; Genetic; Genetic Transcription; Genome; Genomic approach; Human; Human Genome; Individual; Maintenance; Malignant Neoplasms; Mediating; Molecular; Nucleotides; Occupations; Orthologous Gene; Pan Genus; Phenotype; Play; Pluripotent Stem Cells; Pongidae; Pongo pygmaeus; Primates; Process; Protein Microchips; Protein Region; Proteins; Race; Recording of previous events; Regenerative Medicine; Regulation; Regulator Genes; Reporter; Repression; Resolution; Retrotransposition; Retrotransposon; Risk; Role; Signal Transduction; Site-Directed Mutagenesis; Source; Testing; Tetrapoda; Time; Work; Zinc Fingers; arm; base; blastomere structure; cell fate specification; cell type; cellular targeting; comparative; comparative genomics; differential expression; epigenomics; experimental analysis; experimental study; genomic data; human pluripotent stem cell; implantation; innovation; insight; knock-down; natural Blastocyst Implantation; nervous system disorder; overexpression; pluripotency; preimplantation; prevent; programs; promoter; protein expression; recruit; tool; trait; transcription factor; transcriptome; zinc finger nuclease

Project Summary / Abstract This proposal investigates how co-evolution of retrotransposon elements (RTEs) and KRAB zinc finger proteins (KZNFs) have resulted in new gene regulatory modules and how these modules contribute to human embryonic development and pluripotency. KZNFs are the largest family of human transcription factors and have undergone rapid evolution in primates to repress RTE expression. Both RTEs and KZNFs are highly expressed in pluripotent stem cells (PSCs) and are aberrantly expressed in cancers and neurological diseases, suggesting that they play functional roles in these cell types. KZNFs show strong signals of selection and activity even after their target RTEs have lost the ability to mobilize (i.e. generate new insertion events) and therefore no longer pose a threat to their host genome. We hypothesize that over evolutionary time KZNFs are maintained by the host to regulate host gene expression after their job repressing RTEs is finished, and hence tracing the evolution of KZNF-RTE and KZNF-enhancer interactions will not only increase our understanding of the rules governing ZNF-DNA binding, but open a new window on the evolution of and mechanisms in primate/human gene regulatory networks. We will use comparative genomics approaches that take advantage of new, highly contiguous, primate genome assemblies to trace this evolutionary history. This analysis will allow us to apply assays we have developed to dissect the role of evolutionary changes to both KZNFs and their RTE/host targets in controlling transcription in PSCs, and by analogy, in early embryonic cell types. We will focus our experimental analysis on “naive” and “primed” PSCs, which mimic epiblast cells of pre- and post-implantation embryos, respectively. These cell types show high expression of a number of specific RTEs and KZNFs, and these expression signatures differ between closely related species, including between human and non-human apes. Naive and primed PSCs are experimentally tractable and critical for regenerative medicine efforts. We have succeeded in making them in human, chimpanzee and orangutan. We will test the function of KZNF-RTE interactions active in these ape PSCs by modulating both KZNF and RTE expression and will assess the consequences of these manipulations on cell fate specification, maintenance of pluripotency and differentiation potential. By performing these experiments in non-human ape PSCs in addition to human PSCs we can identify conserved and species-specific regulatory programs and dissect the molecular and evolutionary basis for recently evolved differences in pluripotency in humans. The results of this work will reveal how RTEs and KZNFs have influenced human evolution and development and provide important insights into the establishment and maintenance of pluripotent stem cells. ​ ​

项目摘要/摘要 这项建议研究了逆转座子元件(RTES)和KRAB锌指是如何共同进化的 蛋白质(KZNf)已经产生了新的基因调控模块，以及这些模块如何对 人类胚胎发育和多能性。KZNFs是人类转录中最大的家族 因子并在灵长类动物中经历了快速进化以抑制RTE的表达。Rte和kznf都是 在多能干细胞(PSCs)中高表达，在癌症和神经疾病中异常表达 疾病，表明它们在这些细胞类型中发挥功能作用。KZNF表现出强烈的选择信号 和活动，即使在它们的目标RTE已经失去动员能力(即产生新的插入事件)之后 因此不再对它们的宿主基因组构成威胁。我们假设随着进化时间的推移 KZNf在抑制rtes的作用后，由宿主维持以调节宿主基因的表达。 完成，因此追踪KZNF-RTE和KZNF-增强子相互作用的演变不仅将 增加了我们对ZNF-DNA结合规则的理解，但打开了一扇新的窗口 灵长类/人类基因调控网络的进化和机制。我们将使用比较级 基因组学方法利用新的、高度连续的灵长类基因组组装来追踪这一点 进化史。这一分析将使我们能够应用我们开发的分析方法来剖析 KZNFs及其RTE/宿主靶标在控制PSCs转录中的进化变化，以及通过 类比，在早期胚胎细胞类型中。 我们将集中在“幼稚的”和“预激的”PSCs上进行实验分析，它们模仿前和后的上胚层细胞。 分别为植入后胚胎。这些细胞类型显示了许多特定的RTE的高表达 和KZNF，并且这些表达特征在密切相关的物种之间不同，包括在人类之间 以及非人类的类人猿。幼稚和启动的PSCs在实验上是容易驯化的，对再生至关重要 医药方面的努力。我们已经成功地在人类、黑猩猩和猩猩身上制造了它们。我们将测试 KZNF-RTE相互作用在这些类人猿PSCs中的作用 表达，并将评估这些操作对细胞命运指定的后果， 维持多能性和分化潜能。通过在非人类身上进行这些实验 除了人类的PSCs之外，我们还可以识别保守的和物种特有的调节程序和 剖析人类最近进化出的多能性差异的分子和进化基础。 这项工作的结果将揭示rtes和kznf如何影响人类的进化和发展 并为建立和维持多能干细胞提供了重要的见解。 ​ ​