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 该提案调查了逆转座子元件（RTE）和KRAB锌指的共同进化 蛋白质（KZNF）导致了新的基因调节模块，以及这些模块如何促进 人类胚胎发育和多能。 KZNF是人类转录的最大家族 因素并在抑制RTE表达的主要中经历了快速演变。 RTE和KZNF是 在多能干细胞（PSC）中高度表达，在癌症和神经系统中异常表达 疾病，表明它们在这些细胞类型中起功能作用。 KZNFS显示出很强的选择信号 即使在目标RTE失去动员的能力之后（即产生新的插入事件）， 因此，不再对他们的宿主基因组构成威胁。我们假设在进化时期 KZNF由宿主维护以调节宿主基因表达后的作业抑制RTES是 完成，因此追踪KZNF-RTE和KZNF-ENHANCER互动的演变不仅将 提高我们对管理ZnF-DNA绑定规则的理解，但请在该规则上打开一个新窗口 灵长类/人类基因调节网络中的发展和机制的演变。我们将使用比较 基因组学方法利用了新的，高度连续的灵长类动物基因组组件来追踪这一点 进化史。这种分析将使我们能够应用我们开发的测定法以剖析 KZNF及其RTE/宿主目标的进化变化在控制PSC中的转录以及通过 类比，在早期的胚胎细胞类型中。 我们将将实验分析集中在“天真”和“启动” PSC上，这些PSC模仿了前和前的e培细胞。 植入后胚胎。这些细胞类型显示出许多特定RTE的高表达 和KZNF，这些表达的特征在密切相关的物种之间不同，包括人之间 和非人类猿。幼稚和底漆的PSC在实验上是可探讨的，对于再生至关重要 医学努力。我们成功地将它们制作到人类，黑猩猩和猩猩中。我们将测试 通过调节KZNF和RTE，KZNF-RTE相互作用在这些APE PSC中活跃的功能 表达并将评估这些操纵对细胞脂肪规范的后果， 维持多能性和差异潜力。通过在非人类中进行这些实验 除人类PSC外，APE PSC我们还可以识别保守和规格的特定监管程序，并且 剖析了最近进化的人类多能性差异的分子和进化基础。 这项工作的结果将揭示RTE和KZNF如何影响人类的进化和发展 并为多能干细胞的建立和维护提供重要的见解。 になったんです。英语：您可以做的第一件事就是找到最好的方法。 になったんです。英语：您可以做的第一件事就是找到最好的方法。