mRNA regulation, localization, and dynamics in C. elegans embryogenesis

秀丽隐杆线虫胚胎发生中的 mRNA 调控、定位和动态

• 批准号: 10674715
• 负责人: Erin Osborne Nishimura
• 金额: $ 39.09万
• 依托单位: COLORADO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-18 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10674715
• 关键词: Biological Assay; Biological Models; Caenorhabditis elegans; Cell Differentiation process; Cell Shape; Cells; Cellular biology; Complex; Cytoplasm; Cytoplasmic Granules; Cytoskeleton; Databases; Development; Disease; Embryo; Embryology; Embryonic Development; Ensure; Exhibits; Family; Fertility; Funding; Gene Expression; Genetic Transcription; Genomics; Human; Link; Locales; Malignant Neoplasms; Maternal Messenger RNA; Membrane; Messenger RNA; Modeling; Molecular; Neurobiology; Organism; Pattern; Phase; Physical condensation; Post-Transcriptional Regulation; Production; Proteins; RNA-Binding Proteins; Regulation; Research; Resolution; Shapes; Signal Transduction; Specificity; Subcellular structure; Sum; Technology; Transcript; Translating; Translations; Work; cell growth regulation; genome-wide; innovation; member; nano; novel; programs; transcriptome

PROJECT SUMMARY/ABSTRACT: Cells of the Caenorhabditis elegans early embryo diversify their mRNA content even in the absence of de novo transcription. This remarkable feat has given my lab a unique vantage from which to study post- transcriptional regulation. Surprisingly, we found that many mRNA transcripts which exhibit cell-specific patterning also localize to discrete subcellular structures such as biomolecular condensates or membranes. My lab aims to understand how subcellular mRNA patterning arises mechanistically, how it functionally links to protein production, and how it impacts development. Recent advances have identified 190,000 localized mRNA transcripts found at 44 subcellular locales across 65 species (RNALocate Database). These transcripts include many that impact human neurobiology and whose mislocalization is associated with disease. Many more represent mRNAs that accumulate at cellular regions through unknown mechanisms and for undefined purposes, underscoring the potential for new discoveries that we aim to make. In the first funding phase, my group determined mechanisms that localize mRNAs to P granules (cytoplasmic condensates important for germline development and fertility). Transcripts that associate with P granules undergo either temporary sequestration or permanent decay. In the next phase, we will address the signals, mechanisms, and dynamics that distinguish P granule-associated mRNA sequestration from decay. Specifically, we will differentiate between competing models explaining how the conserved transcript nos-2 (nanos) exits P granules and initiates its translation to ensure fertility. Previously, we identified several mRNA transcripts that localize to membranes along with the proteins they encode, a finding echoed in other organisms. Among these were erm-1 a member of a conserved family of cytoskeletal membrane linker proteins that impacts cell shape and cancer. We found that erm-1’s mRNA localization is translation-dependent. Next, we will address the mechanisms and principles explaining how and why complexes of translating erm-1 move to membranes. We will also use genomics to characterize the membrane-enriched transcriptome to better understand localized translation at membranes. Maternal mRNA transcripts undergo decay in early embryos often creating cell-specific patterns that direct cell differentiation. In the first funding cycle, we demonstrated a requirement for the RNA binding protein SPN-4 in the clearance and cell-specificity of some transcripts. In the next phase, we will determine how SPN-4 shapes the transcriptome and works in concert with other mechanisms of mRNA clearance. The sum of these projects will be to create an overarching research program aimed at describing how mRNA transcripts organize spatially within the cell and how that organization can impact gene expression and embryogenesis.

项目总结/摘要： 秀丽隐杆线虫早期胚胎的细胞即使在缺乏 从头转录。这一非凡的壮举给了我的实验室一个独特的Vantage，从其中研究后- 转录调控令人惊讶的是，我们发现许多表现出细胞特异性的mRNA转录本， 图案化还定位于离散的亚细胞结构，例如生物分子凝聚物或膜。我 该实验室旨在了解亚细胞mRNA模式是如何在机制上产生的， 与蛋白质生产的联系，以及它如何影响发展。最新的研究发现， 在65个物种的44个亚细胞位置发现的定位mRNA转录物（RNALocate数据库）。这些 转录本包括许多影响人类神经生物学的转录本，其错误定位与 疾病更多的代表通过未知机制在细胞区域积累的mRNA， 用于未定义的目的，强调了我们旨在进行的新发现的潜力。 在第一个资助阶段，我的小组确定了mRNA定位于P颗粒的机制， （细胞质凝聚物对生殖系发育和生育力很重要）。与P相关的转录本 颗粒经历暂时的隔离或永久的衰变。在下一阶段，我们将 区分P颗粒相关mRNA隔离的信号、机制和动力学 从腐烂。具体来说，我们将区分竞争模型，解释保守的 转录本nos-2（nanos）离开P颗粒并启动其翻译以确保能育性。 以前，我们鉴定了几种mRNA转录物，它们与蛋白质一起沿着定位于细胞膜 这一发现在其他生物体中得到了回应。其中包括一个保守家族的成员， 影响细胞形状和癌症的细胞骨架膜连接蛋白。我们发现， 定位是依赖于预防的。接下来，我们将讨论解释 翻译β-1的复合物如何以及为什么移动到膜上。我们还将利用基因组学， 表征膜富集的转录组，以更好地理解膜上的定位翻译。 母体mRNA转录物在早期胚胎中经历衰变，通常产生细胞特异性模式， 直接细胞分化。在第一个资助周期中，我们证明了RNA结合蛋白的需求， SPN-4在某些转录物的清除和细胞特异性中的作用。在下一阶段，我们将确定如何 SPN-4塑造转录组，并与mRNA清除的其他机制协同工作。 这些项目的总和将创建一个总体研究计划，旨在 描述mRNA转录本如何在细胞内进行空间组织以及该组织如何 影响基因表达和胚胎发生。

项目成果

Hyper-active RAS/MAPK introduces cancer-specific mitotic vulnerabilities.

过度活跃的 RAS/MAPK 会引入癌症特异性的有丝分裂漏洞。

• DOI: 10.1073/pnas.2208255119
• 发表时间: 2022-10-11
• 期刊: Proceedings of the National Academy of Sciences of the United States of America
• 影响因子: 11.1

The ERM-1 membrane-binding domain directs erm-1 mRNA localization to the plasma membrane in the C. elegans embryo.

ERM-1膜结合结构域将ERM-1 mRNA定位定位到秀丽隐杆线虫胚胎中的质膜。

• DOI: 10.1242/dev.200930
• 发表时间: 2022-11-15
• 期刊: Development (Cambridge, England)

Improved Methods for Single-Molecule Fluorescence In Situ Hybridization and Immunofluorescence in Caenorhabditis elegans Embryos.

• DOI: 10.1002/cpz1.299
• 发表时间: 2021-11
• 期刊: Current protocols
• 作者: Parker, Dylan M;Winkenbach, Lindsay P;Parker, Annemarie;Boyson, Sam;Nishimura, Erin Osborne
• 通讯作者: Nishimura, Erin Osborne

It's Just a Phase: Exploring the Relationship Between mRNA, Biomolecular Condensates, and Translational Control.

• DOI: 10.3389/fgene.2022.931220
• 发表时间: 2022
• 期刊: Frontiers in genetics
• 影响因子: 3.7

A Strategy To Isolate Modifiers of Caenorhabditis elegans Lethal Mutations: Investigating the Endoderm Specifying Ability of the Intestinal Differentiation GATA Factor ELT-2.

• DOI: 10.1534/g3.118.200079
• 发表时间: 2018-05-04
• 期刊: G3 (Bethesda, Md.)
• 作者: Wiesenfahrt T;Duanmu J;Snider F;Moerman D;Au V;Li-Leger E;Flibotte S;Parker DM;Marshall CJ;Nishimura EO;Mains PE;McGhee JD
• 通讯作者: McGhee JD