The Role of mRNA Degradation in Embryonic Cell Fate Specification

mRNA 降解在胚胎细胞命运规范中的作用

• 批准号: 10604512
• 负责人: Felicia Peng
• 金额: $ 4.77万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-04-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10604512
• 关键词: 3' Untranslated Regions; Address; Affect; Alternative Splicing; Animals; Auxins; Binding; Binding Proteins; Caenorhabditis elegans; Cell Culture System; Cell Lineage; Cells; Codon Nucleotides; Complex; Data; Data Analyses; Defect; Deposition; Development; Developmental Gene; Developmental Process; Disease; Dissociation; Embryo; Embryonic Development; Ensure; Eukaryota; Exoribonucleases; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic Transcription; Half-Life; Health; Human; Image; Invertebrates; Kinetics; Knowledge; Label; Link; Maps; Maternal Messenger RNA; Measurement; Measures; Mediating; Messenger RNA; Metabolic; Methods; Modification; Nematoda; Neurodegenerative Disorders; Organism; Pathway interactions; Pattern; Phenotype; Physiologic pulse; Poly A; Polyadenylation; Post-Transcriptional Regulation; Process; Proteins; RNA; RNA Decay; RNA Degradation; RNA Polymerase II; RNA-Binding Proteins; Regulation; Regulatory Element; Resolution; Role; Shapes; Small RNA; Specific qualifier value; Specificity; System; Testing; Time; Tissues; Transcript; Transcriptional Regulation; Transgenes; Transgenic Organisms; Translations; blastomere structure; cell fate specification; cell type; comparison control; egg; embryo cell; exosome; gene product; inhibitor; innovation; live cell imaging; mRNA Decay; mRNA Stability; mRNA Transcript Degradation; model organism; osteosarcoma; progenitor; programs; single-cell RNA sequencing; spatiotemporal; temporal measurement; transcriptome; transcriptome sequencing

Project Summary During development, cells undergo dynamic changes in gene expression that are required for appropriate cell fate specification. Although developmental gene expression is best studied in terms of transcriptional regulation, the regulation of mRNA degradation may also have important contributions to these expression patterns. Defects in mRNA decay machinery have been linked to diseases with distinct phenotypes, such as osteosarcoma and neurodegenerative diseases. In addition, the widespread degradation of maternal mRNAs in all animals during early embryogenesis is critical for the control of development to switch from maternally provided to zygotically encoded products. Studies of maternal and zygotic mRNA decay dynamics have established that transcript stability is largely regulated by the binding of protein or RNA factors to cis-regulatory elements within the 3’ untranslated region (3’ UTR) of transcripts. Codon usage is another major determinant of mRNA stability, as translation can affect mRNA stability in a codon-dependent manner. Considering the great diversity of RNA- binding proteins and small RNAs in eukaryotes, along with alternative splicing and polyadenylation, the regulation of mRNA degradation has the potential to be highly complex. This complexity may shape precise gene expression patterns during development, though the extent of developmentally regulated zygotic mRNA degradation is unclear. To explore this, I am studying zygotic mRNA degradation in Caenorhabditis elegans throughout embryonic development. In Aim 1, I will generate a transcriptome-wide map of mRNA decay rates throughout embryogenesis with spatial and temporal resolution. Transcript half-lives will be determined using single cell RNA-sequencing to measure mRNA abundance in embryonic cells treated with a transcription inhibitor. To validate half-lives measured by this transcription inhibition approach, I will use metabolic labeling and degradation of RNA polymerase II as two orthogonal methods to measure decay rates. Mechanisms of differential mRNA degradation, namely genes with different rates of decay in different cell types, will be explored using a transgene approach. In Aim 2, I will establish the roles of the major 5′ to 3′ and 3′ to 5′ mRNA decay pathways in development. I will identify mRNA targets of both pathways through RNA-sequencing of staged embryos depleted of the cognate exoribonuclease. Genes that are significantly upregulated compared to control embryos will be treated as putative targets. Additionally, I will determine the roles of both pathways in cell fate specification by analyzing cell fate marker expression in exoribonuclease-depleted embryos using live imaging. By characterizing mRNA decay rates across cell types and developmental stages and establishing mechanisms of differential mRNA degradation, I will begin to uncover the role of zygotic mRNA turnover in embryonic cell fate specification. Such findings will provide a more comprehensive understanding of regulatory strategies used during embryogenesis to mediate developmental transitions and patterning.

项目总结