PROJECT SUMMARY/ ABSTRACT
Gene expression is a complex process involving transcription, translation, and the turnover of mRNAs
and proteins. Proper spatiotemporal regulation of gene expression and protein abundance plays a crucial role
in guiding the differentiation of the fertilized egg into a complex animal. Understanding the regulation of protein
dynamics can provide valuable insights into the differentiation of germ layers (endoderm, mesoderm,
ectoderm), as well as the development of specialized cells and tissues.
However, quantifying lineage-specific protein dynamics in developing embryos is challenging due to
technical limitations in single-cell proteomics and the inherent heterogeneity of embryonic tissues. As a result,
researchers have often used mRNA levels as a proxy for protein expression, but this approach has significant
limitations due to the poor correlation between mRNA and protein levels. This discrepancy highlights the
importance of posttranscriptional mechanisms, such as protein degradation and translation efficiencies, in
determining cell fate.
To address these issues and enhance our understanding of embryogenesis, it is crucial to measure
proteome dynamics during cell differentiation directly. These measurements will provide a more
comprehensive and accurate view of the intricate processes at play during embryonic development. This study
proposes using genetically modified morphogen-flattened Drosophila embryos expressing four morphogens
uniformly. These embryos contain a uniform cell type at gastrulation, different for each morphogen-flattened
embryo. The focus will be on quantifying protein dynamics and posttranscriptional regulation within the
ectoderm germ layer. My approach involves deep multiplexed proteomics and single-cell RNAseq to analyze
proteome differentiation and stochastic cell fate diversification (Aim 1 & 2). Additionally, by achieving the
desired outcomes of measuring posttranscriptional regulation (translation efficiency and protein turnover) in
Aim 3, the proposed mathematical model will provide valuable insights into mRNA-protein dynamics during cell
differentiation in developing embryos, which will address some of the discrepancies between the two.
In conclusion, this proposal aims to decipher the mechanisms of embryonic cell-type differentiation by
using morphogen-flattened embryos and employing an integrative analysis of genomics and proteomics
measurements. This comprehensive approach will yield valuable insights into the intricate interplay of
transcriptional and posttranscriptional regulation during development, enhancing our understanding of the
fundamental principles in embryonic development and informing strategies for manipulating cell fate in
regenerative medicine and tissue engineering.