This project aims to systematically decipher the roles and mechanisms of post-transcriptional RNA degradation within embryonic gene expression programs. Its successful implementation will address important questions in developmental biology and regulation of RNA degradation.
Aim 1: This aim will generate two large datasets: (1) catalogues of cis-elements that regulate mRNA degradation across different positions, lengths and modifications, and (2) a high-resolution atlas of RNA regulatory dynamics during early embryogenesis. Based on this data, we will (1) build novel computational tools to systematically map mRNA degradation profiles and their cis-regulatory determinants, (2) develop a predictive model of genomic information within native mRNA sequences and define regulatory rules of maternal mRNA degradation and (3) provide design tools to predict the impact of genetic variations on mRNA stability and expression patterns in early embryos, and determine the effects of variants that are associated with disease or positive selection and to design synthetic mRNAs with pre-defined stabilities.
Aim 2: This aim will develop a technology to monitor the regulation of mRNA stability in early embryogenesis at single-cell resolution on a genome-scale. The technology is based on single-cell resolution metabolic labeling and reporter assays, in combination with novel computational tools for the analysis of those datasets to map both mRNA degradation rates and cis-element activities within single cells and cell-types of developing zebrafish embryos. We will use this data to investigate key questions on mRNA stability and its roles during development: (1) Decode differential mRNA stabilities and cis-element activities between cell-types and spatially restricted embryonic cell populations. (2) Determine cell-to-cell variability of mRNA stabilities, its stochastic variation and its functional roles in regulation of cellular population. (3) Provide an improved resolution and a refined cis-regulatory code for decoding mRNA degradation patterns within specific developmental cell-types in early embryos. (4) Decode regulation of mRNA stability within developmental gene expression programs that define and maintain cellular states.
Aim 3: This aim will generate comprehensive gene network models of the maternal mRNA decay programs in zebrafish embryos, a key regulatory event in early embryogenesis that is shared in all animals. These gene network models will describe known regulatory interactions, predict novel regulators and reveal missing components. We will use these models to (1) characterize the molecular mechanisms, functions and physiological roles of maternal RNA degradation (2) implement and apply a screening strategy for maternal mRNAs, and uncover physiological roles for their timely degradation during early embryogenesis.
These outcomes have important practical implications on understanding disease mechanisms, drug discovery, and therapeutics. The resulting technology will provide principled and unbiased tools to decode regulation of RNA stability across many systems and processes, ranging from disease mechanisms to the engineering of RNA-protein interactions.
