טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentHarel Zalts
SubjectDevelopmental Constraints and the Evolution of Embryonic
Development
DepartmentDepartment of Biology
Supervisors Full Professor Kishony Roy
Professor Yanai Itai
Full Thesis textFull thesis text - English Version


Abstract

Embryogenesis is a tightly regulated process consisting of different stages and milestones that can be monitored at the gene expression level. During this process, the timing and localization of gene expression are crucial for proper development. Embryonic development can be studied from a comparative aspect. Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. By measuring gene expression for all genes throughout development in twenty C. elegans strains, I found that variations were dramatically uneven throughout development, with a significant depletion during mid-embryogenesis. This data further shows that genes responsible for the integration of germ layers during morphogenesis are the most constrained class of genes, providing strong evidence for developmental constraints as the mechanism underlying the hourglass model of animal evolution.

The crucial embryonic gene expression program is also regulated post-transcriptionally, in part by factors binding to the 3'UTR of messenger RNAs. During embryogenesis, transcripts may have alternative polyadenylatiuon sites, thus different 3' UTRs. Here, I introduce APA-Seq, an RNA-Seq method to measure the expression levels of alternatively polyadenylated (APA) isoforms at a global level. APA-Seq is applied to study individual C. elegans embryos and study the patterns of isoform expression throughout development. We found that global changes in APA usage demarcate developmental stages, and in particular reveal a prominent use of shorter isoforms starting at the specification stage. Surprisingly, genes with an overall constitutive expression throughout development generally show highly dynamic expression for individual 3’ UTR isoforms. This led us to distinguish between two classes of genes with APA isoforms, depending upon the expression correlation among their isoforms. Genes with uncorrelated isoforms have significantly more miRNA binding sites and higher correlations with the expression profiles of miRNA and canonical polyadenylation factors. We propose that the use of APA is under stronger selective pressures in this group of genes than in genes with correlated isoforms, and consequently more likely to have functional consequences. Collectively, these results suggest that correspondence among the regulatory programs of 3’ UTR variants is a proxy for the functional relevance of APA isoforms.