טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
Ph.D Thesis
Ph.D StudentAvital Gal
SubjectUnderstanding Gene Regulatory Programs Involving Non
Poly-A Transcripts in Dynamic Processes
DepartmentDepartment of Biology
Supervisors Professor Roy Kishony
Professor Itai Yanai
Full Thesis textFull thesis text - English Version


Abstract

While RNA was historically relegated to an intermediary role by the “central dogma”, it is now clear that a myriad RNA classes play central roles in a large number of cellular processes including catalytic, structural and regulatory functions. Systems biology has made tremendous strides in understanding dynamic systems in terms of complex and comprehensive gene regulatory pathways. However, as detailed and comprehensive as these pathways attempt to be, they hardly integrate the non poly-A RNA classes, thereby exposing a blind side of our understanding of different pathways. In this research we examined the roles and regulation of different RNA classes within two dynamic systems; embryogenesis and infection.

We adopt an evolutionary developmental approach to study miRNA function by examining their expression throughout embryogenesis in both C. elegans and D. melanogaster. We find that, in both species, miRNA transcriptomic shifts in a punctuated fashion during the mid-developmental transition, specifying two dominant modes of early and late expression profiles. Strikingly, late-expressed miRNAs are enriched for phylogenetic conservation and function by fine-tuning the expression of their targets, implicating a role in the canalization of cell-types during differentiation. In contrast, early-expressed miRNAs are inversely expressed with their targets suggesting strong target-inhibition. Taken together, our work exposes a bimodal role for miRNA function during animal development, involving late-expressed physiological roles and early-expressed repressive roles.

In order to get a better understanding of the infection process, we have developed a single-cell RNA-Seq method (scDual-Seq) that simultaneously captures both host and pathogen transcriptomes and use it to study the process of infection of individual mouse macrophages with the intracellular pathogen Salmonella typhimurium. We found a previously unreported class of macrophages with a partial induction of an immune response to infection. Among those macrophages exhibiting a full immune response, we detected two distinct classes of expression among Salmonella contained within these macrophages. We show evidence for a linear progression through these states, supporting a model in which these three states correspond to consecutive stages of infection.