טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
M.Sc Thesis
M.Sc StudentMostov Natalia
SubjectDifferential 3'UTR Isoform Expression across Space and
Time in the C. elegans Embryo
DepartmentDepartment of Biology
Supervisors Professor Yael Mandel-Gutfreun
Professor Itai Yanai
Full Thesis textFull thesis text - English Version


Abstract

The 3’UTR is a key determinant of post-transcriptional gene regulation. It exerts a tremendous effect over a vast variety of the transcript’s characteristics, such as its stability, translation rate, and even the cellular localization. For example, degradation of the transcript can be controlled by regions such as AU-rich elements (AREs) and microRNA binding sites located in the 3'UTR region. The same exact transcript can have different 3’UTR variants. Those variants are referred to as isoforms, and arise by a mechanism of alternative poly Adenylation (APA). During the last decade, a huge progress has been made in studying APA, and widespread APA changes were detected during a huge assortment of biological, developmental, physiological and even pathological processes. The APA was recognized as a widespread and evolutionary conserved mechanism; the percentage of estimated alternatively poly-Adenylated genes varies between 30%-70% in different species. In our lab, we study the embryogenesis of the nematode C. elegans. We have been using CEL-Seq, a high throughput sequencing method developed in our lab to obtain gene expression profiles in a single cell resolution. In order to adapt our method for studying APA, we had to make adjustments in the bioinformatics pipeline. First, we have switched to using the R1, which specifically captures the poly-A tails of mRNAs, to detect the APA sites. Next, to deal with the R1s bad quality, we mapped it to the gene of origin instead of to the whole genome, to elevate the mapping percentage. This computational approach, together with a unique dataset -a time course of in vitro cultured five blastomeres (AB, MS, E, C and P3), allowed us to study the influence of both the spatial and the temporal factors on APA. Our recent results imply that developmental stage exerts greater influence over 3’UTR isoform expression patterns than the cell lineage, in all cases except PD. In the PD cell lineage, which later on will follow both mesodermal and germline specification programs, we observe a universal shift towards using the shorter 3’UTR isoforms in later developmental stages. In the C and in the MS cell lineage, which later on will develop to mesoderm and ectoderm, there is a statistically significant elongation of the 3’UTR isoforms in the later developmental stages. However, overall in all the cell lineages, including PD there are more elongating than shortening genes. In most cases, genes with similar APA profiles tend to perform similar functions. Moreover, we have been able to recreate previous results of a research conducted on human tissues, showing that ubiquitously transcribed genes tend to have more 3’UTR isoforms than tissue-restricted genes. Hence, APA patterns are sufficiently conserved to allow us to project the findings in C. elegans on other eukaryotes.