Ph.D Thesis

Ph.D StudentIdit Kosti
SubjectStudying Co-Regulation in the Human Gene Expression
DepartmentDepartment of Biology
Supervisor Professor Mandel-Gutfreun Yael
Full Thesis textFull thesis text - English Version


Traditionally the gene expression pathway has been regarded as being comprised of independent steps, such as chromatin remodelling, transcription, RNA processing, RNA degradation, translation and protein degradation. To date there is increasing evidence for coupling between the different processes of the pathway.

In my thesis I focused on two main projects. The first project investigates the role of co-regulation of gene-body DNA methylation and histone modifications by using data of human fibroblast cell-line and primary B-cells. Consistent with previous work we found that gene-body methylation is positively correlated with gene expression and that intragenic exons are more methylated than their neighboring intronic environment. Intriguingly, we found that the overall elevated DNA methylation at exons relative to their surrounding introns is primarily a characteristic of silenced genes. These results were independent of the inclusion rate of the exons, suggesting a novel role for exon methylation that does not directly relate to active transcription or splicing processes. Furthermore, we observed a negative correlation between gene-body exon methylation and the density of the majority of histone modifications. We specifically demonstrated a positive correlation between exon expression, hypomethylated exons and a characteristic histone code comprised of significantly high levels of histone markings.

In the second project I explored the role of co-regulation of transcription and alternative splicing in the gene expression pathway. In order to learn about co-regulation we derived a transcription-splicing integrated network with transcription factors, splicing factors and kinases as nodes, and predicted transcriptional and alternative splicing regulation as edges. Analysis of the network indicated pervasive cross-regulation among the nodes; specifically, splicing factors were observed to be significantly more connected by alternative splicing regulatory edges relative to the two other subgroups, while transcription factors were more extensively controlled by transcriptional regulation. Consistent with the network results, our bioinformatics analyses showed that the subgroup of kinases had the highest density of predicted phosphorylation sites. Interestingly this trend was not human specific and was also found for S. cerevisiae and D. melanogaster genomes. Based on our results we proposed a new regulatory paradigm postulating that gene expression regulation of the master regulators in the cell is predominantly achieved by cross-regulation between regulatory stages.