Transcriptome dynamics in early zebrafish embryogenesis

The aim of this PhD study was to obtain a deeper insight in transcriptome dynamics, by investigating on an omics scale the changing gene-expression during early zebrafish embryogenesis. A number of gene-expression experiments were carried out in which zebrafish eggs and embryos were used as model system. A new RNA isolation method for the transcriptomics profiling of single zebrafish eggs or embryos was developed, as well as a methodology to integrate heterogeneous sequence information for transcriptome-wide microarray design is. Next, the discovery of a mother-specific signature in the maternal transcriptome composition of unfertilized zebrafish eggs is shown. This was achieved by determining the transcriptomes of individual eggs from five sibling mothers and measuring the differences within and between spawns. In zebrafish oogenesis, the gene-expression appears to be tightly regulated and at the same time the transcriptome shows a mother-specific signature. Next, the transcriptome dynamics of early zebrafish embryogenesis during the late blastula and early gastrula stages in 180 individual zebrafish embryos was studied by a high-resolution time series analysis. Along this developmental time course on average one individual embryo per minute was profiled. The transcriptome dynamics, as well as cellular factors influencing these transcriptome dynamics were extensively studied. Again a tight gene-expression regulation with a spawn specific signature was observed. Finally, possible gene-expression regulating factors were studied such as transcription factor binding sites and miRNAs. To study the latter, two small-RNA next-generation sequencing experiments were carried out, which showed a strict gene-expression regulation of the miR-430 family. Gene expression in these developmental stages appears to be regulated by many cellular processes.