Although being the focus of much research worldwide, the temporal and spatial dynamics of the transcriptome are still largely unknown. The primary challenges here are the complexity of the transcriptome and the limitations of omics experimentation.
Gene expression and degradation regulation
Not only is the transcriptome highly complex, changes in the transcriptome occur relatively quickly, orchestrated by a intertwined system of gene expression and RNA degradation. However, most omics experiments use a quite low-resolution temporal and spatial sampling, which will severely hamper correct interpretation. Usually practical or budgetary constraints result in sub-optimal experiments and subsequent sub-optimal results. We will approach transcriptomes by a large, high-resolution time series (e.g. 200 single Zebrafish embryos, 1 per 12 seconds) and subsequent in-situ hybridizations to dissect the transcriptome complexity into a manageable number of activated genes per cell type at each time point.
Although non-coding RNAs such as tRNA and rRNA are known for a long time, the discovery of small microRNA and long ncRNA have sparked a renewed interest. In view of the recent discoveries of sponge-RNA, it is anticipated that many types of (regulatory) RNA are still unknown. Given the potential of next-generation sequencing technology, we will explore transcriptomes for novel RNA molecules and try to determine their role in the regulation of the transcriptome.