| Schmidtea mediterranea is being established as a standard model system for studying regeneration and adult stem cells (ASCs). This is largely due to the developmental plasticity of the planarian and the abundant distribution and experimental accessibility of the ASCs. Techniques such as whole mount in situ hybridization (WISH), dsRNA-mediated interference (RNAi), utilization of halogenated thymidine analogs, and fluorescence activated cell sorting (FACS) allow for studying ASCs in vivo. The development of bioinformatic tools is also required for this to be a reality. Before the genome was sequenced, the main bioinformatic resource was a web-accessible database containing a large collection of expressed sequence tags (ESTs), up-to-date annotations, and expression data (SmedDb). With the sequencing of the genome and genome assembly available, it was feasible to create and use tools to annotate (MAKER) and distribute the genome, annotations and experimental data (SmedGD). With these tools in place it was possible to proceed with investigating biological questions, specifically epigenetic states and regulation of ASCs. Given the role chromatin architecture plays in defining the genomic output of a given cell, the multipotentiality found in the stem cells of S. mediterranea is likely to be no different. Canonical histones, H3, H4, H2A, H2B, the linker H1 and the variants H3.3, H2A.X, H2A.Z are present in the S. mediterranea genome. Immuno-cytochemistry has confirmed differential levels of histone posttranslational modifications in different cell types, specially acetylation and methylation of histone H3. My aims were to develop the necessary bioinformatic tools, establish protocols for studying epigenetics in planarian, to determine if any epigenetic modifying enzymes are localized to ASCs, and identify if any of these enzymes have specific roles in ASC function. I assisted in the development of systems to keep SmedDb up-to-date, in the annotation (MAKER) of the genome, and the web accessibility of the genome and associated data (SmedGD). I created a library of genes for approximately 90 epigenetic modifying enzymes. The expression patterns of these genes were visualized with WISH and their function was perturbed with RNAi. Six genes were identified that are likely to have key roles in stem cell self-renewal, maintenance, and differentiation. |
