The small RNA complement of salamander limb regeneration

The exceptional regenerative capacities of the Mexican axolotl (Ambystoma mexicanum) have made it one of the most prominent organisms in the study of vertebrate regeneration. Here we present results of a genomic survey of small RNAs during limb regeneration using 454 high-throughput sequencing technology. We mapped small RNAs to an axolotl transcriptome assembly and to a representative library of repetitive DNA sequences sampled from the axolotl genome. Intriguingly, the majority of the axolotl small RNAs (~72%) mapped to repetitive DNA elements while only ~8% corresponded to microRNAs, some of which are differentially expressed following limb amputation. We also observed a novel class of small RNAs that have some of the features of transposon-related piRNAs, a RNA class that so far has been found predominantly in germ cells in other organisms. Other unusual small RNAs identified are likely to be endogenous siRNAs that emerge during the regenerative process; several of these were successfully mapped to assembled, protein-coding transcripts. These observations suggest that axolotl limb regeneration is associated with a diverse, small RNA repertoire that may reflect germinal tissues and stem cells.