Large scale gene expression profiling during intestine and body wall regeneration in the sea cucumber Apostichopus japonicus.

Sea cucumbers are fascinating invertebrate organisms because of their ability to rapidly regenerate many organs and appendages. In this study 454 cDNA sequencing method was used to characterize transcriptome in Apostichopus japonicus in order to investigate genes that are active in regeneration. Based on sequence similarity with known genes, our analysis identified 6590 genes expressed in the early stages of regeneration of the intestine and body wall. Assembled sequences were annotated with gene names and gene ontology terms. The transcription of genes associated with structural molecule activity was abundant during regeneration compared with the control sample (based on tissues from an uninjured animal). Many important genes involved in major intercellular signaling pathways associated with regeneration were identified, based on a KEGG database search. Our investigation also indicated the expression profiles of many genes associated with development, muscle dedifferentiation, ECM remolding and epigenetic reprogramming. During the early stages of regeneration we found that 324 genes were significantly up-regulated and 80 genes were significantly down-regulated. The top 25 genes that demonstrated the most significant differential expression during regeneration were verified using real-time PCR, which identified 90% consistency between these two approaches. The new candidate gene sequences, discovered for the first time in this study, will greatly enable future research - using the sea cucumber model - into the molecular mechanisms associated with intestine and body wall regeneration.