The eukaryotic TRIM (TRIpartite Motif) super-family represents one of the largest classes of
putative E3 ubiquitin ligases involved in several processes, including epigenetic control of
development and disease. In the post-genomic era, new approaches allow genome-wide studies
of gene family. In particular, we performed a comprehensive analysis of the TRIM repertoire in
selected sea urchin species. By combining iterations of ab initio predictions and pairwise
comparative methods, we first retrieved the full complement of TRIM genes in
Strongylocentrotus purpuratus, whose full genome sequence was available. Interestingly, such a
DNA sequence set includes not previously classified, echinoderm-specific, TRIM genes as well
as multiple copies of known ones. We also retrieved a landscape of cDNA sequences from staged
EST libraries, indicating that most of these genes are actively transcribed during development.
Phylogenetic analysis of the deduced proteins, using set of TRIMs from various species, revealed
a degree of genetic variation between species. Worth of mention, we predicted the occurrence of
transposition events involving some of these genes, according with the documented rapid
evolution of this family. Next, we adopted heuristic algorithms and post-processing steps to
investigate the evolutionarily distant Paracentrotus lividus, Allocentrotus fragilis and Lytechinus
variegatus genomes, whose sequencing projects are actually in progress. We assembled partial
pools of TRIM genes and specifically associated them to EST-derived cDNA sequences. Such a
collection of data should provide a framework for unravel gene regulatory networks involving
TRIM genes from an evolutionary perspective. Indeed, in the Pl species, we have previously
isolated and functionally characterized the cDNA sequence encoding the first echinoderm
TRIM factor, Strim1. Here, we identified five strim1 genes, all sharing a intronless organization,
and roughly located their cis-regulatory apparatus