subtractive hybridization strategy for the identification of differentially expressed genes was performed between LPSchallenged
and naive Ciona intestinalis. This strategy allowed the characterization of two transcripts (Ci8short and Ci8long)
generated by the use of two Alternative Polyadenylation sites. The Ci8long transcript contains a protein domain with
relevant homology to several components of the Receptor Transporting Protein (RTP) family not present in the Ci8short
mRNA. By means of Real Time PCR and Northern Blot, the Ci8short and Ci8long transcripts showed a different pattern of
gene expression with the Ci8short mRNA being strongly activated after LPS injection in the pharynx. In situ hybridization
analysis demonstrated that the activation of the APA site also influenced the tissue localization of the Ci8short transcript.
This analysis showed that the Ci8long mRNA was expressed in hemocytes meanwhile the Ci8short mRNA was highly
transcribed also in vessel endothelial cells and in the epithelium of pharynx. These findings demonstrated that regulation of
gene expression based on different polyadenylation sites is an ancestral powerful strategy influencing both the level of
expression and tissue distribution of alternative transcripts