Motivation: Phosphodiesterase 4 (PDE4) is an enzyme that has been targeted for inflammatory disorders, including asthma, chronic obstructive pulmonary disease, and central nervous system (CNS) injury/disease. PDE4 has a large number of potential isoforms with apparent tissue and functional specificity. Potential roles of the different PDE4 isoforms within the central nervous system and other tissue types were studied using all four known rat PDE4 paralogs (PDE4a, PDE4b, PDE4c and PDE4d). Splicing patterns of each of these genes were examined using a computational method to align rat ESTs to the corresponding chromosomal and mRNA sequences. Each EST was examined for its corresponding splice pattern and tissue type in order to gain more insight into PDE4 isoform tissue specificity.

Results: A total of 812,497 rat EST sequences were extracted from GenBank/dbEST (dated 7-17-06). Comparisons of these ESTS to the four PDE4 paralogs resulted in 4 single-exon and 11 spliced, multi-exon patterns in PDE4a; 10 single-exon and 13 spliced, multi-exon patterns in PDE4b; 4 single-exon and 25 multiple exon patterns in PDE4c; and 14 single-exon and 9 spliced, multi-exon patterns in PDE4d. Computational analysis of the multi-exon hits yield a total of 18 previously undetected exons from isoforms within thePDE4a, PDE4b, and PDE4d classes typically associated with the central nervous system that also appear to have some level of tissue specificity. Twelve of these occur between the first two exons in the variable region of the PDE4 gene. An additional six previously undetected exons are found in the PDE4c class. These novel exons are expressed in the 3’ end of the gene, which has been previously thought to be a region of low variability. One of these PDE4c exons appears to have a heart tissue specificity for expression.

Keywords: PDE4, bioinformatics, computational biology, EST, splicing pattern