BMC Genomics 2009, 10:295 http://www.biomedcentral.com/1471-2164/10/295 sRFceirgaiupl-trtsiem)a3enRdTn-oPnC-cRoedxinpgresstrsiaonndspr(Bofi–leadnutirsienngseB.tnranpsucsrsipetesd) doefvaegloropmupenotf nuasipnign parnidmnearpsisnp-reecliafitcefdotrrtahnesccroipdtisng (A – sense tran- Real-time RT-PCR expression profile during B. napus seed development using primers specific for the coding (A – sense transcripts) and non-coding strands (B – antisense transcripts) of a group of napin and napin-related transcripts. Square symbols represent napin transcripts most similar to 2S seed storage proteins AT4G27140, AT4G27150, AT4G27160, AT4G27170, while triangular symbols represent napin-related transcripts most similar to protease inhibitor/seed storage/lipid transfer protein AT5G54740. strongly represented within the 30 most abundantly expressed genes at 23 DAP and 35 DAP, e.g. a δ-vascular processing enzyme (δ-VPE) at 23 DAP. VPEs are cysteine- type proteases which were originally discovered to be responsible for maturation of seed storage proteins. In A. thaliana δ-VPE was found to be involved in developmental cell death during embryogenesis [26]. In general, pro- teases are considered to be key regulators of plant devel- opment involved in post-translational modification or activation of proteins and enzymes of diverse biological processes. Proteases play a role both in general protein turnover and in highly specific regulation of plant devel- opment. Dong et al. [27] also described an elevated expression of genes coding for subtilisin-like protease and vacuolar processing enzymes (VPE), consistent with seed endosperm development, along with early expression of lipid transfer proteins that are required for embryo pattern formation [28,29]. The high transcription levels of genes encoding seed storage proteins are also consistent with the results of Dong et al. [27] based on cDNA cloning and Northern blot expression profiling. On the other hand, our LongSAGE analysis revealed that transcripts encoded by the peroxidase gene AT4G21960 (Protein ID CAA66957) had a high abundance at 23 DAP and a sub- sequent drop in expression at 35 DAP, whereas Northern blot analysis appeared to reveal the opposite expression pattern. Such differences might be due to different specif- icities and resolutions of the two techniques, e.g. cross- hybridization of Northern blot probes with other closely related peroxidase transcripts. Antisense transcripts and sense-antisense transcript pairs (natural antisense transcripts, NATs) were found to be prevalent at both developmental stages investigated. Anti- sense transcripts were observed earlier in A. thaliana and rice cDNA/EST databases and confirmed using tag-based expression profiling approaches like SAGE or Massively Parallel Signature Sequencing [30], with matching to the sequenced genomes. In some of these studies it was noted that the sense and antisense transcripts of an overlapping NAT pair (cis-NATs) tend to be expressed in different tis- sues or different conditions. Furthermore, in cases where the sense and antisense transcripts of a NAT pair were expressed in the same library, one type of transcript was usually more abundant than the other. One speculation is that cis-antisense transcripts could be involved in down- regulating the expression levels of their target mRNA to achieve a low protein concentration by interfering with the transcription of their sense transcript. Due to the matching strategy we applied, the sense-antisense pair matches we found to the A. thaliana proteome might either indicate natural sense-antisense pair expression from one B. napus gene, or a concurrent expression of sense and antisense transcripts from paralogous B. napus genes. Either way, the results clearly indicate that a signif- icant number of antisense transcripts are expressed during Page 12 of 16 (page number not for citation purposes)