Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite

Serial analysis of gene expression (SAGE) was applied to the malarial paras ite Plasmodium falciparum to characterize the comprehensive transcriptional profile of erythrocytic stages. A SAGE library of similar to 8335 tags rep resenting 4866 different genes was generated from 3D7 strain parasites. Bas ic local alignment search tool analysis of high abundance SAGE tags reveale d that a majority (88%) corresponded to 3D7 sequence, and despite the low c omplexity of the genome, 70% of these highly abundant tags matched unique l oci. Characterization of these suggested the major metabolic pathways that are used by the organism under normal culture conditions. Furthermore sever al tags expressed at high abundance (30% of tags matching to unique loci of the 3D7 genome) were derived from previously uncharacterized open reading frames, demonstrating the use of SAGE in genome annotation. The open platfo rm "profiling" nature of SAGE also lead to the important discovery of a nov el transcriptional phenomenon in the malarial pathogen: a significant numbe r of highly abundant tags that were derived from annotated genes (17%) corr esponded to antisense transcripts. These SAGE data were validated by two in dependent means, strand specific reverse transcription-polymerase chain rea ction and Northern analysis, where antisense messages were detected in both asexual and sexual stages. This finding has implications for transcription al regulation of Plasmodium gene expression.