Monitoring the chromosome 2 intraerythrocytic transcriptome of Plasmodium falciparum using oligonucleotide arrays.
To test the feasibility of using short oligonucleotide probes to monitor transcript levels in Plasmodium falciparum, a microarray was manufactured containing 4,167 (25 base single-stranded) probes derived from the predicted coding region of P. falciparum chromosome 2. RNA samples from three asexual stages (rings, trophozoites, and schizonts) were labeled and hybridized to the arrays. These results were reproducible, and transcripts were detected for 69% of the 210 genes on chromosome 2. In addition, of the 145 expressed genes, 1/3 appeared to be differentially transcribed during the asexual cycle. Some regions of the chromosome appeared to be transcriptionally silent. Results were confirmed by Northern blot analysis and by quantitative reverse transcriptase-polymerase chain reaction. These data validate the use of relatively short 25-mers for monitoring the expression of a genome that is 82% AT rich.
Le Roch
Karine G
KG
Department of Cell Biology, The Scripps Research Institute, La Jolla, Calif 92037, USA. leroch@scripps.edu
Zhou
Yingyao
Y
Batalov
Sergei
S
Winzeler
Elizabeth A
EA
D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D002875:Chromosomes; D017931:DNA Primers; D004912:Erythrocytes / Q000469:parasitology*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010963:Plasmodium falciparum / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D017931:DNA Primers; D012333:RNA, Messenger