Nucleic Acids Research Advance Access published online on October 28, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp895
RNA |
A global view of the nonprotein-coding transcriptome in Plasmodium falciparum
1Institute of Experimental Pathology, ZMBE, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, 2Abteillung Parasitologie Hygiene Institut, Im Neuenheimer Feld 324, 69120 Heidelberg, 3MPI Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin-Dahlem, Germany and 4Advanced Medical and Dental Institute (AMDI), Institute for Molecular Research (INFORMM), USM 11800 Malaysia
*To whom correspondence should be addressed. Tel: +49 251 8358607; Fax: +49 251 8352134; Email: rozhdest{at}uni-muenster.de
Correspondence may also be addressed to Juergen Brosius. Tel: +49 251 8358511; Fax: +49 251 8358512; Email: RNA.world{at}uni-muenster.de
Correspondence may also be addressed to Thean-Hock Tang. Tel: +604 5622302; Fax: +6045792960; Email: tangth{at}amdi.usm.edu.my
Received August 25, 2009. Revised October 2, 2009. Accepted October 5, 2009.
Nonprotein-coding RNAs (npcRNAs) represent an important class of regulatory molecules that act in many cellular pathways. Here, we describe the experimental identification and validation of the small npcRNA transcriptome of the human malaria parasite Plasmodium falciparum. We identified 630 novel npcRNA candidates. Based on sequence and structural motifs, 43 of them belong to the C/D and H/ACA-box subclasses of small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). We further observed the exonization of a functional H/ACA snoRNA gene, which might contribute to the regulation of ribosomal protein L7a gene expression. Some of the small npcRNA candidates are from telomeric and subtelomeric repetitive regions, suggesting their potential involvement in maintaining telomeric integrity and subtelomeric gene silencing. We also detected 328 cis-encoded antisense npcRNAs (asRNAs) complementary to P. falciparum protein-coding genes of a wide range of biochemical pathways, including determinants of virulence and pathology. All cis-encoded asRNA genes tested exhibit lifecycle-specific expression profiles. For all but one of the respective sense–antisense pairs, we deduced concordant patterns of expression. Our findings have important implications for a better understanding of gene regulatory mechanisms in P. falciparum, revealing an extended and sophisticated npcRNA network that may control the expression of housekeeping genes and virulence factors.