A global view of the nonprotein-coding transcriptome in Plasmodium falciparum.
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.
Institute of Experimental Pathology, ZMBE, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany.
Carsten A
CA
Raabe
Cecilia P
CP
Sanchez
Gerrit
G
Randau
Thomas
T
Robeck
Boris V
BV
Skryabin
Suresh V
SV
Chinni
Michael
M
Kube
Richard
R
Reinhardt
Guey Hooi
GH
Ng
Ravichandran
R
Manickam
Vladimir Y
VY
Kuryshev
Michael
M
Lanzer
Juergen
J
Brosius
Thean Hock
TH
Tang
Timofey S
TS
Rozhdestvensky
D000818:Animals; D001483:Base Sequence; D005091:Exons; D020869:Gene Expression Profiling; D015723:Gene Library; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000235:genetics / Q000378:metabolism; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016615:Telomere / Q000737:chemistry
D016372:RNA, Antisense; D000077278:RNA, Mitochondrial; D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated; D012313:RNA