Institute of Experimental Pathology, ZMBE, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany.
Nucleic Acids Res. 2010 Jan;38(2):608-17. doi: 10.1093/nar/gkp895. Epub 2009 Oct 28.
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.
非蛋白编码 RNA（npcRNA）是一类重要的调控分子，它们在许多细胞途径中发挥作用。在这里，我们描述了人类疟原虫 Plasmodium falciparum 小非编码 RNA 转录组的实验鉴定和验证。我们鉴定了 630 个新的 npcRNA 候选物。基于序列和结构基序，其中 43 个属于小核仁 RNA（snoRNA）和小 Cajal 体特异性 RNA（scaRNA）的 C/D 和 H/ACA 盒亚类。我们进一步观察到一个功能性 H/ACA snoRNA 基因的外显子化，这可能有助于核糖体蛋白 L7a 基因表达的调控。一些小 npcRNA 候选物来自端粒和端粒旁重复区域，表明它们可能参与维持端粒完整性和端粒基因沉默。我们还检测到 328 个顺式编码反义非编码 RNA（asRNA），与广泛的生化途径中的 P. falciparum 蛋白编码基因互补，包括毒力和病理学决定因素。所有顺式编码的 asRNA 基因都表现出生命周期特异性的表达谱。除了一对相应的 sense-antisense 对中的一个外，我们推断出表达的一致性模式。我们的发现对更好地理解 P. falciparum 中的基因调控机制具有重要意义，揭示了一个扩展和复杂的 npcRNA 网络，可能控制管家基因和毒力因子的表达。
