A global view of the nonprotein-coding transcriptome in Plasmodium falciparum

Application of genomics to field investigations of malaria by the international centers of excellence for malaria research

Success of the global research agenda toward eradication of malaria will depend on development of new tools, including drugs, vaccines, insecticides and diagnostics. Genomic information, now available for the malaria parasites, their mosquito vectors, and human host, can be leveraged to both develop these tools and monitor their effectiveness. Although knowledge of genomic sequences for the malaria parasites, Plasmodium falciparum and Plasmodium vivax, have helped advance our understanding of malaria biology, simply knowing this sequence information has not yielded a plethora of new interventions to reduce the burden of malaria. Here we review and provide specific examples of how genomic information has increased our knowledge of parasite biology, focusing on P. falciparum malaria. We then discuss how population genetics can be applied toward the epidemiological and transmission-related goals outlined by the International Centers of Excellence for Malaria Research groups recently established by the National Institutes of Health. Finally, we propose genomics is a research area that can promote coordination and collaboration between various ICEMR groups, and that working together as a community can significantly advance the value of this information toward reduction of the global malaria burden.

PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites

In Plasmodium falciparum, perinuclear subtelomeric chromatin conveys monoallelic expression of virulence genes. However, proteins that directly bind to chromosome ends are poorly described. Here we identify a novel DNA/RNA-binding protein family that bears homology to the archaeal protein Alba (Acetylation lowers binding affinity). We isolated three of the four PfAlba paralogs as part of a molecular complex that is associated with the P. falciparum-specific TARE6 (Telomere-Associated Repetitive Elements 6) subtelomeric region and showed in electromobility shift assays (EMSAs) that the PfAlbas bind to TARE6 repeats. In early blood stages, the PfAlba proteins were enriched at the nuclear periphery and partially co-localized with PfSir2, a TARE6-associated histone deacetylase linked to the process of antigenic variation. The nuclear location changed at the onset of parasite proliferation (trophozoite-schizont), where the PfAlba proteins were also detectable in the cytoplasm in a punctate pattern. Using single-stranded RNA (ssRNA) probes in EMSAs, we found that PfAlbas bind to ssRNA, albeit with different binding preferences. We demonstrate for the first time in eukaryotes that Alba-like proteins bind to both DNA and RNA and that their intracellular location is developmentally regulated. Discovery of the PfAlbas may provide a link between the previously described subtelomeric non-coding RNA and the regulation of antigenic variation.

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

BACKGROUND

It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene models for those expressed in sexual or mosquito stages have not been validated. Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown.

RESULTS

We have sequenced seven bidirectional libraries from ring, early and late trophozoite, schizont, gametocyte II, gametocyte V, and ookinete, and four strand-specific libraries from late trophozoite, schizont, gametocyte II, and gametocyte V of the 3D7 parasites. Alignment of the cDNA sequences to the 3D7 reference genome revealed stage-specific antisense transcripts and novel intron-exon splicing junctions. Sequencing of strand-specific cDNA libraries suggested that more genes are expressed in one direction in gametocyte than in schizont. Alternatively spliced genes, antisense transcripts, and stage-specific expressed genes were also characterized.

CONCLUSIONS

It is necessary to continue to sequence cDNA from different developmental stages, particularly those of non-erythrocytic stages. The presence of antisense transcripts in some gametocyte and ookinete genes suggests that these antisense RNA may play an important role in gene expression regulation and parasite development. Future gene expression studies should make use of directional cDNA libraries. Antisense transcripts may partly explain the observed discrepancy between levels of mRNA and protein expression.

How old are RNA networks?

Some major classes of RNAs (such as mRNA, rRNA, tRNA and RNase P) are ubiquitous in all living systems so are inferred to have arisen early during the origin of life. However, the situation is not so clear for the system of RNA regulatory networks that continue to be uncovered, especially in eukaryotes. It is increasingly being recognised that networks of small RNAs are important for regulation in all cells, but it is not certain whether the origin of these networks are as old as rRNAs and tRNA. Another group of ncRNAs, including snoRNAs, occurs mainly in archaea and eukaryotes and their ultimate origin is less certain, although perhaps the simplest hypothesis is that they were present in earlier stages of life and were lost from bacteria. Some RNA networks may trace back to an early stage when there was just RNA and proteins, the RNP-world; before DNA.

Noncoding RNA, antigenic variation, and the virulence genes of Plasmodium falciparum

Long non-coding RNAs (lncRNA) are being increasingly recognized as important regulators of gene expression. A recent paper in Genome Biology reports the identification of a lncRNA family in Plasmodium falciparum, the cause of the most deadly form of malaria, that may help to explain the mechanism of antigenic variation in virulence genes of this important pathogen.

The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome

New deep RNA sequencing methodologies in transcriptome analyses identified a wealth of novel nonprotein-coding RNAs (npcRNAs). Recently, deep sequencing was used to delineate the small npcRNA transcriptome of the human pathogen Vibrio cholerae and 627 novel npcRNA candidates were identified. Here, we report the detection of 223 npcRNA candidates in V. cholerae by different cDNA library construction and conventional sequencing methods. Remarkably, only 39 of the candidates were common to both surveys. We therefore examined possible biasing influences in the transcriptome analyses. Key steps, including tailing and adapter ligations for generating cDNA, contribute qualitatively and quantitatively to the discrepancies between data sets. In addition, the state of 5'-end phosphorylation influences the efficiency of adapter ligation and C-tailing at the 3'-end of the RNA. Finally, our data indicate that the inclusion of sample-specific molecular identifier sequences during ligation steps also leads to biases in cDNA representation. In summary, even deep sequencing is unlikely to identify all RNA species, and caution should be used for meta-analyses among alternatively generated data sets.

A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs

BACKGROUND

Mounting evidence suggests a major role for epigenetic feedback in Plasmodium falciparum transcriptional regulation. Long non-coding RNAs (lncRNAs) have recently emerged as a new paradigm in epigenetic remodeling. We therefore set out to investigate putative roles for lncRNAs in P. falciparum transcriptional regulation.

RESULTS

We used a high-resolution DNA tiling microarray to survey transcriptional activity across 22.6% of the P. falciparum strain 3D7 genome. We identified 872 protein-coding genes and 60 putative P. falciparum lncRNAs under developmental regulation during the parasite's pathogenic human blood stage. Further characterization of lncRNA candidates led to the discovery of an intriguing family of lncRNA telomere-associated repetitive element transcripts, termed lncRNA-TARE. We have quantified lncRNA-TARE expression at 15 distinct chromosome ends and mapped putative transcriptional start and termination sites of lncRNA-TARE loci. Remarkably, we observed coordinated and stage-specific expression of lncRNA-TARE on all chromosome ends tested, and two dominant transcripts of approximately 1.5 kb and 3.1 kb transcribed towards the telomere.

CONCLUSIONS

We have characterized a family of 22 telomere-associated lncRNAs in P. falciparum. Homologous lncRNA-TARE loci are coordinately expressed after parasite DNA replication, and are poised to play an important role in P. falciparum telomere maintenance, virulence gene regulation, and potentially other processes of parasite chromosome end biology. Further study of lncRNA-TARE and other promising lncRNA candidates may provide mechanistic insight into P. falciparum transcriptional regulation.

Highly conserved gene arrangement of the mitochondrial genomes of 23 Plasmodium species

Mitochondrial (mt) genomes from diverse phylogenetic groups vary considerably in size, structure and organization. The genus Plasmodium, the causative agent of malaria, has the smallest mt genome in the form of a tandemly repeated, linear element of 6 kb. The Plasmodium mt genome encodes only three protein genes (cox1, cox3 and cob) and large- and small-subunit ribosomal RNA (rRNA) genes, which are highly fragmented with 19 identified rRNA pieces. The complete mt genome sequences of 21 Plasmodium species have been published but a thorough investigation of the arrangement of rRNA gene fragments has been undertaken for only Plasmodium falciparum, the human malaria parasite. In this study, we determined the arrangement of mt rRNA gene fragments in 23 Plasmodium species, including two newly determined mt genome sequences from P. gallinaceum and P. vinckei vinckei, as well as Leucocytozoon caulleryi, an outgroup of Plasmodium. Comparative analysis reveals complete conservation of the arrangement of rRNA gene fragments in the mt genomes of all the 23 Plasmodium species and L. caulleryi. Surveys for a new rRNA gene fragment using hidden Markov models enriched with recent mt genome sequences led us to suggest the mtR-26 sequence as a novel candidate LSU rRNA fragment in the mt genomes of the 24 species. Additionally, we found 22-25 bp-inverted repeat sequences, which may be involved in the generation of lineage-specific mt genome arrangements after divergence from a common ancestor of the genera Eimeria and Plasmodium/Leucocytozoon.

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

Over 50% of genes in Plasmodium falciparum, the deadliest human malaria parasite, contain predicted introns, yet experimental characterization of splicing in this organism remains incomplete. We present here a transcriptome-wide characterization of intraerythrocytic splicing events, as captured by RNA-Seq data from four timepoints of a single highly synchronous culture. Gene model-independent analysis of these data in conjunction with publically available RNA-Seq data with HMMSplicer, an in-house developed splice site detection algorithm, revealed a total of 977 new 5' GU-AG 3' and 5 new 5' GC-AG 3' junctions absent from gene models and ESTs (11% increase to the current annotation). In addition, 310 alternative splicing events were detected in 254 (4.5%) genes, most of which truncate open reading frames. Splicing events antisense to gene models were also detected, revealing complex transcriptional arrangements within the parasite's transcriptome. Interestingly, antisense introns overlap sense introns more than would be expected by chance, perhaps indicating a functional relationship between overlapping transcripts or an inherent organizational property of the transcriptome. Independent experimental validation confirmed over 30 new antisense and alternative junctions. Thus, this largest assemblage of new and alternative splicing events to date in Plasmodium falciparum provides a more precise, dynamic view of the parasite's transcriptome.

H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3

Epigenetic regulatory mechanisms and their enzymes are promising targets for malaria therapeutic intervention; however, the epigenetic component of gene expression in P. falciparum is poorly understood. Dynamic or stable association of epigenetic marks with genomic features provides important clues about their function and helps to understand how histone variants/modifications are used for indexing the Plasmodium epigenome. We describe a novel, linear amplification method for next-generation sequencing (NGS) that allows unbiased analysis of the extremely AT-rich Plasmodium genome. We used this method for high resolution, genome-wide analysis of a histone H2A variant, H2A.Z and two histone H3 marks throughout parasite intraerythrocytic development. Unlike in other organisms, H2A.Z is a constant, ubiquitous feature of euchromatic intergenic regions throughout the intraerythrocytic cycle. The almost perfect colocalisation of H2A.Z with H3K9ac and H3K4me3 suggests that these marks are preferentially deposited on H2A.Z-containing nucleosomes. By performing RNA-seq on 8 time-points, we show that acetylation of H3K9 at promoter regions correlates very well with the transcriptional status whereas H3K4me3 appears to have stage-specific regulation, being low at early stages, peaking at trophozoite stage, but does not closely follow changes in gene expression. Our improved NGS library preparation procedure provides a foundation to exploit the malaria epigenome in detail. Furthermore, our findings place H2A.Z at the cradle of P. falciparum epigenetic regulation by stably defining intergenic regions and providing a platform for dynamic assembly of epigenetic and other transcription related complexes.

Plasmodium falciparum is a unicellular pathogen that is responsible for the most severe form of malaria. Similar to other eukaryotic organisms, its genome is organized into chromosomes by proteins called histones. Modification or replacement of these histones has marked effects on the packaging grade of DNA and instructs the recruitment of protein complexes, thereby regulating essential cellular processes such as gene expression and replication. Here we unveil the genome-wide localization of two histone H3 modifications (K9ac/K4me3) and a histone variant, H2A.Z, during development of the parasite in the human red blood cells. We find that all three epigenetic features are predominantly present in intergenic regions of the P. falciparum genome, suggesting an interconnecting role in regulation of gene expression. H2A.Z levels appear to be largely invariable throughout intraerythrocytic development while placement/removal of the histone marks is dynamic with H3K9ac and H3K4me3 being transcription-coupled and stage-specific, respectively. These observations support a model in which H2A.Z-containing nucleosomes serve to demarcate regulatory regions in the parasite's genome and promote transcription initiation by guiding chromatin modifying and transcription initiating complexes. The findings and methodological developments presented in this paper provide a cornerstone for future epigenome research in eukaryotic pathogens and vital information to understand and to interfere with parasite development and survival.

Long- and short-term selective forces on malaria parasite genomes

Plasmodium parasites, the causal agents of malaria, result in more than 1 million deaths annually. Plasmodium are unicellular eukaryotes with small ∼23 Mb genomes encoding ∼5200 protein-coding genes. The protein-coding genes comprise about half of these genomes. Although evolutionary processes have a significant impact on malaria control, the selective pressures within Plasmodium genomes are poorly understood, particularly in the non-protein-coding portion of the genome. We use evolutionary methods to describe selective processes in both the coding and non-coding regions of these genomes. Based on genome alignments of seven Plasmodium species, we show that protein-coding, intergenic and intronic regions are all subject to purifying selection and we identify 670 conserved non-genic elements. We then use genome-wide polymorphism data from P. falciparum to describe short-term selective processes in this species and identify some candidate genes for balancing (diversifying) selection. Our analyses suggest that there are many functional elements in the non-genic regions of these genomes and that adaptive evolution has occurred more frequently in the protein-coding regions of the genome.

Epigenetics in Plasmodium: what do we really know?

In the burgeoning field of Plasmodium gene expression, there are--to borrow some famous words from a former U.S. Secretary of Defense--"known knowns, known unknowns, and unknown unknowns." This is in itself an important achievement, since it is only in the past decade that facts have begun to move from the third category into the first. Nevertheless, much remains in the middle ground of known or suspected "unknowns." It is clear that the malaria parasite controls vital virulence processes such as host cell invasion and cytoadherence at least partly via epigenetic mechanisms, so a proper understanding of epigenetic transcriptional control in this organism should have great clinical relevance. Plasmodium, however, is an obligate intracellular parasite: it operates not in a vacuum but rather in the complicated context of its metazoan hosts. Therefore, as valuable data about the parasite's basic epigenetic machinery begin to emerge, it becomes increasingly important to relate in vitro studies to the situation in vivo. This review will focus upon the challenge of understanding Plasmodium epigenetics in an integrated manner, in the human and insect hosts as well as the petri dish.

Non-coding RNA in apicomplexan parasites

In recent years it has became evident that the transcriptome of most species has little protein-coding capacity and that the abundance of non-coding RNA was previously overlooked. Non-coding RNAs were initially thought to be transcriptional noise, however, a growing number of studies is showing that many of these RNAs have important regulatory functions. Here, we review the progress done in apicomplexan parasites in this rapidly growing field.

Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi

We experimentally identified and characterized 97 novel, non-protein-coding RNA candidates (npcRNAs) from the human pathogen Salmonella enterica serovar Typhi (hereafter referred to as S. typhi). Three were specific to S. typhi, 22 were restricted to Salmonella species and 33 were differentially expressed during S. typhi growth. We also identified Salmonella Pathogenicity Island-derived npcRNAs that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of S. typhi. An in-depth characterization of S. typhi StyR-3 npcRNA showed that it specifically interacts with RamR, the transcriptional repressor of the ramA gene, which is involved in the multidrug resistance (MDR) of Salmonella. StyR-3 interfered with RamR–DNA binding activity and thus potentially plays a role in regulating ramA gene expression, resulting in the MDR phenotype. Our study also revealed a large number of cis-encoded antisense npcRNA candidates, supporting previous observations of global sense–antisense regulatory networks in bacteria. Finally, at least six of the npcRNA candidates interacted with the S. typhi Hfq protein, supporting an important role of Hfq in npcRNA networks. This study points to novel functional npcRNA candidates potentially involved in various regulatory roles including the pathogenicity of S. typhi.