ArticleBMC genomics2013
Analysis of the spatial and temporal arrangement of transcripts over intergenic regions in the human malarial parasite Plasmodium falciparum.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing.PloS one · 2022Article
- Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.PLoS computational biology · 2021Article
- In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework.Malaria journal · 2021Article
- Identifying transcript 5' capped ends inPeerJ · 2021Article
- Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms.BMC genomics · 2020Article
- High-Resolution Mapping of Transcription Initiation in the Asexual Stages ofFrontiers in cellular and infection microbiology · 2020Article
- Translational Control in the Latency of Apicomplexan Parasites.Trends in parasitology · 2017Review
- Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum.BMC genomics · 2017Article
- Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva.BMC genomics · 2016Article
- Article
- Triaging informative cis-regulatory elements for the combinatorial control of temporal gene expression during Plasmodium falciparum intraerythrocytic development.Parasites & vectors · 2015Article
- Genome-wide analysis in Plasmodium falciparum reveals early and late phases of RNA polymerase II occupancy during the infectious cycle.BMC genomics · 2014Article
- Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites.BMC genomics · 2014Article
- Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum.Nature methods · 2014Article
- Transcript maturation in apicomplexan parasites.Current opinion in microbiology · 2014Review
- Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum.Genome biology · 2013Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe ability of the human malarial parasite Plasmodium falciparum to invade, colonise and multiply within diverse host environments, as well as to manifest its virulence within the human host, are activities tightly linked to the temporal and spatial control of gene expression. Yet, despite the wealth of high throughput transcriptomic data available for this organism there is very little information regarding the location of key transcriptional landmarks or their associated cis-acting regulatory elements. Here we provide a systematic exploration of the size and organisation of transcripts within intergenic regions to yield surrogate information regarding transcriptional landmarks, and to also explore the spatial and temporal organisation of transcripts over these poorly characterised genomic regions.
resultsUtilising the transcript data for a cohort of 105 genes we demonstrate that the untranscribed regions of mRNA are large and apportioned predominantly to the 5' end of the open reading frame. Given the relatively compact size of the P. falciparum genome, we suggest that whilst transcriptional units are likely to spatially overlap, temporal co-transcription of adjacent transcriptional units is actually limited. Critically, the size of intergenic regions is directly dependent on the orientation of the two transcriptional units arrayed over them, an observation we extend to an analysis of the complete sequences of twelve additional organisms that share moderately compact genomes.
conclusionsOur study provides a theoretical framework that extends our current understanding of the transcriptional landscape across the P. falciparum genome. Demonstration of a consensus gene-spacing rule that is shared between P. falciparum and ten other moderately compact genomes of apicomplexan parasites reveals the potential for our findings to have a wider impact across a phylum that contains many organisms important to human and veterinary health.
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