Analysis of the Spatial and Temporal Arrangement of Transcripts over Intergenic Regions in the Human Malarial Parasite Plasmodium Falciparum

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2013 Apr 23

PMID 23601558

Citations 16

Authors

Karen Russell

Sandra Hasenkamp

Richard Emes

Paul Horrocks

Affiliations

Soon will be listed here.

Abstract

Background: The 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.

Results: Utilising 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.

Conclusions: Our 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.

Citing Articles

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing.

Shaw P, Kaewprommal P, Wongsombat C, Ngampiw C, Taechalertpaisarn T, Kamchonwongpaisan S PLoS One. 2022; 17(11):e0276956.

PMID: 36331983 PMC: 9635732. DOI: 10.1371/journal.pone.0276956.

Identifying transcript 5' capped ends in .

Shaw P, Piriyapongsa J, Kaewprommal P, Wongsombat C, Chaosrikul C, Teeravajanadet K PeerJ. 2021; 9:e11983.

PMID: 34527439 PMC: 8401752. DOI: 10.7717/peerj.11983.

Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes.

Menichelli C, Guitard V, Martins R, Lebre S, Lopez-Rubio J, Lecellier C PLoS Comput Biol. 2021; 17(4):e1008909.

PMID: 33861755 PMC: 8081344. DOI: 10.1371/journal.pcbi.1008909.

High-Resolution Mapping of Transcription Initiation in the Asexual Stages of .

Markus B, Waldman B, Lorenzi H, Lourido S Front Cell Infect Microbiol. 2021; 10:617998.

PMID: 33553008 PMC: 7854901. DOI: 10.3389/fcimb.2020.617998.

In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework.

Gunnarsson S, Prabakaran S Malar J. 2021; 20(1):71.

PMID: 33546698 PMC: 7866754. DOI: 10.1186/s12936-021-03598-1.

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