Triaging informative cis-regulatory elements for the combinatorial control of temporal gene expression during Plasmodium falciparum intraerythrocytic development

Particle and Fibre Toxicology

Paul Horrocks²  Richard Emes¹  Karen Russell² 

[1] Advanced Data Analysis Centre, University of Nottingham, Leicestershire LE12 5RD, UK;Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK

关键词: Stage-specific expression;    Malaria;    Finding informative regulatory elements;    Combinatorial control;    Cis-acting DNA motifs;    Bioinformatics;    AP2 transcription factor;   

Others  :  1147049
DOI  :  10.1186/s13071-015-0701-0

 received in 2014-11-21, accepted in 2015-01-27,  发布年份 2015

【 摘 要 】

Background

Over 2700 genes are subject to stage-specific regulation during the intraerythrocytic development of the human malaria parasite Plasmodium falciparum. Bioinformatic analyses have identified a large number of over-represented motifs in the 5′ flanking regions of these genes that may act as cis-acting factors in the promoter-based control of temporal expression. Triaging these lists to provide candidates most likely to play a role in regulating temporal expression is challenging, but important if we are to effectively design in vitro studies to validate this role.

Methods

We report here the application of a repeated search of variations of 5′ flanking sequences from P. falciparum using the Finding Informative Regulatory Elements (FIRE) algorithm.

Results

Our approach repeatedly found a short-list of high scoring DNA motifs, for which cognate specific transcription factors were available, that appear to be typically associated with upregulation of mRNA accumulation during the first half of intraerythrocytic development.

Conclusions

We propose these cis-trans interactions may provide a combinatorial promoter-based control of gene expression to complement more global mechanisms of gene regulation that can account for temporal control during the second half of intraerythrocytic development.

【 授权许可】

   
2015 Russell et al.; licensee BioMed Central.

【 图 表 】

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