Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Genome-wide and positional homopolymeric tract enrichment at promoter-exon boundaries and exclusion of nucleosomes in Plasmodium spp. and related parasites

Long poly dA.dT tracts are enriched within the intergenic sequences of eukaryotic genomes where they appear to act as intrinsic regulators of nucleosome positioning. Previous studies of the incomplete genome of the human malarial parasite Plasmodium falciparum, reported a high enrichment of long poly dA.dT tracts, far above that expected for this AT rich genome (Zhou, et.al. 2004, Dechering, et.al. 1998). We report an analysis of the relative frequency, length and spatial arrangement of homopolymer tracts for the complete P. falciparum genome, extending this analysis to 12 additional Apicomplexan parasite genomes (Russell, et.al., 2014). Using nucleosome positioning data available for P. falciparum, we explore the correlation of poly dA.dT tracts with nucleosome positioning over key expression landmarks within intergenic regions. We describe three lineage-specific patterns of homopolymeric tract intergenic organization within these Apicomplexan parasites. Moreover, a striking enrichment pattern of long poly dA.dT tracts apparent in the intergenic regions of Plasmodium spp. uniquely extends into protein coding sequences. Also observed was a conserved spatial arrangement of elevated poly dA.dT frequencies immediately flanking translational start and stop sites (solid colored lines, Fig 1.) and over predicted core promoter sites (not shown). These three expression landmarks are all relatively depleted in nucleosomes (dashed line, Fig 1 panels) in P. falciparum (Ponts et.al. 2011) as would be expected for long poly dA.dT tracts acting as nucleosome exclusion sequences.


Fig. 1. Spatial distribution of nucleosome occupancy and poly dA.dT tracts over translational start and stop sites of P. falciparum ORF. Spatial distribution of observed tract frequencies (Fobs, right Y-axis) of N=5 (10 base bins) length dA (red line) and dT (blue line) over 400bp centered over translational start (A) and stop (B) sites. Experimental nucleosome occupancy (dashed line) presented as a log2 ratio of FAIRE to MAINE sequence reads (left Y-axis) increase in ratio indicates regions relatively deficient in nucleosomes.

    Y. Zhou, J. Bizzaro & K.A. Marx (2004) BMC Genomics 5:95-103

    K. Dechering et al. (1998) Nucleic Acids Research 26:4056-4062

    N. Ponts et al. (2011) Infection Genetics and Evolution 11:716-724.

Karen Russell 1
Chia-Ho Cheng2
Jeffrey W. Bizzaro2
Nadia Ponts3
Richard Emes4
Kenneth A. Marx2
Karine Le Roch3
Paul Horrocks1

1Institute of Science and Technology in Medicine, Keele University, Staffordshire, ST5 5BG, 2Department of Chemistry
University of Massachusetts
Lowell, MA, USA,
3Department of Biol. & Neurosci.
University of California at Riverside, CA, USA
4School of Veterinary Med. and Sci., University of Nottingham
Leicestershire, LE12 5RD

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