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Artículo

Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions

Dalmasso, Maria CarolinaIcon ; Carmona, Santiago JavierIcon ; Ángel, Sergio OscarIcon ; Agüero, Fernan GonzaloIcon
Fecha de publicación: 13/01/2014
Editorial: BioMed Central
Revista: BMC Genomics
ISSN: 1471-2164
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Otras Ciencias de la Computación e Información; Bioquímica y Biología Molecular

Resumen

Background Chromosome ends are composed of telomeric repeats and subtelomeric regions, which are patchworks of genes interspersed with repeated elements. Although chromosome ends display similar arrangements in different species, their sequences are highly divergent. In addition, these regions display a particular nucleosomal composition and bind specific factors, therefore producing a special kind of heterochromatin. Using data from currently available draft genomes we have characterized these putative Telomeric Associated Sequences in Toxoplasma gondii. Results An all-vs-all pairwise comparison of T. gondii assembled chromosomes revealed the presence of conserved regions of ∼ 30 Kb located near the ends of 9 of the 14 chromosomes of the genome of the ME49 strain. Sequence similarity among these regions is ∼ 70%, and they are also highly conserved in the GT1 and VEG strains. However, they are unique to Toxoplasma with no detectable similarity in other Apicomplexan parasites. The internal structure of these sequences consists of 3 repetitive regions separated by high-complexity sequences without annotated genes, except for a gene from the Toxoplasma Specific Family. ChIP-qPCR experiments showed that nucleosomes associated to these sequences are enriched in histone H4 monomethylated at K20 (H4K20me1), and the histone variant H2A.X, suggesting that they are silenced sequences (heterochromatin). A detailed characterization of the base composition of these sequences, led us to identify a strong long-range compositional bias, which was similar to that observed in other genomic silenced fragments such as those containing centromeric sequences, and was negatively correlated to gene density. Conclusions We identified and characterized a region present in most Toxoplasma assembled chromosomes. Based on their location, sequence features, and nucleosomal markers we propose that these might be part of subtelomeric regions of T. gondii. The identified regions display a unique trinucleotide compositional bias, which is shared (despite the lack of any detectable sequence similarity) with other silenced sequences, such as those making up the chromosome centromeres. We also identified other genomic regions with this compositional bias (but no detectable sequence similarity) that might be functionally similar.
Palabras clave: Toxoplasma Gondii , Telomeric Associated Sites (Tas) , Subtelomeric Heterochromatin , Trinucleotide Compositional Bias
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/24842
URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-21
DOI: http://dx.doi.org/10.1186/1471-2164-15-21
Colecciones
Articulos(CCT - LA PLATA)
Articulos de CTRO.CIENTIFICO TECNOL.CONICET - LA PLATA
Articulos(IIB-INTECH)
Articulos de INST.DE INVEST.BIOTECNOLOGICAS - INSTITUTO TECNOLOGICO CHASCOMUS
Citación
Dalmasso, Maria Carolina; Carmona, Santiago Javier; Ángel, Sergio Oscar; Agüero, Fernan Gonzalo; Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions; BioMed Central; BMC Genomics; 15; 21; 13-1-2014; 21-36
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