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Centromere sequence and dynamics in Dictyostelium discoideum.

Glöckner G, Heidel AJ - Nucleic Acids Res. (2009)

Bottom Line: They mainly consist of one type of transposons that is confined to centromeric regions.Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum.In addition to insights into the centromere organization and dynamics of a protist eukaryote, this work also provides a starting point for the analysis of the evolution of centromere structures in social amoebas by comparative genomics.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany. gernot@fli-leibniz.de

ABSTRACT
Centromeres play a pivotal role in the life of a eukaryote cell, perform an essential and conserved function, but this has not led to a standard centromere structure. It remains currently unclear, how the centromeric function is achieved by widely differing structures. Since centromeres are often large and consist mainly of repetitive sequences they have only been analyzed in great detail in a handful of organisms. The genome of Dictyostelium discoideum, a valuable model organism, was described a few years ago but its centromere organization remained largely unclear. Using available sequence information we reconstructed the putative centromere organization in three of the six chromosomes of D. discoideum. They mainly consist of one type of transposons that is confined to centromeric regions. Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum. One centromere probably has expanded recently, whereas another underwent major rearrangements. In addition to insights into the centromere organization and dynamics of a protist eukaryote, this work also provides a starting point for the analysis of the evolution of centromere structures in social amoebas by comparative genomics.

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Centromere structures. Symbols above each chromosome's center line show features oriented towards the core of the chromosome, features below the line are oriented towards the upper end of the chromosome. The DIRS elements are depicted as green half-arrows. DNA transposons are in blue and skipper and DGLT elements in brown. The red triangles show the rDNA palindrome sequence whereas the orange hue indicates nonunique sequences not derived from transposons. Black triangles above the figures indicate gap locations.
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Figure 1: Centromere structures. Symbols above each chromosome's center line show features oriented towards the core of the chromosome, features below the line are oriented towards the upper end of the chromosome. The DIRS elements are depicted as green half-arrows. DNA transposons are in blue and skipper and DGLT elements in brown. The red triangles show the rDNA palindrome sequence whereas the orange hue indicates nonunique sequences not derived from transposons. Black triangles above the figures indicate gap locations.

Mentions: Most elements are highly fragmented (Table 2), mainly due to subsequent insertions of further transposable elements. DIRS elements and DDT/Tdd elements show a pronounced preference to be located in regions enriched for the respective elements. For example in the centromere of chromosome 3 the region from 17 kb to 35 kb is occupied by DDT and Tdd elements only, whereas the region from 85 kb to 100 kb is comprised solely of DIRS elements (Figure 1). Skipper and Dictyostelium Gypsy like Transposon (DGLT) elements apparently show no such preference.Figure 1.


Centromere sequence and dynamics in Dictyostelium discoideum.

Glöckner G, Heidel AJ - Nucleic Acids Res. (2009)

Centromere structures. Symbols above each chromosome's center line show features oriented towards the core of the chromosome, features below the line are oriented towards the upper end of the chromosome. The DIRS elements are depicted as green half-arrows. DNA transposons are in blue and skipper and DGLT elements in brown. The red triangles show the rDNA palindrome sequence whereas the orange hue indicates nonunique sequences not derived from transposons. Black triangles above the figures indicate gap locations.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665215&req=5

Figure 1: Centromere structures. Symbols above each chromosome's center line show features oriented towards the core of the chromosome, features below the line are oriented towards the upper end of the chromosome. The DIRS elements are depicted as green half-arrows. DNA transposons are in blue and skipper and DGLT elements in brown. The red triangles show the rDNA palindrome sequence whereas the orange hue indicates nonunique sequences not derived from transposons. Black triangles above the figures indicate gap locations.
Mentions: Most elements are highly fragmented (Table 2), mainly due to subsequent insertions of further transposable elements. DIRS elements and DDT/Tdd elements show a pronounced preference to be located in regions enriched for the respective elements. For example in the centromere of chromosome 3 the region from 17 kb to 35 kb is occupied by DDT and Tdd elements only, whereas the region from 85 kb to 100 kb is comprised solely of DIRS elements (Figure 1). Skipper and Dictyostelium Gypsy like Transposon (DGLT) elements apparently show no such preference.Figure 1.

Bottom Line: They mainly consist of one type of transposons that is confined to centromeric regions.Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum.In addition to insights into the centromere organization and dynamics of a protist eukaryote, this work also provides a starting point for the analysis of the evolution of centromere structures in social amoebas by comparative genomics.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany. gernot@fli-leibniz.de

ABSTRACT
Centromeres play a pivotal role in the life of a eukaryote cell, perform an essential and conserved function, but this has not led to a standard centromere structure. It remains currently unclear, how the centromeric function is achieved by widely differing structures. Since centromeres are often large and consist mainly of repetitive sequences they have only been analyzed in great detail in a handful of organisms. The genome of Dictyostelium discoideum, a valuable model organism, was described a few years ago but its centromere organization remained largely unclear. Using available sequence information we reconstructed the putative centromere organization in three of the six chromosomes of D. discoideum. They mainly consist of one type of transposons that is confined to centromeric regions. Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum. One centromere probably has expanded recently, whereas another underwent major rearrangements. In addition to insights into the centromere organization and dynamics of a protist eukaryote, this work also provides a starting point for the analysis of the evolution of centromere structures in social amoebas by comparative genomics.

Show MeSH