Sequence Analysis of a Functional Drosophila Centromere

Abstract

Centromeres are the site for kinetochore formation and spindle attachment and are embedded in heterochromatin in most eukaryotes. The repeat-rich nature of heterochromatin has hindered obtaining a detailed understanding of the composition and organization of heterochromatic and centromeric DNA sequences. Here, we report the results of extensive sequence analysis of a fully functional centromere present in the Drosophila Dp1187 minichromosome. Approximately 8.4% (31 kb) of the highly repeated satellite DNA (AATAT and TTCTC) was sequenced, representing the largest data set of Drosophila satellite DNA sequence to date. Sequence analysis revealed that the orientation of the arrays is uniform and that individual repeats within the arrays mostly differ by rare, single-base polymorphisms. The entire complex DNA component of this centromere (69.7 kb) was sequenced and assembled. The 39-kb "complex island" Maupiti contains long stretches of a complex A+T rich repeat interspersed with transposon fragments, and most of these elements are organized as direct repeats. Surprisingly, five single, intact transposons are directly inserted at different locations in the AATAT satellite arrays. We find no evidence for centromere-specific sequences within this centromere, providing further evidence for sequence-independent, epigenetic determination of centromere identity and function in higher eukaryotes. Our results also demonstrate that the sequence composition and organization of large regions of centric heterochromatin can be determined, despite the presence of repeated DNA.

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

“…There are very limited data sets on the literature concerning the analysis of satDNA junctions under this context, but they generally support the expectations of the model (McAllister and Werren, 1999;Schueler et al, 2001;Mravinac and Plohl, 2007). The homogeneity of a junction between the AATAT and TTCTC satellites in the D. melanogaster Dp1187 minichromosome is an exception (Sun et al, 2003). Probably other molecular mechanisms, such as replication slippage, might be important in the homogenization and amplification of simple satDNA repeats.…”

“…For example, in D. melanogaster, a different set of satDNA families are often located near one another on the same chromosome (Lohe et al, 1993) and sequence analysis of a 31 kb DNA centromeric region from the X-derived Dp1187 minichromosome revealed that the highly repeated satellites AATAT and TTCTC are organized in uniform arrays directly juxtaposed, with neither interspersion nor intervening DNA (Sun et al, 2003). In humans, the centromeric region of each chromosome contains at least one a-satellite DNA together with a unique combination of other satDNAs.…”

“…Whole-genome projects have many sharp junctions of satellites with generally uncharacterized genomic DNA, although accurate assembly of individual sequence reads into satDNA arrays may be extremely difficult (see Lee et al, 2006 for care required for assembly of blocks of HORs). Nevertheless, in examples that have been verified, abrupt transitions involving satDNA Â satDNA or satDNA Â defined non-satDNA junctions have been reported in a number of organisms, such as humans (Gaff et al, 1994), plants (Alkhimova et al, 2004;Lee et al, 2006) and insects (McAllister and Werren, 1999;Sun et al, 2003;Krzywinski et al, 2005).…”

The role of repetitive DNA in structure and evolution of sex chromosomes in plants

“…Centromeres are regions with lower recombination frequency (Beadle, 1932;Clarke and Carbon, 1980) and often exhibit interspersion of satellite sequences and TEs, as in cereals (Zhong et al, 2002), Arabidopsis (Copenhaver et al, 1999), insects (Sun et al, 2003) and fungi (Cambareri et al, 1998). There are indications of the evolutionary link between the centromere structure and TE's activity: centromeric satellite repeats may arise from DNA transposons (Kapitonov and Jurka, 1999).…”

Identification and Preliminary Analysis of Several Centromere‐associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

“…In contrast, the centromeres in eukaryotes that have been investigated are regions that vary in size from several hundred kilobases to a few megabases, such as fission yeast (S. pombe;Baum et al 1994), fruitfly (Drosophila melanogaster; Sun et al 1997Sun et al , 2003, and A. Kumekawa et al 2000Kumekawa et al , 2001Hosouchi et al 2002).…”