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The Small Chromosomes of Trypanosoma brucei Involved in Antigenic Variation Are Constructed Around Repetitive Palindromes

¹ Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom ² School of Biological Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom

Most eukaryotic genomes contain large regions of satellite DNA. These arrays are often associated with essential chromosomal functions, but remain largely absent from genome projects because of difficulties in cloning and sequence assembly. The numerous small chromosomes of the parasite Trypanosoma brucei fall into this category, yet are critical to understanding the genome because of their role in antigenic variation. Their relatively small size, however, makes them particularly amenable to physical mapping. We have produced fine-resolution maps of 17 complete minichromosomes and partial maps of two larger intermediate-sized chromosomes. This revealed a canonical structure shared by both chromosomal classes based around a large central core of 177-bp repeats. Around the core are variable-length genic regions, the lengths of which define chromosomal class. We show the core region to be a repetitive palindrome with a single inversion point common to all the chromosomes of both classes, suggesting a mechanism of genesis for these chromosomes. Moreover, palindromy appears to be a feature of (peri)centromeres in other species that can be easily overlooked. We propose that sequence inversion is one of the higher-order sequence motifs that confer chromosomal stability.

³ Present address: Department of Biological Sciences, University of Hull, Hull, HU6 7RX, UK.

⁴ Corresponding author.
E-MAIL keith.gull{at}pathology.oxford.ac.uk; FAX 44-1865-285-691.

[Supplemental material is available online at www.genome.org. The following people kindly provided reagents, samples, or unpublished information as indicated in the paper: S. Melville and P. Borst.]

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