We have applied established state-of-the-art tools to a variety challenging biological questions.

Most plants and animals have two copies of each chromosome in the normal chromosome set. Unbalanced numerical changes resulting from gains or losses of individual chromosomes (aneuploidy) usually have deleterious consequences. For example, Down syndrome in humans is caused by an extra (triplicate) copy of chromosome 21. Human tumor cells usually display numerous alterations in chromosome number and structure. Little is known about how changes in chromosome number influence gene activity and chromosome integrity, thereby perturbing physiology and development. The current literature, moreover, seems to be divided regarding the question whether in an organism with an extra chromosome most of the genes on the extra chromosome reflect the dosage increase. In such assessments, classical analyses face the problem that a large number of genes change in an asymmetric way, invalidating most commonly used normalization approaches. Using appropriate transforms, however, we could show in Huettel et al. (2008) that most genes indeed reflect the dosage increase, with only a small percentage being regulated differentially from this trend.

In Kanno et al. (2008), we could identify and, by way of domain-based sequence analysis, discuss a novel protein involved in RNA-directed DNA methylation. The protein is interesting in that it contains the SMC hinge but no other SMC domains.

References

1. Huettel B,^* Kreil DP,^* Matzke M, Matzke AJ (2008) Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana. PLoS Genet. 4, e1000226. (read more | Supplement)
2. Kanno T, Bucher E, Daxinger L, Huettel B, Böhmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet. 40, 670–5 (preprint on request)

[^*=joint first]

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