The Evolution of Functional Gene Clusters in Eukaryote Genomes. In: Pontarotti P, editor. Evolutionary Biology. Berlin: Springer Berlin Heidelberg; 2009. pp. 185-94. [DOI: 10.1007/978-3-642-00952-5_11]

The clustering of functionally related genes contributes to CNV-mediated disease

Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10⁻³). Using three different functional networks, we identified unexpectedly large numbers of functionally related genes within de novo CNVs from two large independent cohorts of individuals with developmental disorders. The presence of multiple functionally related genes was a significant predictor of a CNV's pathogenicity when compared to CNVs from apparently healthy individuals and a better predictor than the presence of known disease or haploinsufficient genes for larger CNVs. The functionally related genes found in the de novo CNVs belonged to 70% of all clusters of functionally related genes found across the genome. De novo CNVs were more likely to affect functional clusters and affect them to a greater extent than benign CNVs (P = 6 × 10⁻⁴). Furthermore, such clusters of functionally related genes are phenotypically informative: Different patients possessing CNVs that affect the same cluster of functionally related genes exhibit more similar phenotypes than expected (P < 0.05). The spanning of multiple functionally similar genes by single CNVs contributes substantially to how these variants exert their pathogenic effects.

Clustering of Pathogen-Response Genes in the Genome of Arabidopsis thaliana

Previously, we used heterologous expressed sequence tag (EST) mapping to generate a profile of 4 935 pathogen-response genes of Arabidopsis thaliana. In this work, we performed a computer analysis of this profile, revealing 1 594 non-homologous clustered genes distributed among all A. thaliana chromosomes, whose co-regulation may be related to host responses to pathogens. To supplement computer data, we arbitrarily selected two clusters and analyzed their expression levels in A. thaliana ecotypes Col-0 and C24 during infection with the yellow strain of Cucumber mosaic virus CMV(Y). Ecotype Col-0 is susceptible to CMV(Y), whereas C24 contains the dominant resistance gene RCY1. Upon infection with CMV(Y), all clustered genes were significantly activated in the resistant ecotype C24. In addition, we demonstrated that posttranslational histone modifications associated with trimethylation of histone H3 lysine 27 are most likely involved in regulation of several cluster genes described in this study. Overall, our experiments indicated that pathogen-response genes in the genome of A. thaliana may be clustered and co-regulated.