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Evolution of chromosome organization driven by selection for reduced gene expression noise

Nature Genetics volume 39, pages 945–949 (2007)Cite this article

Abstract

The distribution of genes on eukaryotic chromosomes is nonrandom, but the reasons behind this are not well understood. The commonly observed clustering of essential genes is a case in point. Here we model and test a new hypothesis. Essential proteins are unusual in that random fluctuations in abundance (noise) can be highly deleterious. We hypothesize that persistently open chromatin domains are sinks for essential genes, as they enable reduced noise by avoidance of transcriptional bursting associated with chromatin remodeling. Simulation of the model captures clustering and correctly predicts that (i) essential gene clusters are associated with low nucleosome occupancy (ii) noise-sensitive nonessential genes cluster with essential genes (iii) nonessential genes of similar knockout fitness are physically linked (iv) genes in domains rich in essential genes have low noise (v) essential genes are rare subtelomerically and (vi) essential gene clusters are preferentially conserved. We conclude that different noise characteristics of different genomic domains favors nonrandom gene positioning. This has implications for gene therapy and understanding transgenic phenotypes.

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Figure 1: Essential gene clusters are in open chromatin regions.
Figure 2: The evolution of essential gene clusters along a chromosome.
Figure 3: Dependence of essential gene clustering on the noise sensitivities of nonessential genes.
Figure 4: Influence of density of essential genes flanking a given gene on the noise level of the focal gene.

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Acknowledgements

N.B. is funded by a fellowship from the Canadian Institutes for Health Research.

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  1. Nizar N. Batada and Laurence D. Hurst are in the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. l.d.hurst@bath.ac.uk or nizar.batada@gmail.com,

    Nizar N Batada & Laurence D Hurst

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Supplementary Figures 1–3, Supplementary Tables 1–3, Supplementary Methods, Supplementary Discussion (PDF 591 kb)

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Batada, N., Hurst, L. Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet 39, 945–949 (2007). https://doi.org/10.1038/ng2071

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