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Epigenetic regulation and the variability of gene expression

Nature Genetics volume 40, pages 141–147 (2008)Cite this article

Abstract

We characterized the genetic variability of gene expression in terms of trans and cis variability for each yeast transcript. Genes that are highly regulated by nucleosomes showed a high degree of trans variability. From the expression profiles of mutants for various chromatin modifiers, we found that trans-variable genes are distinctly regulated at the chromatin level. The effect of chromatin regulators was highly significant, even when compared with that of transcription factors. The DNA-binding activities of transcription factors had a low influence on trans variability. In the case of the basal transcription factor TBP and TBP-associated factor TAF1, expression variability was coupled with the histone acetyltransferase activities of TAF1 and other factors, rather than with the binding of TBP to DNA. Additionally, we found that the correlation of TATA-box presence and expression variability could be explained in terms of chromatin regulation. The lack of activating histone modifications may subject TATA-containing promoters to chromatin regulation processes. Our results propose that epigenetic regulation has a central role in the variation and evolution of gene expression.

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Figure 1: Schematic of cis- and trans-variability identification.
Figure 2: Correspondence between expression variability and expression divergence.
Figure 3: Impact of chromatin regulation on expression variability.
Figure 4: Effects of transcription factors on expression variability.
Figure 5: High expression variability of TATA-containing genes explained by chromatin regulation effects.

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Acknowledgements

We thank R. Brem for valuable comments and suggestions and M. Kupiec for providing the chromatin modifier compendium. This work was supported by grants from the Korean Ministry of Science and Technology to Y.-J.K. (Creative Research Initiatives and Epigenomic Research of Human Disease).

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Authors and Affiliations

  1. Genome Regulation Center, Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul, 120-749, Korea

    Jung Kyoon Choi & Young-Joon Kim

  2. Department of Biochemistry, Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul, 120-749, Korea

    Young-Joon Kim

Authors
  1. Jung Kyoon Choi
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  2. Young-Joon Kim
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Contributions

J.K.C. designed the methodology, performed the analysis and wrote the paper; Y.-J.K. helped with the analysis and wrote and revised the paper.

Corresponding author

Correspondence to Young-Joon Kim.

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The authors declare no competing financial interests.

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Supplementary Table 1 (XLS 390 kb)

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Choi, J., Kim, YJ. Epigenetic regulation and the variability of gene expression. Nat Genet 40, 141–147 (2008). https://doi.org/10.1038/ng.2007.58

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