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Is the “Histone Code” an Organic Code?

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Abstract

Post-translational histone modifications and their biological effects have been described as a ‘histone code’. Independently, Barbieri used the term ‘organic code’ to describe biological codes in addition to the genetic code. He also provided the defining criteria for an organic code, but to date the histone code has not been tested against these criteria. This paper therefore investigates whether the histone code is a bona fide organic code. After introducing the use of the term ‘code’ in biology, the criteria a putative organic code such as the histone code must conform to in order to be recognised as an organic code are described. Our current knowledge of histones and their major post-translational modifications, and the specific protein binding domains that recognise and translate these into specific biological effects, is then reviewed in detail. The histone modification system is then placed in the context of an organic code and it is concluded that it fulfils all the requirements of an organic code. The marks produced on histones by processes such as acetylation and methylation act as organic signs that are translated into unique biological effects, their biological meanings. These translations are accomplished by effector proteins that consist of a binding domain that recognises a specific histone mark and a regulatory domain that mediates the biological effect. Crucially, these domains can be experimentally interchanged between different effector proteins, thus altering the rules that specify the relationships between sign and meaning. The effector proteins therefore fulfil the role of adaptor molecules.

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Acknowledgements

The authors thank Marcello Barbieri and Joachim de Beule for their boundless support and guidance. The authors acknowledge financial support from the South African National Research Foundation (NRF). Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors, and therefore the NRF does not accept any liability in regard thereto.

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  1. Department of Biochemistry, Stellenbosch University, Stellenbosch, 7600, South Africa

    Stefan Kühn & Jan-Hendrik S. Hofmeyr

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  1. Stefan Kühn
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  2. Jan-Hendrik S. Hofmeyr
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Correspondence to Jan-Hendrik S. Hofmeyr.

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Kühn, S., Hofmeyr, JH.S. Is the “Histone Code” an Organic Code?. Biosemiotics 7, 203–222 (2014). https://doi.org/10.1007/s12304-014-9211-2

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