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Organization of the Genetic System: Proteins as Vehicles of Distinction

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DNA Information: Laws of Perception

Part of the book series: SpringerBriefs in Biochemistry and Molecular Biology ((BRIEFSBIOCHEM))

Abstract

The transcriptional regulatory networks (TRNs) integrate all the known interactions between the numerous transcription factors and their target genes. However, in the TRN, the DNA sites mediating the effects of the transcription factors appear as purely static entities providing the unique “addresses” for their cognate binding proteins, whereas in fact all these gene regulatory interactions are embedded in the physical chromosome, and are modulated by its configuration dynamics. By virtue of its construction, the TRN lacks all information about the structural dynamics of the DNA and its role in regulating the genetic activity. Notably, a gene is a discontinuous entity that can be expressed or not, thus being subject to “on or off” logic and therefore, belonging to the digital information type. Conversely, the physicochemical properties of DNA are determined not by individual base pairs, but by the additive interactions of successive base steps. The thermodynamic stability and superhelical density of the DNA are by definition continuous variables subject to “more or less” logic and belong to analog information type. It is this latter information that largely determines the chromosomal configuration dynamics, interactions between the remote DNA sites, and ultimately, the expression of the linear genetic code. Analysis of genetic regulation is greatly facilitated by introducing a formalism, allowing the dissection, and quantification of the inputs of digital and analog control mechanisms.

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Notes

  1. 1.

    We cannot elaborate here on the topic of various effects of small regulatory RNAs; for recent reviews see, e.g., Li and Izpisua Belmonte (2015), Ipsaro and Joshua-Tor (2015).

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  1. School of Engineering and Science, Jacobs University, Bremen, Germany

    Georgi Muskhelishvili

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  1. Georgi Muskhelishvili
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Muskhelishvili, G. (2015). Organization of the Genetic System: Proteins as Vehicles of Distinction. In: DNA Information: Laws of Perception. SpringerBriefs in Biochemistry and Molecular Biology. Springer, Cham. https://doi.org/10.1007/978-3-319-17425-9_4

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