INSTITUTIONAL DIGITAL REPOSITORY

Anticipating response function in gene regulatory networks

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dc.contributor.author Gautam, P.
dc.contributor.author Sinha, S. K.
dc.date.accessioned 2021-11-29T06:25:55Z
dc.date.available 2021-11-29T06:25:55Z
dc.date.issued 2021-11-29
dc.identifier.uri http://localhost:8080/xmlui/handle/123456789/3259
dc.description.abstract The origin of an ordered genetic response of a complex and noisy biological cell is intimately related to the detailed mechanism of protein–DNA interactions present in a wide variety of gene regulatory (GR) systems. However, the quantitative prediction of genetic response and the correlation between the mechanism and the response curve is poorly understood. Here, we report in silico binding studies of GR systems to show that the transcription factor (TF) binds to multiple DNA sites with high cooperativity spreads from specific binding sites into adjacent non-specific DNA and bends the DNA. Our analysis is not limited only to the isolated model system but also can be applied to a system containing multiple interacting genes. The controlling role of TF oligomerization, TF–ligand interactions, and DNA looping for gene expression has been also characterized. The predictions are validated against detailed grand canonical Monte Carlo simulations and published data for the lac operon system. Overall, our study reveals that the expression of target genes can be quantitatively controlled by modulating TF–ligand interactions and the bending energy of DNA. en_US
dc.language.iso en_US en_US
dc.subject gene regulation en_US
dc.subject protein–DNA networks en_US
dc.subject statistical mechanics en_US
dc.subject response function en_US
dc.subject GCMC simulation en_US
dc.title Anticipating response function in gene regulatory networks en_US
dc.type Article en_US


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