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Theory of site-specific interactions of the combinatorial transcription factors with DNA
Published in
2010
Volume: 43
   
Issue: 19
Abstract
We derive a functional relationship between the mean first passage time associated with the concurrent binding of multiple transcription factors (TFs) at their respective combinatorial cis-regulatory module sites (CRMs) and the number n of TFs involved in the regulation of the initiation of transcription of a gene of interest. Our results suggest that the overall search time τs that is required by the n TFs to locate their CRMs which are all located on the same DNA chain scales with n as τs∝n α where α ∼ (2/5). When the jump size k that is associated with the dynamics of all the n TFs along DNA is higher than that of the critical jump size kc that scales with the size of DNA N as kc ∼ N2/3, we observe a similar power law scaling relationship and also the exponent α. When k < kc, α shows a strong dependence on both n and k. Apparently there is a critical number of combinatorial TFs nc ∼ 20 that is required to efficiently regulate the initiation of transcription of a given gene below which (2/5) < α < 1 and beyond which α > 1. These results seem to be independent of the initial distances between the TFs and their corresponding CRMs and also suggest that the maximum number of TFs involved in a given combinatorial regulation of the initiation of transcription of a gene of interest seems to be restricted by the degree of condensation of the genomic DNA. The optimum number mopt of roadblock protein molecules per genome at which the search time associated with these n TFs to locate their binding sites is a minimum seems to scale as mopt ∝ Ln α/2 where L is the sliding length of TFs whose maximum value seems to be such that L ≤ 104 bps for the E. coli bacterial genome. © 2010 IOP Publishing Ltd.
About the journal
JournalJournal of Physics A: Mathematical and Theoretical
ISSN17518113
Open AccessNo