The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites (SBSs). It is an intriguing question how the naturally occurring TFs and their SBSs are designed to manage the retarding effects of such randomly occurring traps. We develop a simple random walk model on the site-specific binding of TFs with genomic DNA in the presence of sequence traps. Our dynamical model predicts that (a) the retarding effects of traps will be minimum when the traps are arranged around the SBS such that there is a negative correlation between the binding strength of TFs with traps and the distance of traps from the SBS and (b) the retarding effects of sequence traps can be appeased by the condensed conformational state of DNA. Our computational analysis results on the distribution of sequence traps around the putative binding sites of various TFs in mouse and human genome clearly agree well the theoretical predictions. We propose that the distribution of traps can be used as an additional metric to efficiently identify the SBSs of TFs on genomic DNA. © 2016 IOP Publishing Ltd.

Rajamanickam Murugan

Department Of Biotechnology

Gnanapragasam Niranjani

protein binding

transcription factor

Animal

binding site

biological model

chemistry

Human

HUMAN GENOME

mouse

Animals

Binding sites

GENOME, HUMAN

Humans

Mice

Models, Genetic

Transcription Factors

Fulltext

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IIT Madras

Physical Biology

We show that nucleosomes exert a maximal amount of hindrance to the one-dimensional diffusion of transcription factors (TFs) when they are present between TFs and their cognate sites on DNA. The effective one-dimensional diffusion coefficient of TFs (χTF) decreases with a rise in the free-energy barrier (μNU) of the sliding of nucleosomes as χTF∝exp(−μNU). The average time (ηL) required by TFs to slide over L sites on DNA increases with μNU as ηL∝exp(μNU). When TFs move close to nucleosomes, then they exhibit typical subdiffusion. Nucleosomes can enhance the search dynamics of TFs when TFs are present between nucleosomes and TF binding sites. These results suggest that nucleosome-depleted regions around the cognate sites of TFs are mandatory for efficient site-specific binding of TFs. Remarkably, the genome-wide in vivo positioning pattern of TFs shows a maximum at their specific binding sites where the occupancy of nucleosomes shows a minimum. This could be a consequence of an increasing level of breathing dynamics of nucleosome cores and decreasing levels of fluctuations in the DNA binding domains of TFs as they move across TF binding sites. The dynamics of TFs becomes slow as they approach their cognate sites so that TFs form a tight site-specific complex, whereas the dynamics of nucleosomes becomes rapid so that they quickly pass through the cognate sites of TFs. Several in vivo data sets on the genome-wide positioning pattern of nucleosomes and TFs agree well with our arguments. The retarding effects of nucleosomes can be minimized when the degree of condensation of DNA is such that it can permit a jump size associated with the dynamics of TFs beyond ∼160–180 bp. © 2018 Biophysical Society

Biophysical Journal

Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks

We develop a generalized theoretical framework on the binding of transcription factor proteins (TFs) with specific sites on DNA that takes into account the interplay of various factors regarding overall electrostatic potential at the DNAprotein interface, occurrence of kinetic traps along the DNA sequence, presence of other roadblock protein molecules along DNA and crowded environment, conformational fluctuations in the DNA binding domains (DBDs) of TFs, and the conformational state of the DNA. Starting from a Smolochowski type theoretical framework on site-specific binding of TFs we logically build our model by adding the effects of these factors one by one. Our generalized two-step model suggests that the electrostatic attractive forces present inbetween the positively charged DBDs of TFs and the negatively charged phosphate backbone of DNA, along with the counteracting shielding effects of solvent ions, is the core factor that creates a fluidic type environment at the DNAprotein interface. This in turn facilitates various one-dimensional diffusion (1Dd) processes such as sliding, hopping and intersegmental transfers. These facilitating processes as well as flipping dynamics of conformational states of DBDs of TFs between stationary and mobile states can enhance the 1Dd coeffcient on a par with three-dimensional diffusion (3Dd). The random coil conformation of DNA also plays critical roles in enhancing the site-specific association rate. The extent of enhancement over the 3Dd controlled rate seems to be directly proportional to the maximum possible 1Dd length. We show that the overall site-specific binding rate scales with the length of DNA in an asymptotic way. For relaxed DNA, the specific binding rate will be independent of the length of DNA as length increases towards infinity. For condensed DNA as in in vivo conditions, the specific binding rate depends on the length of DNA in a turnover way with a maximum. This maximum rate seems to scale with the maximum possible 1Dd length of TFs in a square root manner. Results suggest that 1Dd processes contribute much less to the enhancement of specific binding rate under in vivo conditions for condensed DNA. There exists a critical length of binding stretch of TFs beyond which the probability associated with the random occurrence of similar specific binding sites will be close to zero. TFs in natural systems from prokaryotes to eukaryotes seem to handle sequencemediated kinetic traps via increasing the length of their recognition stretch or combinatorial binding. TFs overcome the hurdles of roadblocks via switching effciently between sliding, hopping and intersegmental transfer modes. The site-specific binding rate as well as the maximum possible 1Dd length seem to be directly proportional to the square root of the probability (pR) of finding a nonspecific binding site to be free from dynamic roadblocks. Here pR seems to be a function of the number of nsbs available per DNA binding protein (φ) inside the living cell. It seems that pR > 0.8 when φ > 10 which is true for the Escherichia coli cell system. © 2016 IOP Publishing Ltd and SISSA Medialab srl.

Journal of Statistical Mechanics: Theory and Experiment

Generalized theory on the mechanism of site-specific DNA-protein interactions

Eukaryotic genes are typically split into exons that need to be spliced together to form the mature mRNA. The splicing process depends on the dynamics and interactions among transcription by the RNA polymerase II complex (RNAPII) and the spliceosomal complex consisting of multiple small nuclear ribonucleo proteins (snRNPs). Here we propose a biophysically plausible initial theory of splicing that aims to explain the effects of the stochastic dynamics of snRNPs on the splicing patterns of eukaryotic genes. We consider two different ways to model the dynamics of snRNPs: pure three-dimensional diffusion and a combination of three- and one-dimensional diffusion along the emerging pre-mRNA. Our theoretical analysis shows that there exists an optimum position of the splice sites on the growing pre-mRNA at which the time required for snRNPs to find the 5′ donor site is minimized. The minimization of the overall search time is achieved mainly via the increase in non-specific interactions between the snRNPs and the growing pre-mRNA. The theory further predicts that there exists an optimum transcript length that maximizes the probabilities for exons to interact with the snRNPs. We evaluate these theoretical predictions by considering human and mouse exon microarray data as well as RNAseq data from multiple different tissues. We observe that there is a broad optimum position of splice sites on the growing pre-mRNA and an optimum transcript length, which are roughly consistent with the theoretical predictions. The theoretical and experimental analyses suggest that there is a strong interaction between the dynamics of RNAPII and the stochastic nature of snRNP search for 5′ donor splicing sites. © 2012 Murugan, Kreiman.

PLoS Computational Biology

Theory on the Coupled Stochastic Dynamics of Transcription and Splice-Site Recognition

DNA-binding proteins recognize their cognate sites on the template DNA more efficiently when the thermally driven flipping of their DNA-binding domains between the fast- and slow-moving conformations is coupled to the search dynamics. We show that there exists an optimum barrier height (kBT ln2) that separates these fast- and slow-moving states of DNA-binding domains, at which the efficiency associated with the thermodynamic coupling of thermally driven flipping and the overall search dynamics is the maximum. Furthermore, the dynamics of DNA-binding domains resembles that of typical downhill folding proteins at their midpoint denaturation temperatures. We further show that the average one-dimensional scanning lengths of slow- and fast-moving states of DNA-binding domains of LacI repressor protein are tuned to minimize the overall search time that is required to locate its cognate sites on DNA. © 2011 IOP Publishing Ltd.

Journal of Physics A: Mathematical and Theoretical

Theory on thermodynamic coupling of site-specific DNA-protein interactions with fluctuations in DNA-binding domains

We develop a theory that explains how the thermally driven conformational fluctuations in the DNA binding domains (DBDs) of the DNA binding proteins (DBPs) are effectively coupled to the one-dimensional searching dynamics of DBPs for their cognate sites on DNA. We show that the rate γopt, associated with the flipping of conformational states of DBDs beyond which the maximum search efficiency of DBPs is achieved, varies with the one-dimensional sliding length L as γopt ∝ L-2 and with the number of roadblock protein molecules present on the same DNA m as γopt ∝ m2. The required free energy barrier ERTO associated with this flipping transition seems to be varying with L as ERTO ∝ In L2. When the barrier height associated with the conformational flipping of DBDs is comparable with that of the thermal free energy, then the possible value of L under in vivo conditions seems to be L ≤ 70 bps. © 2010 by the Biophysical Society.

Theory of site-Specific DNA-Protein interactions in the presence of conformational fluctuations of DNA binding domains

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 &lt; 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) &lt; α &lt; 1 and beyond which α &gt; 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.

Theory of site-specific interactions of the combinatorial transcription factors with DNA

Theory on the mechanism of site-specific DNA-protein interactions in the presence of traps

Journal	Physical Biology
Publisher	Institute of Physics Publishing
ISSN	14783967
Open Access	No