Understanding the Target Search by Multiple Transcription Factors on Nucleosomal DNA

Abstract

The association of multiple Transcription Factors (TFs) in the cis‐regulatory region is imperative for developmental changes in eukaryotes. The underlying process is exceedingly complex, and it is not at all clear what orchestrates the overall search process by multiple TFs. In this study, by developing a theoretical model based on a discrete‐state stochastic approach, we investigated the target search mechanism of multiple TFs on nucleosomal DNA. Experimental kinetic rate constants of different TFs are taken as input to estimate the Mean‐First‐Passage time to recognize the binding motifs by two TFs on a dynamic nucleosome model. The theory systematically analyzes when the TFs search their binding motifs hierarchically and when simultaneously by proceeding via the formation of a protein‐protein complex. Our results, validated by extensive Monte Carlo simulations, elucidate the molecular basis of the complex target search phenomenon of multiple TFs on nucleosomal DNA.

How Do Nucleosome Dynamics Regulate Protein Search on DNA?

“…The present study is based on a discrete state stochastic model to demonstrate the target search mechanism of TFs on nucleosomal DNA. A similar method has been used previously by us and others to investigate the kinetic origin of nucleosome invasion by PFs, 82 target search mechanism of multiple proteins on nucleosomal DNA, 81 protein diffusion on supercoiled DNA 86 and linear DNA with sequence heterogeneity, 87 conformational fluctuations, 88 and loop formation. 89 In the present study, we probe how the two most prominent nucleosome dynamics, namely sliding and breathing, modulate the target search efficiency of PFs and NPFs.…”

“…To this end, it is noteworthy that not all TFs can invade nucleosomes and bind to target DNA sites, rather a fraction of transcription factors (TFs) known as pioneer factors (PFs) ,− are able to do so. By replacing the histone-DNA contacts with equivalent DNA-PF nonspecific contacts, they can create permissive states for transcription, translation, and other regulatory processes as well as recruit other nonpioneer factors (NPFs) for complex DNA metabolic pathways. In our recent studies, we have explored the kinetic origin of PFs binding to nucleosomal DNA during its breathing dynamics and how the same may regulate the subsequent association of another TF. , In this work, we go further and provide a theoretical framework to investigate the role of symmetric and asymmetric DNA breathing and sliding dynamics on the target search mechanism of TFs.…”

“…By replacing the histone-DNA contacts with equivalent DNA-PF nonspecific contacts, they can create permissive states for transcription, translation, and other regulatory processes as well as recruit other nonpioneer factors (NPFs) for complex DNA metabolic pathways. In our recent studies, we have explored the kinetic origin of PFs binding to nucleosomal DNA during its breathing dynamics and how the same may regulate the subsequent association of another TF. , In this work, we go further and provide a theoretical framework to investigate the role of symmetric and asymmetric DNA breathing and sliding dynamics on the target search mechanism of TFs. Our inputs for the theory are the available experimental kinetic rates of PFs and NPFs on nucleosomal DNA, which help us to estimate the Mean First Passage Time (MFPT) , to reach the target sites by a TF.…”

smFRET Detection of Cis and Trans DNA Interactions by the BfiI Restriction Endonuclease

“…Proteins with a single DNA target binding domain utilize mechanisms from one (or a combination) of the target search classes. − However, proteins with two DNA binding domains may simultaneously interact with two targets on a single DNA molecule (i.e., in cis interaction) or on two separate molecules (i.e., in trans interaction) and with different mechanisms . Temporal interactions with two target sites in cis and in trans often play an important role in target search and are critical in many cellular mechanisms. − For example, precise timing of two DNA target binding events is important for transposons and transposases (such as the prototypical Tn7 family) in finding safe sites for insertion, efficient spread of the element, and avoiding unregulated insertion events. − …”