Mondal, AnupamFelipe, CaykeKolomeisky, Anatoly B.2023-07-182023-07-182023Mondal, Anupam, Felipe, Cayke and Kolomeisky, Anatoly B.. "Nucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factors." <i>The Journal of Physical Chemistry Letters,</i> 14, no. 17 (2023) American Chemical Society: 4096-4103. https://doi.org/10.1021/acs.jpclett.3c00529.https://hdl.handle.net/1911/114937Transfer of genetic information starts with transcription factors (TFs) binding to specific sites on DNA. But in living cells, DNA is mostly covered by nucleosomes. There are proteins, known as pioneer TFs, that can efficiently reach the DNA sites hidden by nucleosomes, although the underlying mechanisms are not understood. Using the recently proposed idea of interaction-compensation mechanism, we develop a stochastic model for the target search on DNA with nucleosome breathing. It is found that nucleosome breathing can significantly accelerate the search by pioneer TFs in comparison to situations without breathing. We argue that this is the result of the interaction-compensation mechanism that allows proteins to enter the inner nucleosome region through the outer DNA segment. It is suggested that nature optimized pioneer TFs to take advantage of nucleosome breathing. The presented theoretical picture provides a possible microscopic explanation for the successful invasion of nucleosome-buried genes.engThis work is protected by copyright, and is made available here for research and educational purposes. Permission to reuse, publish, or reproduce the work beyond the bounds of Fair Use or other exemptions to copyright law must be obtained from the copyright holder.Journal articlehttps://doi.org/10.1021/acs.jpclett.3c00529