Nucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factors

Simple item page
dc.citation.firstpage4096en_US
dc.citation.issueNumber17en_US
dc.citation.journalTitleThe Journal of Physical Chemistry Lettersen_US
dc.citation.lastpage4103en_US
dc.citation.volumeNumber14en_US
dc.contributor.authorMondal, Anupamen_US
dc.contributor.authorFelipe, Caykeen_US
dc.contributor.authorKolomeisky, Anatoly B.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2023-07-18T16:29:40Zen_US
dc.date.available2023-07-18T16:29:40Zen_US
dc.date.issued2023en_US
dc.description.abstractTransfer 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.en_US
dc.identifier.citationMondal, 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.en_US
dc.identifier.doihttps://doi.org/10.1021/acs.jpclett.3c00529en_US
dc.identifier.urihttps://hdl.handle.net/1911/114937en_US
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
dc.rightsThis 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.en_US
dc.titleNucleosome Breathing Facilitates the Search for Hidden DNA Sites by Pioneer Transcription Factorsen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Nucleosome_Breathing_Facilitates_the_Search_for_Hidden_DNA_Sites_by_Pioneer_Transcription_Factors_JPC_Letter.pdf
Size:
850.3 KB
Format:
Adobe Portable Document Format
Description:
Download
Collections
Faculty Publications
Chemical and Biomolecular Engineering Publications
Chemistry Publications
Physics and Astronomy Publications