DNA looping by protamine follows a nonuniform spatial distribution

DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes proteins such as condensin. Here, however, we are interested in a...

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Autores principales: McMillan, Ryan B., Kuntz, Victoria D., Devenica, Luka M., Bediako, Hilary, Carter, Ashley R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Biophysical Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8390855/
https://www.ncbi.nlm.nih.gov/pubmed/34023297
http://dx.doi.org/10.1016/j.bpj.2021.04.022
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author McMillan, Ryan B.
Kuntz, Victoria D.
Devenica, Luka M.
Bediako, Hilary
Carter, Ashley R.
author_facet McMillan, Ryan B.
Kuntz, Victoria D.
Devenica, Luka M.
Bediako, Hilary
Carter, Ashley R.
author_sort McMillan, Ryan B.
collection PubMed
description DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes proteins such as condensin. Here, however, we are interested in a different looping method whereby condensing agents (charge ≥+3) such as protamine proteins neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (≤1 μm) DNA fragments using atomic force microscopy. We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine’s in vivo role for looping DNA into toroids and the mechanism of DNA condensation by condensing agents more broadly.
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spelling pubmed-83908552022-06-15 DNA looping by protamine follows a nonuniform spatial distribution McMillan, Ryan B. Kuntz, Victoria D. Devenica, Luka M. Bediako, Hilary Carter, Ashley R. Biophys J Article DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors like lac repressor or by structural maintenance of chromosomes proteins such as condensin. Here, however, we are interested in a different looping method whereby condensing agents (charge ≥+3) such as protamine proteins neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (≤1 μm) DNA fragments using atomic force microscopy. We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine’s in vivo role for looping DNA into toroids and the mechanism of DNA condensation by condensing agents more broadly. The Biophysical Society 2021-06-15 2021-05-21 /pmc/articles/PMC8390855/ /pubmed/34023297 http://dx.doi.org/10.1016/j.bpj.2021.04.022 Text en © 2021 Biophysical Society. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
McMillan, Ryan B.
Kuntz, Victoria D.
Devenica, Luka M.
Bediako, Hilary
Carter, Ashley R.
DNA looping by protamine follows a nonuniform spatial distribution
title DNA looping by protamine follows a nonuniform spatial distribution
title_full DNA looping by protamine follows a nonuniform spatial distribution
title_fullStr DNA looping by protamine follows a nonuniform spatial distribution
title_full_unstemmed DNA looping by protamine follows a nonuniform spatial distribution
title_short DNA looping by protamine follows a nonuniform spatial distribution
title_sort dna looping by protamine follows a nonuniform spatial distribution
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8390855/
https://www.ncbi.nlm.nih.gov/pubmed/34023297
http://dx.doi.org/10.1016/j.bpj.2021.04.022
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