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Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search

We previously demonstrated that the polycomb repressive complex 2 chromatin–modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermediate state. Simulations suggested that such a direct transfer mechanism may be generally necessary for RNA to recruit proteins to chrom...

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Autores principales: Hemphill, Wayne O., Voong, Calvin K., Fenske, Regan, Goodrich, James A., Cech, Thomas R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10293810/
https://www.ncbi.nlm.nih.gov/pubmed/37339225
http://dx.doi.org/10.1073/pnas.2220537120
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author Hemphill, Wayne O.
Voong, Calvin K.
Fenske, Regan
Goodrich, James A.
Cech, Thomas R.
author_facet Hemphill, Wayne O.
Voong, Calvin K.
Fenske, Regan
Goodrich, James A.
Cech, Thomas R.
author_sort Hemphill, Wayne O.
collection PubMed
description We previously demonstrated that the polycomb repressive complex 2 chromatin–modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermediate state. Simulations suggested that such a direct transfer mechanism may be generally necessary for RNA to recruit proteins to chromatin, but the prevalence of direct transfer capability is unknown. Herein, we used fluorescence polarization assays and observed direct transfer for several well-characterized nucleic acid–binding proteins: three-prime repair exonuclease 1, heterogeneous nuclear ribonucleoprotein U, Fem-3-binding factor 2, and MS2 bacteriophage coat protein. For TREX1, the direct transfer mechanism was additionally observed in single-molecule assays, and the data suggest that direct transfer occurs through an unstable ternary intermediate with partially associated polynucleotides. Generally, direct transfer could allow many DNA- and RNA-binding proteins to conduct a one-dimensional search for their target sites. Furthermore, proteins that bind both RNA and DNA might be capable of readily translocating between those ligands.
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spelling pubmed-102938102023-06-28 Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search Hemphill, Wayne O. Voong, Calvin K. Fenske, Regan Goodrich, James A. Cech, Thomas R. Proc Natl Acad Sci U S A Biological Sciences We previously demonstrated that the polycomb repressive complex 2 chromatin–modifying enzyme can directly transfer between RNA and DNA without a free-enzyme intermediate state. Simulations suggested that such a direct transfer mechanism may be generally necessary for RNA to recruit proteins to chromatin, but the prevalence of direct transfer capability is unknown. Herein, we used fluorescence polarization assays and observed direct transfer for several well-characterized nucleic acid–binding proteins: three-prime repair exonuclease 1, heterogeneous nuclear ribonucleoprotein U, Fem-3-binding factor 2, and MS2 bacteriophage coat protein. For TREX1, the direct transfer mechanism was additionally observed in single-molecule assays, and the data suggest that direct transfer occurs through an unstable ternary intermediate with partially associated polynucleotides. Generally, direct transfer could allow many DNA- and RNA-binding proteins to conduct a one-dimensional search for their target sites. Furthermore, proteins that bind both RNA and DNA might be capable of readily translocating between those ligands. National Academy of Sciences 2023-06-20 2023-06-27 /pmc/articles/PMC10293810/ /pubmed/37339225 http://dx.doi.org/10.1073/pnas.2220537120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Biological Sciences
Hemphill, Wayne O.
Voong, Calvin K.
Fenske, Regan
Goodrich, James A.
Cech, Thomas R.
Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
title Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
title_full Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
title_fullStr Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
title_full_unstemmed Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
title_short Multiple RNA- and DNA-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
title_sort multiple rna- and dna-binding proteins exhibit direct transfer of polynucleotides with implications for target-site search
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10293810/
https://www.ncbi.nlm.nih.gov/pubmed/37339225
http://dx.doi.org/10.1073/pnas.2220537120
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