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Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA

A human protein heterogeneous ribonucleoprotein U (hnRNP U) also known as Scaffold attachment factor A (SAF-A) and its orthologous rat protein SP120 are abundant and multifunctional nuclear protein that directly binds to both DNA and RNA. The C-terminal region of hnRNP U enriched with arginine and g...

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Autores principales: Miyaji, Mary, Kawano, Shinji, Furuta, Ryohei, Murakami, Emi, Ikeda, Shogo, Tsutsui, Kimiko M., Tsutsui, Ken
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10403129/
https://www.ncbi.nlm.nih.gov/pubmed/37540655
http://dx.doi.org/10.1371/journal.pone.0289599
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author Miyaji, Mary
Kawano, Shinji
Furuta, Ryohei
Murakami, Emi
Ikeda, Shogo
Tsutsui, Kimiko M.
Tsutsui, Ken
author_facet Miyaji, Mary
Kawano, Shinji
Furuta, Ryohei
Murakami, Emi
Ikeda, Shogo
Tsutsui, Kimiko M.
Tsutsui, Ken
author_sort Miyaji, Mary
collection PubMed
description A human protein heterogeneous ribonucleoprotein U (hnRNP U) also known as Scaffold attachment factor A (SAF-A) and its orthologous rat protein SP120 are abundant and multifunctional nuclear protein that directly binds to both DNA and RNA. The C-terminal region of hnRNP U enriched with arginine and glycine is essential for the interaction with RNA and the N-terminal region of SAF-A termed SAP domain has been ascribed to the DNA binding. We have reported that rat hnRNP U specifically and cooperatively binds to AT-rich DNA called nuclear scaffold/matrix-associated region (S/MAR) although its detailed mechanism remained unclear. In the present study analysis of hnRNP U deletion mutants revealed for the first time that a C-terminal domain enriched with Arg-Gly (defined here as ‘RG domain’) is predominantly important for the S/MAR-selective DNA binding activities. RG domain alone directly bound to S/MAR and coexistence with the SAP domain exerted a synergistic effect. The binding was inhibited by netropsin, a minor groove binder with preference to AT pairs that are enriched in S/MAR, suggesting that RG domain interacts with minor groove of S/MAR DNA. Interestingly, excess amounts of RNA attenuated the RG domain-dependent S/MAR-binding of hnRNP U. Taken together, hnRNP U may be the key element for the RNA-regulated recognition of S/MAR DNA and thus contributing to the dynamic structural changes of chromatin compartments.
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spelling pubmed-104031292023-08-05 Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA Miyaji, Mary Kawano, Shinji Furuta, Ryohei Murakami, Emi Ikeda, Shogo Tsutsui, Kimiko M. Tsutsui, Ken PLoS One Research Article A human protein heterogeneous ribonucleoprotein U (hnRNP U) also known as Scaffold attachment factor A (SAF-A) and its orthologous rat protein SP120 are abundant and multifunctional nuclear protein that directly binds to both DNA and RNA. The C-terminal region of hnRNP U enriched with arginine and glycine is essential for the interaction with RNA and the N-terminal region of SAF-A termed SAP domain has been ascribed to the DNA binding. We have reported that rat hnRNP U specifically and cooperatively binds to AT-rich DNA called nuclear scaffold/matrix-associated region (S/MAR) although its detailed mechanism remained unclear. In the present study analysis of hnRNP U deletion mutants revealed for the first time that a C-terminal domain enriched with Arg-Gly (defined here as ‘RG domain’) is predominantly important for the S/MAR-selective DNA binding activities. RG domain alone directly bound to S/MAR and coexistence with the SAP domain exerted a synergistic effect. The binding was inhibited by netropsin, a minor groove binder with preference to AT pairs that are enriched in S/MAR, suggesting that RG domain interacts with minor groove of S/MAR DNA. Interestingly, excess amounts of RNA attenuated the RG domain-dependent S/MAR-binding of hnRNP U. Taken together, hnRNP U may be the key element for the RNA-regulated recognition of S/MAR DNA and thus contributing to the dynamic structural changes of chromatin compartments. Public Library of Science 2023-08-04 /pmc/articles/PMC10403129/ /pubmed/37540655 http://dx.doi.org/10.1371/journal.pone.0289599 Text en © 2023 Miyaji et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Miyaji, Mary
Kawano, Shinji
Furuta, Ryohei
Murakami, Emi
Ikeda, Shogo
Tsutsui, Kimiko M.
Tsutsui, Ken
Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA
title Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA
title_full Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA
title_fullStr Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA
title_full_unstemmed Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA
title_short Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA
title_sort selective dna-binding of sp120 (rat ortholog of human hnrnp u) is mediated by arginine-glycine rich domain and modulated by rna
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10403129/
https://www.ncbi.nlm.nih.gov/pubmed/37540655
http://dx.doi.org/10.1371/journal.pone.0289599
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