Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures

Ban, Yuki; Ando, Yuka; Terai, Yuma; Matsumura, Risa; Nakane, Keita; Iwai, Shigenori; Sato, Shinichi; Yamamoto, Junpei

doi:https://doi.org/10.1093/nar/gkae1001

Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures

Ban, Yuki; Ando, Yuka; Terai, Yuma et al.

Nucleic Acids Research, 2024, 52(22), 13530-13543

Number of Access:727（2025-10-31 15:13 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/98550

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Title	Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures
Creator	CreatorName Ban, Yuki
	CreatorName Ando, Yuka
	CreatorName Terai, Yuma
	CreatorName Matsumura, Risa
	CreatorName Nakane, Keita
	NRID 1000010168544 1000010168544 researchmap permalink read0076907 read0076907 Scopus Author ID 7201640584 7201640584 CreatorName Iwai, Shigenori
	CreatorName Sato, Shinichi
	NRID 1000090571084 1000090571084 ORCID 0000-0002-5036-991X 0000-0002-5036-991X researchmap permalink yamamotojunpei yamamotojunpei Scopus Author ID 15019956000 15019956000 CreatorName Yamamoto, Junpei
Description	Ban Yuki, Ando Yuka, Terai Yuma, et al. Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures. Nucleic Acids Research 48, 2013 (2024); https://doi.org/10.1093/nar/gkae1001.
Abstract	Non-canonical DNA structures, such as the G-quadruplex (G4) and i-motif (iM), are formed at guanine- and cytosine-rich sequences, respectively, in living cells and involved in regulating various biological processes during the cell cycle. Therefore, the formation and resolution of these non-canonical structures must be dynamically regulated by physiological conditions or factors that can bind G4 and iM structures. Although many G4 binding proteins responsible for tuning the G4 structure have been discovered, the structural regulation of iM by iM-binding proteins remains enigmatic. In this study, we developed a protein-labeling DNA probe bearing an alkyne moiety through a reactive linker, for proximity-labeling of nucleic acid-binding proteins, and searched for new iM-binding proteins. Alkyne-modified proteins in the nuclear extract of HeLa cells were labeled with biotin via a click reaction and then captured with streptavidin-coated magnetic beads. This fingerprint-targeting enrichment, followed by proteome analyses, identified new candidate proteins that potentially bind to the iM structure, in addition to the reported iM-binding proteins. Among the newly identified candidates, we characterized a nucleolar protein, nucleolin, that binds to the iM structure and relaxes it, while nucleolin stabilizes the G4 structure.
Publisher	Oxford University Press (OUP)
Source Title	Nucleic Acids Research
Volume (Issue)	52(22)
Page	13530-13543
Date of Issued	2024-11-19
Language	English
Handle URL	https://hdl.handle.net/11094/98550
PISSN	03051048
eISSN	13624962
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1093/nar/gkae1001
Access Rights	open access
CopyRight	This article is licensed under a Creative Commons Attribution 4.0 International License.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCTERMS.bibliographicCitation	Nucleic Acids Research. 2024, 52(22), p. 13530-13543
DC.title	Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures
DC.creator	Ban, Yuki
	Ando, Yuka
	Terai, Yuma
	Matsumura, Risa
	Nakane, Keita
	Iwai, Shigenori
	Sato, Shinichi
	Yamamoto, Junpei
DC.publisher	Oxford University Press (OUP)
DC.language' scheme='DCTERMS.RFC1766	English
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2024-11-19
DC.identifier	https://doi.org/10.1093/nar/gkae1001
DC.description	Ban Yuki, Ando Yuka, Terai Yuma, et al. Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures. Nucleic Acids Research 48, 2013 (2024); https://doi.org/10.1093/nar/gkae1001.
DCTERMS.abstract	Non-canonical DNA structures, such as the G-quadruplex (G4) and i-motif (iM), are formed at guanine- and cytosine-rich sequences, respectively, in living cells and involved in regulating various biological processes during the cell cycle. Therefore, the formation and resolution of these non-canonical structures must be dynamically regulated by physiological conditions or factors that can bind G4 and iM structures. Although many G4 binding proteins responsible for tuning the G4 structure have been discovered, the structural regulation of iM by iM-binding proteins remains enigmatic. In this study, we developed a protein-labeling DNA probe bearing an alkyne moiety through a reactive linker, for proximity-labeling of nucleic acid-binding proteins, and searched for new iM-binding proteins. Alkyne-modified proteins in the nuclear extract of HeLa cells were labeled with biotin via a click reaction and then captured with streptavidin-coated magnetic beads. This fingerprint-targeting enrichment, followed by proteome analyses, identified new candidate proteins that potentially bind to the iM structure, in addition to the reported iM-binding proteins. Among the newly identified candidates, we characterized a nucleolar protein, nucleolin, that binds to the iM structure and relaxes it, while nucleolin stabilizes the G4 structure.
DC.rights	This article is licensed under a Creative Commons Attribution 4.0 International License.
DC.format	98550
citation_title	Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures
citation_author	Ban, Yuki
	Ando, Yuka
	Terai, Yuma
	Matsumura, Risa
	Nakane, Keita
	Iwai, Shigenori
	Sato, Shinichi
	Yamamoto, Junpei
citation_publisher	Oxford University Press (OUP)
citation_language	English
citation_date	2024-11-19
citation_journal_title	Nucleic Acids Research
citation_volume	52
citation_issue	22
citation_firstpage	13530
citation_lastpage	13543
citation_doi	https://doi.org/10.1093/nar/gkae1001
citation_public_url	https://hdl.handle.net/11094/98550

Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures

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