Evidence map›Paper›PMID 40263610›Full record

ArticleNature plants2025

Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain.

Hirotake Furihata, Zhangliang Zhu, Kaisei Nishida, Yasuhito Sakuraba, Akihiro Tsuji, Hayato Yamashita, Shohei Nosaki, Ryo Tachibana, Ayumi Yamagami, Yoshiki Ikeda and 6 more

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Article in Nature plants, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Hirotake Furihata *Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.ORCID 0000-0002-0171-6751
Zhangliang Zhu *Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.ORCID 0000-0003-2146-9783
Kaisei Nishida *Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
Yasuhito Sakuraba *Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.ORCID 0000-0002-0432-6767
Akihiro TsujiGraduate School of Engineering Science, The University of Osaka, Osaka, Japan.
Hayato YamashitaGraduate School of Engineering Science, The University of Osaka, Osaka, Japan.ORCID 0000-0003-4473-5773
Shohei NosakiDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.ORCID 0000-0001-8493-1299
Ryo TachibanaGraduate School of Biostudies, Kyoto University, Kyoto, Japan.ORCID 0000-0002-8265-7502
Ayumi YamagamiGraduate School of Biostudies, Kyoto University, Kyoto, Japan.ORCID 0000-0003-4222-4769
Yoshiki IkedaInstitute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.
Masayuki AbeGraduate School of Engineering Science, The University of Osaka, Osaka, Japan.
Tatsuya SawasakiProteo-Science Center, Ehime University, Matsuyama, Japan.
Takeshi NakanoGraduate School of Biostudies, Kyoto University, Kyoto, Japan.ORCID 0000-0002-3188-7770
Shuichi YanagisawaAgro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. asyanagi@g.ecc.u-tokyo.ac.jp.ORCID 0000-0002-3758-5933
Masaru TanokuraDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. amtanok@mail.ecc.u-tokyo.ac.jp.ORCID 0000-0001-5072-2480
Takuya MiyakawaDepartment of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan. miyakawa.takuya.7j@kyoto-u.ac.jp.ORCID 0000-0001-5957-3549

Funding

Japan Agency for Medical Research and Development (AMED) JP24ama121010MEXT | Japan Society for the Promotion of Science (JSPS) JP19H04855MEXT | Japan Society for the Promotion of Science (JSPS) JP22H04977MEXT | Japan Society for the Promotion of Science (JSPS) JP22K18945MEXT | Japan Society for the Promotion of Science (JSPS) JP23H01818MEXT | Japan Society for the Promotion of Science (JSPS) JP23H03073MEXT | Japan Society for the Promotion of Science (JSPS) JP23K27467MEXT | Japan Society for the Promotion of Science (JSPS) JP24KJ1579
6 · The paper itself

Abstract

DNA-binding with one-finger (Dof) proteins are a family of plant-specific transcription factors distinguished by the highly conserved Dof DNA-binding domain. Various members play crucial roles in diverse plant biological processes. However, it remains unclear how the Dof domain recognizes a restricted set of promoters for gene regulation by binding to just four nucleotides, AAAG/CTTT. Here we present the crystal structure of the Dof domain of CYCLING DOF FACTOR 1 (CDF1), a well-characterized Dof protein acting as a transcriptional repressor by binding to the CONSTANS promoter to regulate photoperiodic flowering, in complex with DNA containing two cis elements. The data reveal that the Dof domain exhibits a unique zinc ribbon fold that includes a three-stranded antiparallel β-sheet and a carboxy-terminal loop, enabling DNA recognition accompanied by directional expansion of the major groove. These features facilitate binding to contiguous target cis elements in a proper arrangement to effectively regulate gene expression.

Indexed as

ArabidopsisArabidopsis ProteinsDNA-Binding ProteinsPromoter Regions, GeneticTranscription FactorsGene Expression Regulation, PlantProtein DomainsArabidopsis ProteinsCONSTANS protein, ArabidopsisDNA-Binding ProteinsTranscription Factors

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.