PRESS RELEASE
CRC and MYB proteins help activate genes essential for nectary development
Summary
A research team led by Professor Toshiro Ito of the Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST; President: Kazuhiro Shiozaki), has uncovered a mechanism by which DNA looping enhances the activity of a gene required for the growth of nectaries, the small floral organs that produce nectar, in the model plant Arabidopsis thaliana. DNA contains regulatory regions that can increase gene expression. The researchers found evidence that proteins called CRC and MYB bring a gene and a distant regulatory region into closer contact, forming a loop in the intervening DNA and promoting the expression of a gene essential for nectary growth. CRC also regulates genes involved in sugar transport, which supplies materials for nectar production, and the synthesis of terpenes, a class of compounds that includes floral scent components. Together, the findings suggest that CRC coordinates both nectary development and the molecular functions associated with nectar secretion and scent production. The study was published online in Nature Communications (DOI: 10.1038/s41467-026-78943-6).
Background and objectives
Floral nectar is produced by small organs called nectaries, which are located, for example, near the bases of stamens. Nectaries do more than store sugars: they have specialized machinery to transport sugars and secrete them as nectar. Understanding how these organs develop and acquire the capacity to secrete nectar offers insight into how plants form organs with specialized functions.
Previous research in the model plant Arabidopsis thaliana (Note 1) established that a protein called CRC is essential for nectary formation. Genes involved in nectary growth and sugar transport had also been identified individually. However, how CRC regulates these genes to support both organ development and nectar secretion remained unclear.
Nectaries are tiny organs, approximately 100 micrometers across, making them difficult to separate from surrounding tissues. Conventional approaches have therefore had limited ability to determine which genes are active in particular locations. In this study, the researchers combined analyses of gene expression in individual cell nuclei with analyses that retain spatial information to identify key genes and regulatory connections underlying nectary development and function.
Figure. Overview of the Arabidopsis flower and the proposed CRC-MYB-dependent DNA-looping mechanism regulating MAB4. Labels in the original illustration are in Japanese.
Research findings
Mapping gene activity in flowers at cellular and spatial resolution
The team reanalyzed publicly available single-nucleus RNA-sequencing data (Note 2) and confirmed that CRC and MYB genes are expressed in nectary-associated cell populations. Using spatial transcriptomics (Note 3), which measures gene expression while preserving information about tissue location, they further found that genes encoding sugar transporters and terpene biosynthetic enzymes show characteristic expression in nectaries. Comparison with crc mutants, which lack nectaries, helped link these gene-expression patterns to the location of the nectary.
CRC regulates genes involved in nectary growth, sugar transport, and terpene synthesis
The researchers examined where CRC binds to DNA and which genes change their expression when CRC function is lost. They identified CRC-regulated genes associated not only with organ growth but also with sugar transport and the biosynthesis of terpenes (Note 4), some of which contribute to floral fragrance. They also demonstrated that CRC interacts with three MYB proteins--MYB21, MYB24, and MYB57--and that these proteins regulate overlapping sets of genes. Plants lacking the functions of all three MYB proteins developed smaller nectaries, supporting an important role for CRC and MYB proteins in nectary growth.
Among the genes jointly regulated by CRC and MYB proteins, the team focused on MAB4, which contributes to nectary growth. A regulatory DNA region downstream of MAB4 acts as an enhancer (Note 5). Disrupting this region reduced MAB4 expression and resulted in smaller nectaries. Tests of physical proximity between distant DNA regions detected contact between the region near the MAB4 transcription start site and the downstream enhancer. This contact was reduced when CRC function was lost.
These observations support a model in which CRC and MYB proteins facilitate the proximity of the two regions, forming a chromatin loop that enhances MAB4 expression. The researchers further found that MAB4 helps organize the positioning of proteins that transport the plant hormone auxin (Note 6), thereby supporting auxin distribution and growth within the nectary. The study thus connects regulation of gene activity through DNA architecture to the spatial organization of cellular proteins and the growth of a small floral organ.
Future directions
The findings indicate that CRC not only promotes nectary growth but also regulates genes involved in sugar transport and terpene synthesis. CRC may therefore coordinate the processes that build the organ with those that enable it to carry out its specialized functions.
The results also highlight how interactions between distant regions of DNA, beyond the DNA sequence itself, can contribute to organ development. Examining whether similar mechanisms operate in nectaries of other plant species or in different organs may reveal more general principles of plant organ formation.
An important limitation is that contacts between DNA regions were measured using samples containing multiple tissue types; chromatin-loop formation was not directly visualized in individual nectary cells. Future studies will need to examine DNA organization and gene activity across developmental stages and at cellular resolution. It also remains to be determined how CRC-dependent gene regulation affects nectar quantity and composition and the actual production of terpenes.
Glossary
1. Arabidopsis thaliana: A small plant in the mustard family widely used in plant research because it has a short life cycle and extensive genetic resources.
2. Single-nucleus RNA sequencing: A method that isolates individual cell nuclei and measures their RNA, allowing researchers to identify cell populations with characteristic patterns of gene expression in mixed tissues.
3. Spatial transcriptomics: An approach that links gene expression to its location within a tissue. This study used Slide-seq, a technique that measures RNA from thin sections of floral tissue.
4. Terpenes: A diverse class of plant-produced compounds, some of which contribute to floral scent. The study showed that genes encoding enzymes involved in terpene biosynthesis are regulated by CRC.
5. Regulatory DNA region (enhancer): A DNA sequence that controls where or how strongly a gene is expressed. The downstream region studied here acts as an enhancer of MAB4 expression.
6. Auxin: A plant hormone involved in growth and organ formation. Its transport and local accumulation help regulate cell growth and development.
Publication
Title: A CRC-MYB chromatin loop controls auxin-mediated nectary growth in Arabidopsis
Authors: Hideaki Iimura, Makoto Takahashi, Ryosuke Ohta, Asumi Nagamori, Seika Togawa, Yuki Furuta, Koki Nakamura, Febri Yuda Kurniawan, Xuejing Wang, Kie Kumaishi, Samantha Klasfeld, Taiji Kawakatsu, Yasunori Ichihashi, Takamasa Suzuki, Doris Wagner, Toshiro Ito, and Nobutoshi Yamaguchi
Journal: Nature Communications
DOI: 10.1038/s41467-026-78943-6
Contacts
Research inquiries
Professor Toshiro Ito
Laboratory of Molecular Genetics of Floral Development
Division of Biological Science, Graduate School of Science and Technology
Nara Institute of Science and Technology (NAIST)
Tel: +81-743-72-5500 | Email: itot@bs.naist.jp
Lab website: https://bsw3.naist.jp/ito/
Media inquiries
Public Relations and External Affairs Section, Planning and General Affairs Division
Nara Institute of Science and Technology (NAIST)
Tel: +81-743-72-5112 | Fax: +81-743-72-5011
Email: s-kikaku@ad.naist.jp