• Chloroplasts, essential organelles for photosynthesis, can communicate with the cell nucleus to precisely control the activation or repression of specific genes.
• A recent study has now shown that chloroplasts also regulate the genome through epigenetic modifications, acting directly on the chromatin.
• This discovery marks a major step forward in understanding how plants regulate the development of their photosynthetic machinery, and opens the door to future applications in agricultural biotechnology.

Chloroplasts are organelles found in plant cells that play a crucial role in converting sunlight into chemical energy through photosynthesis. Although chloroplasts contain their own DNA, they also depend on the nuclear genome to produce many of the proteins required for proper function.

During early seedling development, especially upon first exposure to light, chloroplasts begin to differentiate and initiate the photosynthetic programme. This process requires tight coordination between chloroplast and nucleus via anterograde signals (from nucleus to chloroplast) and retrograde signals (from chloroplast to nucleus). This two-way communication is essential for ensuring that photosynthesis is activated in the right place and at the right time.

In a recent study published in the prestigious journal Nature Communications, a research collaboration between CRAG and the Umeå Plant Science Centre (UPSC) in Sweden described for the first time how chloroplasts can modulate nuclear gene expression through epigenetic changes, providing a new perspective on retrograde signalling.

Chloroplasts can directly influence nuclear DNA activity

Until now, it was known that chloroplasts could influence the activation or repression of nuclear genes, but it had not been shown that they could do so through changes in chromatin — the compacted form of DNA inside the nucleus. Chromatin consists of DNA wrapped around proteins called histones. These histones can undergo chemical modifications — such as methylation or acetylation — that change how tightly the DNA is packed, thereby determining whether a gene is active or silenced. This layer of regulation is known as epigenetics.

One of the main challenges in studying the onset of photosynthesis is how quickly this process begins once a seedling is exposed to light. To overcome this, the research team used a suspension culture of the model plant Arabidopsis thaliana cells, which allowed them to slow down and synchronise the process known as greening, which marks the formation of functional chloroplasts and the activation of photosynthesis when cells change from dark to light conditions.

Using high-throughput techniques such as ChIP-seq (Chromatin Immunoprecipitation sequencing) to detect histone modifications and transcriptomic analysis to determine gene expression, researchers achieved high-resolution temporal monitoring of epigenetic changes during the process.

A finely tuned sequence of epigenetic changes

The study revealed that, as cells transition from darkness to light, a precise and ordered sequence of epigenetic modifications occurs in genes related to photosynthesis, known as PhANGs (Photosynthesis Associated Nuclear Genes).

Specifically, a repressive histone mark (H3K27me3 methylation) is replaced by an activating mark (H3K27ac acetylation) just as photosynthesis becomes fully established. This key transition had not previously been described in such detail.

The study also identifies several key regulatory proteins in this process, including GUN1, which is essential for transmitting retrograde signals, as well as VAL1, REF6 and GLK1/2, which help orchestrate the activation of photosynthetic genes.

This discovery represents a major breakthrough in understanding how cellular organelles can directly shape nuclear genome activity, since it shows for the first time how chloroplasts can turn genes on or off through epigenetic mechanisms. Such knowledge may have significant applications in biotechnology and agriculture, potentially enabling the optimisation of photosynthesis, improved crop performance under adverse conditions, or the development of plants more resilient to environmental stress.

Reference Article

Marti Quevedo, Ivona Kubalová, Alexis Brun, Luis Cervela-Cardona, Elena Monte & Åsa Strand. Retrograde signals control dynamic changes to the chromatin state at photosynthesis-associated loci. Nature Communications (2025), https://doi.org/10.1038/s41467-025-61831-w

About the authors and funding of the study

Part of this work was supported by grants and financial support to Å.S. from the Swedish Research Council, VR (2020-03958) and Foundation for Strategic Research, SSF (ARC19-0051) and to E.M. from FEDER/Ministerio de Ciencia, Innovación y Universidades – Agencia Estatal de Investigación (Project Reference PID2021-122288NB-I00); from the CERCA Programme/ Generalitat de Catalunya (Project Reference 2021SGR-792), and from the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence” in CEX2019-000902-S funded by MCIN/AEI/ 10.13039/501100011033. M.Q. received postdoctoral funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 945043.