Dissecting the molecular mechanisms of transgenerational epigenetic inheritance

Project Information

MOMENTS

Grant agreement ID: 101109836

DOI

10.3030/101109836

Project closed

EC signature date 9 March 2023

Start date 1 April 2023

End date 31 March 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 195 914,88

Coordinated by

INSTITUT PASTEUR
France

Periodic Reporting for period 1 - MOMENTS (Dissecting the molecular mechanisms of transgenerational epigenetic inheritance)

Reporting period: 2023-04-01 to 2025-03-31

Summary of the context and overall objectives of the project

The successful development and survival of organisms in different environments rely on their ability to regulate gene expression in a precise, timely, and coordinated manner. Genes are not continuously active; instead, they must be turned on or off in specific cells and moments. To achieve this, organisms have evolved sophisticated regulatory systems. Among these, Argonaute proteins, present in several domains of life, play a central regulatory role. They bind to small RNAs to recognize specific messenger RNAs (mRNAs) by sequence complementarity and negatively regulate their expression.
Beyond their regulatory role in animal development, small RNA-mediated silencing can also be inherited across generations. This phenomenon, known as epigenetic inheritance, allows offspring to "remember" and respond to environmental or developmental experiences of their ancestors. However, not all experiences are passed on, nor do these molecular memories persist indefinitely. This raises fundamental questions: How do organisms decide which molecular memories to retain? How long are they maintained? What mechanisms ensure their inheritance?
This project set out to investigate these questions by exploring how nuclear Argonautes and small RNAs can execute their gene silencing and inheritance functions in the germline of Caenorhabditis elegans, a widely used model organism. While the role of nuclear Argonautes in epigenetic inheritance was recognized, the mechanisms remained unclear.
This project aimed to:
1) Identify the factors involved in the maintenance of silencing across generations
2) Decipher the molecular mechanisms underlying small RNA-mediated transcriptional repression
3) Clarify how these regulatory systems work during development and over successive generations.
By deepening our understanding of heritable gene regulation, this research contributes to the broader field of epigenetics and may ultimately inform areas such as developmental biology and intergenerational health.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

To achieve these objectives, I used the worm Caenorhabditis elegans as an experimental model, given its short life cycle and ability to produce large, genetically identical populations ideal for studying epigenetic inheritance. To address the aims of this project, I used a targeted degradation system to deplete a nuclear Argonaute protein specifically in the germline. By inducing its depletion or re-expression at defined time points, I was able to track the resulting molecular changes with unprecedented temporal and generational resolution—something not achievable with traditional genetic mutants.
This approach allowed me to follow the dynamics of gene silencing and reactivation during development and inheritance. I combined it with advanced genomics tools to assess changes in gene expression, small RNA levels, and chromatin changes in a tissue-specific manner.
The main achievements of this project include the demonstration that silencing maintenance in the germline can persist without canonical repressive histone modifications, suggesting an alternative mode of inheritance not solely reliant on chromatin marks. I also identified that the nuclear Argonaute transgenerationally promotes small RNA biogenesis in the cytoplasm, indicating a feedback loop that links nuclear silencing and cytoplasmic small RNA biogenesis. Additionally, I studied the role of known factors in gene silencing by assessing their role in transcriptional silencing or small RNA biogenesis.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

This project has produced several results that challenge prevailing models and open new research directions. Most notably, I found that gene de-silencing can occur even when canonical repressive histone modifications are still present. This observation suggests that histone marks may not be the direct cause of transcriptional silencing, but rather a consequence or correlate of other regulatory mechanisms.
Furthermore, I observed active transcription in genomic regions traditionally considered heterochromatic and transcriptionally inert. These findings align with emerging studies in other organisms, suggesting that repressive chromatin marks alone are not sufficient to silence genes. This challenges long-standing assumptions and has broad implications for how we understand chromatin’s role in gene regulation.
The discovery that the nuclear Argonaute also contributes to cytoplasmic small RNA production reveals a previously unappreciated level of coordination between nuclear and cytoplasmic silencing processes. This dual function ensures the stability and robustness of inherited gene regulation.
The nuclear Argonaute studied in this project has been involved in the maintenance of environmentally triggered epigenetic memory. Moreover, it is the final effector of several endogenous small RNA pathways in C. elegans germline. The results of this project are the particular importance in this context, showing the complexity and versatility of Argonautes as regulatory complexes, as well as key factors for maintaining epigenetic memory across generations.
This project enhances our understanding of how experiences can influence gene expression across generations. Such insights are important for addressing questions about heredity, environmental exposure, and long-term health. By uncovering how epigenetic memory is regulated, this work lays the groundwork for future advances in health, disease prevention, and public awareness around the impact of the environment on genetic regulation.