Periodic Reporting for period 1 - EPIC (Mechanism and significance of de novo gene methylation during reproduction in Marchantia)
Berichtszeitraum: 2023-08-16 bis 2025-12-15
Plants rely on chemical marks added to their DNA to regulate gene activity. One of the most important of these marks is DNA methylation. In most plants, DNA methylation is best known for silencing transposable elements, often described as genomic parasites. However, recent evidence suggests that DNA methylation may also regulate genes during development. How and when this gene-targeted methylation is established, and what it does during plant reproduction, remains poorly understood.
The EPIC project investigates how new DNA methylation patterns are established during reproduction in Marchantia polymorpha, a simple early-diverging land plant. Studying such an evolutionarily ancient species allows researchers to explore how epigenetic regulatory systems emerged and diversified during plant evolution.
The overall objectives of the project are to determine when gene methylation appears during development, identify the molecular mechanisms responsible for targeting it to specific genes, and understand its functional significance in reproductive tissues. By combining single-cell technologies, genome editing, chromatin profiling and comparative genomics, the project aims to provide a mechanistic and evolutionary framework for understanding gene-targeted DNA methylation in plants.
The EPIC project investigates how new DNA methylation patterns are established during reproduction in Marchantia polymorpha, a simple early-diverging land plant. Studying such an evolutionarily ancient species allows researchers to explore how epigenetic regulatory systems emerged and diversified during plant evolution.
The overall objectives of the project are to determine when gene methylation appears during development, identify the molecular mechanisms responsible for targeting it to specific genes, and understand its functional significance in reproductive tissues. By combining single-cell technologies, genome editing, chromatin profiling and comparative genomics, the project aims to provide a mechanistic and evolutionary framework for understanding gene-targeted DNA methylation in plants.
During the project, advanced single-nucleus sequencing approaches were established in Marchantia reproductive tissues. This allowed gene expression and DNA methylation to be analysed simultaneously at single-cell resolution. These analyses revealed that new DNA methylation is gained during early sperm development and is associated with gene repression. Importantly, this relationship was not visible in conventional bulk analyses, demonstrating the importance of high-resolution approaches.
Using CRISPR genome editing, the project generated mutants for all known DNA methyltransferases in Marchantia. This work identified two enzymes, DNMT3A and CMTa, that cooperate to establish gene methylation. Mutant plants lacking DNMT3A display specific reproductive defects, indicating that gene methylation contributes to the correct formation of male reproductive structures.
To understand how methylation is targeted to specific genes, the project performed sequence motif analysis and comparative genomics. Candidate DNA-binding factors potentially involved in recruitment were identified. Comparative analysis with a related species revealed that gene methylation targets are evolutionarily dynamic, suggesting flexible regulatory mechanisms.
Chromatin profiling and multiomic integration further clarified the epigenetic environment of methylated genes and helped refine mechanistic models. Together, these findings provide new insight into how gene-targeted DNA methylation functions during plant reproduction.
Using CRISPR genome editing, the project generated mutants for all known DNA methyltransferases in Marchantia. This work identified two enzymes, DNMT3A and CMTa, that cooperate to establish gene methylation. Mutant plants lacking DNMT3A display specific reproductive defects, indicating that gene methylation contributes to the correct formation of male reproductive structures.
To understand how methylation is targeted to specific genes, the project performed sequence motif analysis and comparative genomics. Candidate DNA-binding factors potentially involved in recruitment were identified. Comparative analysis with a related species revealed that gene methylation targets are evolutionarily dynamic, suggesting flexible regulatory mechanisms.
Chromatin profiling and multiomic integration further clarified the epigenetic environment of methylated genes and helped refine mechanistic models. Together, these findings provide new insight into how gene-targeted DNA methylation functions during plant reproduction.
The project moves beyond the traditional view that plant DNA methylation mainly silences transposable elements. It demonstrates that gene-targeted methylation can arise dynamically during development and may play a direct regulatory role in reproductive tissues.
By establishing single-cell epigenomic technologies in an early land plant, the project expands methodological capabilities in plant biology. The integration of genome editing, chromatin profiling and evolutionary genomics provides a comprehensive framework for understanding how epigenetic regulation evolves.
In the long term, improved understanding of gene-targeted methylation may inform future approaches to epigenetic engineering in crops, potentially contributing to improved developmental control and stress resilience. The knowledge generated also strengthens European expertise in advanced genomics and data-intensive life science research.
By establishing single-cell epigenomic technologies in an early land plant, the project expands methodological capabilities in plant biology. The integration of genome editing, chromatin profiling and evolutionary genomics provides a comprehensive framework for understanding how epigenetic regulation evolves.
In the long term, improved understanding of gene-targeted methylation may inform future approaches to epigenetic engineering in crops, potentially contributing to improved developmental control and stress resilience. The knowledge generated also strengthens European expertise in advanced genomics and data-intensive life science research.