New Study Reveals How Plants Pass Down Genetic Memories

Recent Research Uncovers Mechanisms of Epigenetic Inheritance in Plants

A recent scientific investigation has shed light on the role of the protein DDM1 in facilitating the methylation process that serves to suppress “jumping genes” within plant organisms. Furthermore, the study delves into how DDM1’s interaction with specific histones contributes to the preservation of epigenetic controls across successive generations. These findings hold potential implications not only for the field of agriculture but also for human genetics.

Beyond the genetic code contained within DNA, organisms pass down additional information through chemical markers that provide instructions for the utilization of the genetic material. This transfer of markers to subsequent generations is referred to as epigenetic inheritance. In the realm of plants, this phenomenon is particularly prevalent, rendering the outcomes of this research pertinent to agriculture, food security, and environmental considerations.

The investigation has been carried out by Cold Spring Harbor Laboratory (CSHL) Professors and HHMI Investigators, Rob Martienssen and Leemor Joshua-Tor. Their focus lies in unraveling the mechanisms underlying the transmission of markers that regulate the activity of transposons, also known as jumping genes. When activated, these genes are capable of repositioning themselves within the genome, potentially causing disruptions to other genetic elements. To counteract this, cells employ regulatory markers to specific sites on the DNA through a process called methylation.

The model organism for this study is Arabidopsis thaliana, a plant species widely used in fundamental biological research. With Arabidopsis as their subject, researchers at CSHL have now unearthed the intricate details of a process crucial for controlling inheritance.

Martienssen and Joshua-Tor have elucidated the role of the DDM1 protein in facilitating the placement of these regulatory markers on newly formed DNA strands. This protein is essential for plant cells due to the compact packaging of their DNA. To maintain the orderly arrangement of their genomes, cells wrap DNA around histones, proteins that aid in packaging. However, this packaging inhibits the access of critical enzymes to the DNA. Martienssen explains that prior to methylation, it’s necessary to reposition or displace the histones to allow for the process.

The discovery of DDM1 dates back three decades when Martienssen and his former colleague Eric Richards first identified it. Subsequent research has unveiled that DDM1 slides DNA along the histones, gradually revealing sites on the DNA that require methylation. Martienssen likens this movement to that of a yo-yo gliding along a string – the histones can traverse the DNA, uncovering segments at a time but never dislodging.

Through a combination of genetic experiments and biochemical analyses, Martienssen identified the specific histones that DDM1 interacts with. Joshua-Tor employed cryo-electron microscopy to capture highly detailed images of the enzyme’s interaction with DNA and associated histones. This visual data elucidated how DDM1 binds to distinct histones, leading to a remodeling of the packaged DNA structure. Joshua-Tor highlights that an unexpected link in DDM1’s structure corresponds to an initial mutation discovered years ago.

The research has also exposed how DDM1’s preference for particular histones ensures the persistence of epigenetic controls across multiple generations. The team demonstrated that a histone unique to pollen exhibits resistance to DDM1 and functions as a placeholder during cell division. Martienssen elaborates that this histone retains the memory of its location during plant development, passing this memory to the next generation.

Interestingly, the implications of these findings might extend beyond plants. Human biology also relies on proteins akin to DDM1 to uphold DNA methylation. Thus, this newly uncovered understanding could potentially contribute to our comprehension of how these proteins maintain the functionality and integrity of our genetic makeup.

The study received funding from various sources, including the National Institutes of Health, the National Science Foundation, Howard Hughes Medical Institute, Wellcome Trust, and the H2020 European Research Council. The full study can be referenced under the title “Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation,” authored by Seung Cho Lee, Dexter W. Adams, Jonathan J. Ipsaro, Jonathan Cahn, Jason Lynn, Hyun-Soo Kim, Benjamin Berube, Viktoria Major, Joseph P. Calarco, Chantal LeBlanc, Sonali Bhattacharjee, Umamaheswari Ramu, Daniel Grimanelli, Yannick Jacob, Philipp Voigt, Leemor Joshua-Tor, and Robert A. Martienssen, published on August 28, 2023, in the journal Cell (DOI: 10.1016/j.cell.2023.08.001).

Frequently Asked Questions (FAQs) about Epigenetic Inheritance

More about Epigenetic Inheritance

• Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation – The full study published in the journal Cell.
• Cold Spring Harbor Laboratory (CSHL) – The institution where the research was conducted.
• National Institutes of Health – A funding source for the study.
• National Science Foundation – Another funding source for the research.
• Howard Hughes Medical Institute – A contributor to the study’s funding.
• Wellcome Trust – A funding organization involved in the research.
• H2020 European Research Council – Another funding entity mentioned in the study.
• Arabidopsis thaliana – The plant species used in the study for research purposes.
• Cryo-electron microscopy – The technique used to capture detailed images of molecular structures.