Polycomb Repressive Complex 2, or PRC2, is the enzyme responsible for writing one of biology’s most important repressive marks, the trimethylation of histone H3 at lysine 27, known as H3K27me3. In animals and plants, this mark silences developmental genes and helps cells remember what they are supposed to become. Once PRC2 establishes H3K27me3, the mark can spread along chromosomes through a read-write mechanism in which the complex recognizes the modification it has just deposited and methylates neighboring nucleosomes. Remarkably, in mammals these repressed domains can persist through many rounds of cell division even when the DNA sequences that originally recruited PRC2 are no longer needed, implying that the mark itself carries heritable information.

Fungi present an intriguing simplification of this picture. Polycomb Repressive Complex 1, which in plants and animals helps recruit and reinforce PRC2, was apparently lost early in fungal evolution, yet many filamentous fungi still assemble large H3K27me3 domains that stably repress condition-specific genes. In Neurospora crassa, these domains cover roughly seven percent of the genome and cluster together in three-dimensional nuclear space. The fungus therefore offers a clean experimental system for asking whether H3K27me3 can be inherited across mitosis without PRC1, and which factors make that inheritance possible.

The Georgia team began with a genetic screen, searching RNA-sequencing datasets for knockout strains that had lost repression of H3K27me3-marked genes. RTT109 stood out. This enzyme was originally discovered in budding yeast as a regulator of Ty1 transposition and is best known for acetylating histone H3 at lysine 56 on newly synthesized histones during replication-coupled nucleosome assembly, the process by which old histones are recycled and new ones deposited behind the replication fork. When the researchers deleted the rtt109 gene, a reporter gene embedded in a facultative heterochromatin domain switched on, mimicking the effect of destroying PRC2 itself.

Transcriptomic analysis confirmed the breadth of the defect. Of 573 genes normally marked with H3K27me3, 136 were significantly upregulated in the rtt109 deletion strain, and the misexpressed genes were strongly enriched for functions normally activated during fruiting body development, including fungal cell wall synthesis and chitin metabolism. Importantly, deleting other histone acetyltransferases did not reproduce this pattern, showing that the effect is specific to RTT109 rather than a generic consequence of altered histone acetylation. Across the whole genome, 705 of 722 differentially expressed genes were upregulated, consistent with a loss of repression rather than a broad transcriptional collapse.

Chromatin immunoprecipitation sequencing revealed that the transcriptional defects were accompanied by structural erosion of the repressed domains themselves. In the deletion strain, 102 of 281 H3K27me3 domains lost at least half of their signal, and the median domain size shrank from 6.1 kilobases in wild type to 4.5 kilobases. The losses were regional rather than uniform: domains near telomeres, which act as strong recruitment sites for PRC2, retained or even gained the mark, while losses increased with distance from chromosome ends. Introducing a tagged wild-type copy of rtt109 restored both the methylation pattern and the DNA-damage repair defect characteristic of the mutant, confirming that RTT109 was directly responsible.

The team then dissected the mechanism with a series of elegant controls. RTT109 is known to work with histone chaperones, and affinity purification coupled to mass spectrometry identified NAF-2, the Neurospora homolog of yeast Vps75, as a high-confidence interactor, with AlphaFold 3 predicting a detailed contact interface between the two proteins. Yet deleting naf-2 did not disrupt H3K27me3 or gene repression, and neither did reducing levels of the essential chaperone ASF-1. More strikingly, histone H3 mutants that either abolish or mimic acetylation at lysine 56, RTT109’s canonical substrate, left H3K27me3 patterns essentially intact. In contrast, engineered catalytically dead versions of RTT109 failed to rescue the methylation defects and even worsened them, suggesting a dominant-negative effect. The conclusion is that RTT109’s enzymatic activity is required for Polycomb-repressed chromatin, but its famous product, H3K56 acetylation, is not the relevant output.

To test whether RTT109 safeguards epigenetic memory over time, the researchers passaged a freshly backcrossed deletion strain through successive rounds of asexual reproduction, each passage representing roughly 25 to 30 mitotic divisions. H3K27me3 declined progressively with each passage, indicating that the mark decays without RTT109 rather than being lost instantly. A second repressive mark, H3K36me3 deposited by the methyltransferase ASH1 within the same facultative heterochromatin domains, was lost much more rapidly, appearing already depleted in the earliest isolate. Because ASH1-dependent H3K36 methylation is known to support gene silencing and proper H3K27me3 patterning in Neurospora, the authors propose that its early loss may trigger the slower decay of H3K27me3 downstream.

The most decisive experiment used a synthetic system to separate establishment from maintenance. The team tethered a PRC2 subunit, SUZ12, to an array of tet operator sequences inserted at a defined genomic locus, allowing them to direct de novo H3K27me3 deposition at will. Adding tetracycline released the tether, and the researchers could then ask whether the native PRC2 complex could maintain the mark without sequence-specific recruitment. In wild-type cells, H3K27me3 persisted at the array for at least 24 hours, an interval estimated to span 10 to 12 rounds of nuclear division, demonstrating true epigenetic inheritance in an organism that lacks PRC1. In cells lacking RTT109, establishment at the array was normal, but maintenance after release of the tether failed, with significantly reduced H3K27me3 levels.

Together, these results establish RTT109 as a replication-linked factor essential for the mitotic stability of Polycomb-repressed chromatin, and they reveal a PRC1-independent route to epigenetic memory in fungi. The relevant substrate of RTT109 remains unknown. It may acetylate a histone residue other than lysine 56, transiently opening the H3 tail to facilitate methylation, or it may modify a non-histone protein; the Neurospora acetylome contains hundreds of acetylated proteins, including chromatin regulators such as the remodeler ISW and the deacetylase RPD3. Because RTT109 is fungal-specific and required for virulence in pathogens such as Candida albicans and Aspergillus fumigatus, the discovery that it underpins epigenetic plasticity also marks it as a potential therapeutic target. More broadly, the work adds to mounting evidence that the machinery of DNA replication is not merely a bystander in epigenetics but an active custodian of cellular memory.

Subject of Research: Epigenetic maintenance of PRC2-repressed chromatin by the histone acetyltransferase RTT109 in Neurospora crassa

Article Title: Epigenetic maintenance of PRC2-repressed chromatin requires RTT109 but not H3K56 acetylation

Article References: Yap, R. E., Ebot-Ojong, F., Ameri-Solanky, A. J., & Lewis, Z. A. (2026). Epigenetic maintenance of PRC2-repressed chromatin requires RTT109 but not H3K56 acetylation. PLOS Genetics, 22(10), e1012327. https://doi.org/10.1371/journal.pgen.1012327

Image Credits: AI Generated

DOI: 10.1371/journal.pgen.1012327

Keywords: epigenetics, PRC2, H3K27me3, RTT109, chromatin, Neurospora crassa, histone acetylation, facultative heterochromatin, DNA replication, gene silencing, epigenetic memory, PLOS Genetics

The core idea of epigenetics is deceptively simple: chemical tags and structural changes to chromatin, the complex of DNA and proteins in which our genes are packaged, can switch genes on or off, and some of these regulatory networks are reversible while still leaving a form of memory. That combination of plasticity and persistence, the editors argue, underlies the potential of epigenetics to influence physiological and pathological mechanisms across all kingdoms of life. But the simplicity ends there. The regulatory machinery is convoluted, and exploiting the continuously improving genomics technology portfolio, epigenome-wide association studies have produced extensive databases with nucleotide resolution and single cell precision at increasingly affordable costs. These datasets, spanning many organisms, reveal both differences and similarities across species, and integrating them is expected to deepen our understanding of functional epigenomics.

One of the most significant accelerants has been the CRISPR revolution. Nuclease-inactivated Cas9 proteins can now be fused to epigenetic writers or erasers, enzymes that add or remove chromatin marks, allowing researchers to interfere with specific epigenetic modifications at any given chromatin context. According to the editorial, such epigenetic editing studies have already yielded agricultural and preclinical therapeutic successes, alongside the essential scientific insights they provide. The ability to target the epigenome with the same precision that CRISPR brought to genome editing suggests a future in which gene expression itself becomes a programmable therapeutic and biotechnological target.

Yet the editors are candid about the bottlenecks. While individual epigenetic modifications have been mined and functionally studied one by one, the systems and networks they form, and the ways those networks become deregulated, remain far from understood. The intrinsic dynamic nature of chromatin, and the potentially rapid transitions between active euchromatin and silent heterochromatin, still pose formidable technological challenges. Complicating matters further, the so-called epi-players that regulate these transitions switch between chromatin-bound and unbound states, and chromatin modifications show not only rapid state changes but an intrinsic deposition or transition order with functional consequences. Understanding these epidynamic transitions, their spatial deconvolution within the cell, and their impact on genome functioning and organismal adaptation is, the editors write, work that has yet to be done.

That is why the interpretation of the dynamic epigenome and its spatiotemporal organization in different biological systems may prove to be a crucial layer of knowledge in physiology and pathology, from basic research through preclinical and biotechnological applications. Unveiling the networks of epimodulatory events and their precise order, using novel computational methods capable of analysis at the single cell level, holds the key to understanding how gene expression is regulated and how the causal, rather than casual, order of cellular events leads to chromatin organization while preserving the stability and maintenance of cellular function. The study of what the editors call network epigenetics may advance mechanistic understanding of epigenetic dynamics within the three-dimensional structure of cells and tissues, topics that receive dedicated sections in the new journal.

Metabolism adds another layer of complexity. Chromatin epiregulators may take advantage of the abundance of metabolic cofactors, supporting the concept that the availability of those cofactors might determine, to some extent, the prioritization of cellular events. Integrating basic epigenome information with the dynamics and metabolic status of cells, the editors suggest, could bridge fundamental research and preclinical information in the fight against disease. It is a vision of epigenetics as a systems science, one in which chemical marks, three-dimensional genome architecture, metabolic state and time itself are read together rather than in isolation.

The journal also takes a deliberate stance on a problem that has long plagued the field: reproducibility. Given the explosion of epigenetic-based studies, the editors argue it is crucial to distinguish reproducible from irreproducible approaches, and to recognize that technically sound studies can fail to prove a scientific hypothesis without being failures at all. Epigenetics Communications intends to act as a forum for showcasing and discussing alternative conclusions and interpretations of well-established epigenetic phenomena, based on reanalyses of published data or new experiments. The journal welcomes systematic studies whether their outcomes are positive and expected or negative and unexpected, a policy its associate editors greeted with enthusiasm in interviews conducted by Vanessa Tse of the University of Bath.

Several of those editors emphasized how unusual and valuable such a platform is. Karl Ekwall noted that negative results are quite common in research and often hard to publish, and that sharing them saves others in the community from repeating the same experiments. Torsten Plösch observed that many researchers are often afraid of showing results that contradict their expectations, and argued that publishing wrong expectations and negative data is a very important part of the scientific process, helping the field in the same way positive data do. Pernette J. Verschure added a note of caution, pointing out that publishing such data is a new attempt that needs critical reviewing, but that a thorough, well-performed study that contradicts its own hypothesis could turn out to be a genuinely interesting new finding deserving follow-up. Kimberly Glass and Frank Johannes both highlighted the journal’s role in filling a gap for important studies that contribute to understanding epigenetics without yet having specific clinical implications, work that can be used to build something larger with eventual clinical impact.

The associate editors were equally forthcoming about the changing landscape of scientific publishing. On the question of whether preprint servers such as bioRxiv pose a serious challenge to peer review, opinions diverged in interesting ways. Verschure called bioRxiv interesting for its flexibility in putting data out early for comments, but insisted peer review remains critical because researchers cannot keep track of so much data without knowing whether it is trustworthy. Plösch described the current peer review system as not ideal, comparing open commenting platforms to social media and suggesting that honest comments from colleagues are the best way to help authors publish good manuscripts. Ekwall was more emphatic, arguing that anything can be posted on bioRxiv without quality control, that peer review works very well in molecular biology and should not be abandoned, and that expert colleagues can judge quality before publication.

Looking ahead five to ten years, the editors’ associates sketched a field on the cusp of transformation. Glass predicted a recognition of the complexity of biological systems and the need to integrate across different types of data, examining how everything works together to produce networks and emergent properties. Andy Lau anticipated that advances in mass spectrometry and sequencing technologies will continue to reveal novel epimodifications, and that deciphering and manipulating epigenomes might open new avenues in drug design for better treatment of human diseases. Frank Dekker expected data science to play a growing role alongside large epigenome mapping initiatives, yielding new drug targets, new pathways and links to new diseases, and ultimately innovations in diagnosis and therapy. Frank Johannes foresaw the field remaining dominated by technological advances, particularly in single cell epigenomic sequencing assays, which will provide unprecedented insights into functional variation across cell types and development, while dropping sequencing costs allow epigenomic projects to scale up to population level surveys. With its first volume now open, Epigenetics Communications is betting that the next chapter of epigenetics will be written not in isolated discoveries but in the connections between them.

Subject of Research: Epigenetic gene regulation, chromatin dynamics and the launch of a journal for fundamental epigenomics research

Article Title: Epigenetics Communications: where are we?

Article References: Altucci, L., & Rots, M. G. (2021). Epigenetics Communications: where are we?. Epigenetics Communications, 1(1), Article 1. https://doi.org/10.1186/s43682-021-00006-2

Image Credits: AI Generated

DOI: 10.1186/s43682-021-00006-2

Keywords: epigenetics, chromatin, CRISPR epigenetic editing, epigenome-wide association studies, single cell sequencing, network epigenetics, negative results publishing, peer review, bioRxiv, metabolic cofactors, gene expression, Clinical Epigenetics