Popmihaylova, A.-M. | Search bioRxiv

bioRxiv2025

Looping specificity of Polycomb response elements requires GAF and a combinatorial code of looping factors

Chromatin looping between cis-regulatory elements is essential for precise developmental gene expression, and its disruption is frequently linked to disease. Polycomb Response Elements (PREs) are specialized tethering elements that mediate chromatin loops and are bound by transcription factors like GAGA-associated factor (GAF), contributing to the recruitment of Polycomb group (PcG) proteins. While both PcG proteins and GAF have been implicated in looping, their specific roles and the mechanisms of loop specificity remain unresolved. Using genome-wide and locus-specific approaches, we show that high GAF occupancy is required for chromatin looping and gene regulation. However, GAF alone cannot establish loops without additional factors. Surprisingly, PRE looping does not require the PcG subunit Polyhomeotic (PH) or the repressive histone marks H3K27me3. Intriguingly, orthologous PRE sequences can rescue looping, while unrelated PREs with similar GAF levels cannot. This indicates that looping specificity depends on both GAF levels and compatible factor combinations at loop anchors. Our results support a combinatorial model in which GAF collaborates with additional looping factors, to drive PRE-specific interactions. We propose the existence of a "looping code" as a mechanistic basis that might explain why only a subset of PREs form loops and contribute to Polycomb-mediated gene silencing.

molecular biology↗

bioRxiv2025

A tumor-suppressive role of the PRC1 Polycomb epigenetic complex in the maintenance of adult Drosophila intestinal stem cell identity

Chromatin modulators, like Polycomb group proteins, are key epigenetic regulators of gene expression and are frequently mutated in cancers. In adult stem cells, epigenetic regulation maintains their identity and controls their differentiation during homeostasis or aging, but its direct role in tumorigenesis remains unclear. Here we developed a novel tumor model in Drosophila by exploring the function of Polycomb Repressive Complex 1 (PRC1) in adult intestinal stem cells (ISCs). Disrupting core PRC1 components in ISCs induces the formation of small cell clusters devoid of intestinal markers, a novel phenotype linked to premature mortality under stress. These clusters exhibit neoplastic characteristics such as overproliferation and continuous growth in serial transplantations, leading to their designation as tumor-initiating intestinal cells (TIICs). While JAK/STAT signaling contributes to TIIC growth, the NF-{kappa}B-related Toll/Imd immune pathways restrict their expansion independently of cell death. Altogether, our results highlight PRC1 as an epigenetic tumor suppressor in adult stem cells. AUTHOR SUMMARYOur research explores how stem cells in the adult intestine stay healthy and avoid becoming cancerous. We focused on a group of proteins called Polycomb Repressive Complex 1 (PRC1), which help regulate which genes are turned off in a cell. While these proteins are known to play important roles during development and cancer prevention, their function in the adult intestine has been less clear. Using the fruit fly Drosophila, we discovered that when PRC1 function is lost in intestinal stem cells, abnormal clusters of cells begin to form. These clusters grow uncontrollably, lose their normal identity, and can keep growing when transplanted--traits that are typical of cancer. Interestingly, we also found that parts of the immune system, specifically NF-{kappa}B-related pathways, can act inside these tumor cells to limit their growth--revealing a protective role that hasnt been seen before in the adult gut. This work provides new insights into how epigenetic regulation and immune signaling work together to keep stem cells from turning cancerous. It opens up new possibilities for understanding how cancers begin and how the body may naturally resist them, even at the level of the tissue.

cancer biology↗