Biology subjects

Healy, E.

Publications and source records attributed to Healy, E..

4 recordsLinked to original sources

bioRxiv2025

Accessory subunits of PRC2 mimic H3K27me3 to restrict the spread of Polycomb domains

The Polycomb repressive complex 2 (PRC2) is essential for normal development by maintaining developmental gene repression. PRC2 deposits the repressive chromatin mark H3 lysine 27 tri-methyl (H3K27me3) through a read-write loop that involves direct interactions between PRC2 and H3K27me3. According to current models, the PRC2-H3K27me3 read-write loop is initiated by the PRC2 subunits JARID2 and PALI1 that mimic H3K27me3. However, it is unknown what restricts the PRC2-H3K27me3 read-write loop from spreading H3K27me3 indefinitely. To answer this question, we generated mutant mice where PRC2 subunits cannot mimic H3K27me3. Unexpectedly, the mutations led to delayed Hox genes activation and a homeotic transformation characteristic of a Polycomb gain-of-function in vivo and the spread of H3K27me3 beyond Polycomb domains in stem cells. Collectively, we show that H3K27me3 mimicry evolved to compete against the PRC2-H3K27me3 read-write loop in a process that restrains PRC2 and restricts the spread of Polycomb domains. HighlightsO_LIH3K27me3 mimicry antagonises Polycomb function in vivo. C_LIO_LIJARID2 and PALI1 synergise to allosterically regulate PRC2 during development. C_LIO_LIH3K27me3 mimicry by JARID2 and PALI1 antagonises PRC2 in stem cells. C_LIO_LIJARID2 and PALI1 mimic H3K27me3 to restrict the spread of Polycomb domains. C_LI

molecular biology↗

bioRxiv2025

The MicroMap is a network visualisation resource for microbiome metabolism

The human microbiome plays a crucial role in metabolism and thereby influences health and disease. Constraint-based reconstruction and analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within the computational systems biology community. Unlike for human, no large-scale visualisation resource for microbiome metabolism has been available to date. To address this gap, we created the MicroMap, a manually curated microbiome metabolic network visualisation, which captures the metabolic content of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5,064 unique reactions and 3,499 unique metabolites, including for 98 drugs. The MicroMap allows users to intuitively explore microbiome metabolism, inspect microbial metabolic capabilities, and visualise computational modelling results. Further, the MicroMap shall serve as an educational tool to make microbiome metabolism accessible to broader audiences beyond computational modellers. For example, we utilised the MicroMap to generate a comprehensive collection of 257,429 visualisations, corresponding to the entire scope of our current microbiome reconstruction resources, to enable users to visually compare and contrast the metabolic capabilities for diaerent microbes. The MicroMap seamlessly integrates with the Virtual Metabolic Human (VMH, www.vmh.life) and the COBRA Toolbox (opencobra.github.io), and is freely accessible at the MicroMap dataverse (https://dataverse.harvard.edu/dataverse/micromap), in addition to all the generated reconstruction visualisations.

systems biology↗

bioRxiv2023

The apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion

RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favour and against this idea. RNase treatment of chromatin is a prevalent tool for the study of RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. RNase A treatment during chromatin immunoprecipitation (RNase-ChIP or rChIP) reduces chromatin occupancy of the H3K27me3 methyltransferase PRC2. This led to suggestions of an "RNA bridge" between PRC2 and chromatin. Here we show that RNase A treatment during chromatin immunoprecipitation leads to the apparent loss of all facultative heterochromatin, including both PRC2 and H3K27me3 genome wide. This phenomenon persists in mouse embryonic stem cells, human cancer cells and human-induced pluripotent stem cells. We track this observation to a gain of DNA from non-targeted chromatin, sequenced at the expense of DNA from facultative heterochromatin, which reduces ChIP signals. Our results point to substantial limitations in using RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay. HighlightsO_LIRNA degradation during ChIP-seq is insufficient to displace PRC2 from chromatin. C_LIO_LIRNA degradation led to the artificial depletion of ChIP-seq signals in multiple cell lines. C_LIO_LIArtificially reduced ChIP-seq signals are explained by a gain of non-targeted DNA. C_LIO_LIRNA is critical in maintaining the solubility of chromatin during experimentation. C_LI

molecular biology↗

bioRxiv2022

Programmed cell death-1 receptor mediated regulation of Tbet+ NK1.1- Innate Lymphoid Cells within the Tumor Microenvironment

Innate Lymphoid Cells (ILCs) play a key role in tissue mediated immunity and can be controlled by co-receptor signaling. Here we define a subset of ILCs that are Tbet+NK1.1- and are present within the tumor microenvironment (TME). We show programmed death-1 receptor (PD-1) expression on ILCs within TME is found in Tbet+NK1.1-ILCs. PD-1 significantly controlled the proliferation and function of Tbet+NK1.1-ILCs in multiple murine and human tumors. We found tumor derived lactate enhanced PD-1 expression on Tbet+NK1.1-ILCs within the TME, which resulted in dampened mTOR signaling along with increased fatty acid uptake. In line with these metabolic changes, PD-1 deficient Tbet+NK1.1-ILCs expressed significantly increased IFN{gamma}, granzyme B and K. Furthermore, PD1 deficient Tbet+NK1.1- ILCs contributed towards diminished tumor growth in an experimental murine model of melanoma. These data demonstrate that PD-1 can regulate anti-tumor responses of Tbet+NK1.1-ILCs within the tumor microenvironment. HighlightsO_LITbet+NK1.1- ILCs are found in WT and PD1 ko mice C_LIO_LIPD-1 is expressed on Tbet+NK1.1- ILC1s within multiple TME C_LIO_LIPD-1 controls the proliferation and function of Tbet+NK1.1- ILCs within the tumor microenvironment by modulating fatty acid metabolism. C_LIO_LIPD-1 regulates the proliferation of human Tbet+ ILC1s in human cutaneous squamous cell carcinoma (cSCC) and melanoma tumor microenvironment. C_LI

immunology↗