Gai, K. | Search bioRxiv

bioRxiv2025

Uncovering directionally and temporally variable genes with STAVAG

Spatially variable genes (SVGs) are crucial for understanding spatial heterogeneity in spatial transcriptomics. Yet, SVGs are challenging to align with established biological axes and lack straightforward mechanistic interpretation, thereby limiting their ability to inform downstream experiments or clinical applications. Here, we introduce the concept of directionally variable genes (DVGs) and temporally variable genes (TVGs). Also, we propose a unified framework, STAVAG, that models spatial or temporal information to identify DVGs and TVGs. STAVAG effectively identifies biologically meaningful DVGs for uncovering prognostically relevant gene modules that align with the malignant-immune-stroma structure in the tumor microenvironment, identifying marker genes in three-dimensional brain data, and detecting 12 polarization genes regulating planarian regeneration. Furthermore, by tracking the progression of myocardial infarction and tissue development, STAVAG reveals critical TVGs that can serve as diagnostic biomarkers for the ultra-acute phase of myocardial infarction. STAVAG also identifies both global and local gene modules involved in mouse placentation, as well as tissue-specific and interactive TVG modules that dynamically evolve during mouse embryonic development.

bioinformatics↗

bioRxiv2020

The histone variant H2A.Z is required to establish normal patterns of H3K27 methylation in Neurospora crassa

Neurospora crassa contains a minimal Polycomb repression system, which provides rich opportunities to explore Polycomb-mediated repression across eukaryotes and enables genetic studies that can be difficult in plant and animal systems. Polycomb Repressive Complex 2 is a multi-subunit complex that deposits mono-, di-, and tri-methyl groups on lysine 27 of histone H3, and tri-methyl H3K27 is a molecular marker of transcriptionally repressed facultative heterochromatin. In mouse embryonic stem cells and multiple plant species, H2A.Z has been found to be co-localized with H3K27 methylation. H2A.Z is required for normal H3K27 methylation in these experimental systems, though the regulatory mechanisms are not well understood. We report here that Neurospora crassa mutants lacking H2A.Z or SWR-1, the ATP-dependent histone variant exchanger, exhibit a striking reduction in levels of H3K27 methylation. RNA-sequencing revealed downregulation of eed, encoding a subunit of PRC2, in an hH2Az mutant compared to wild type and overexpression of EED in a {Delta}hH2Az;{Delta}eed background restored most H3K27 methylation. Reduced eed expression leads to region-specific losses of H3K27 methylation suggesting that EED-dependent mechanisms are critical for normal H3K27 methylation at certain regions in the genome. AUTHOR SUMMARYEukaryotic DNA is packaged with histone proteins to form a DNA-protein complex called chromatin. Inside the nucleus, chromatin can be assembled into a variety of higher-order structures that profoundly impact gene expression. Polycomb Group proteins are important chromatin regulators that control assembly of a highly condensed form of chromatin. The functions of Polycomb Group proteins are critical for maintaining stable gene repression during development of multicellular organisms, and defects in Polycomb proteins are linked to disease. There is significant interest in elucidating the molecular mechanisms that regulate the activities of Polycomb Group proteins and the assembly of transcriptionally repressed chromatin domains. In this study, we used a model fungus to investigate the regulatory relationship between a histone variant, H2A.Z, and a conserved histone modifying enzyme complex, Polycomb Repressive Complex 2 (PRC2). We found that H2A.Z is required for normal expression of a PRC2 component. Mutants that lack H2A.Z have defects in chromatin structure at some parts of the genome, but not others. Identification of PRC2-target domains that are differentially dependent on EED provides insights into the diverse mechanisms that regulate assembly and maintenance of facultative heterochromatin in a simple model system. Data Reference NumbersGSE146611

genetics↗

bioRxiv2018

N-terminal degradation activates the Nlrp1b inflammasome

Intracellular pathogens and danger signals trigger the formation of inflammasomes, which activate inflammatory caspases and induce pyroptotic cell death. The anthrax lethal factor metalloprotease and small molecule DPP8/9 inhibitors both activate the Nlrp1b inflammasome, but the molecular mechanism of Nlrp1b activation is not known. Here, we used genome-wide CRISPR/Cas9 knockout screens to identify genes required for Nlrp1b-mediated pyroptosis, and discovered that lethal factor induces cell death via the N-end rule proteasomal degradation pathway. Lethal factor directly cleaves Nlrp1b, which induces the N-end rule-mediated degradation of the Nlrp1b N-terminus and thereby frees the Nlrp1b C-terminus to activate caspase-1. DPP8/9 inhibitors also induce proteasomal degradation of the Nlrp1b N-terminus, but, in contrast, not through the N-end rule pathway. Overall, these data reveal that N-terminal degradation is the common mechanism for activation of this innate immune sensor protein.\n\nOne Sentence SummaryProteasome-mediated degradation of the Nlrp1b N-terminus releases the Nlrp1b C-terminus to activate caspase-1 and induce pyroptotic cell death.

immunology↗