Biology subjects

Kunowska, N.

Publications and source records attributed to Kunowska, N..

6 recordsLinked to original sources

bioRxiv2025

Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33

Eukaryotic ribosome synthesis is a highly complex, multistep process that is best characterized in the yeast Saccharomyces cerevisiae. It is orchestrated by over 200 ribosome assembly factors and 75 small nucleolar ribonucleoproteins (snoRNPs), which guide site-specific chemical modifications of precursor ribosomal RNA (pre-rRNA). While canonical box C/D snoRNPs direct 2-O-methylation, the atypical box C/D snoRNPs snR4 and snR45 mediate acetylation of 18S rRNA residues C1280 and C1773, respectively, catalyzed by the acetyltransferase Kre33. Here, we identify and characterize Ynl050c/Sni445 as a novel ribosome assembly factor and previously unrecognized auxiliary component of the snR4 and snR45 box C/D snoRNPs. Sni445 associates with snR4 and snR45 in their free form and is required for their stable incorporation into 90S pre-ribosomes. Genetic interactions link Sni445 and the snR4 and snR45 snoRNAs to ribosomal proteins Rps20 (uS10) and Rps14 (uS11), which are positioned near the respective acetylation sites in the 40S subunit. Moreover, Sni445 physically interacts with Kre33 within the 90S pre-ribosome, and its absence abolishes acetylation of C1280 and C1773. Our findings suggest that Sni445 facilitates the recruitment of snR4 and snR45 snoRNPs to 90S particles and might promote their interaction with Kre33, thereby enabling the site-specific acetylation of 18S rRNA by Kre33.

molecular biology↗

bioRxiv2023

Spatial and single-cell transcriptomics illuminate bat immunity and barrier tissue evolution

The Egyptian fruit bat displays tolerance to lethal viruses and unique dietary adaptations, but the molecular basis for this is poorly understood. To this end, we generated detailed maps of bat gut, lung and blood cells using spatial and single-cell transcriptomics. We compared bat with mouse and human cells to reveal divergence in genetic programs associated with environmental interactions and immune responses. Complement system genes are transcriptionally divergent, uniquely expressed in bat lung and gut epithelium, and undergo rapid coding-sequence evolution. Specifically in the tip of the gut villus, bat enterocytes express evolutionarily young genes while lacking expression of genes related to specific nutrient absorption. Profiling immune stimulation of PBMCs revealed a monocyte subset with conserved cross-species interferon expression, suggesting strong constraints to avoid an excessive immune response. Our study thus uncovers conserved and divergent immune pathways in bat tissues, providing a unique resource to study bat immunity and evolution.

genomics↗

bioRxiv2021

A human kinase yeast array for the identification of kinases modulating phosphorylation-dependent protein-protein interactions

Protein kinases play an important role in cellular signaling pathways and their dysregulation leads to multiple diseases, making kinases prime drug targets. While more than 500 human protein kinases are known to collectively mediate phosphorylation of over 290,000 S/T/Y sites, the activities have been characterized only for a minor, intensively studied subset. To systematically address this discrepancy, we developed a human kinase array in Saccharomyces cerevisiae as a simple readout tool to systematically assess kinase activities. For this array, we expressed 266 human kinases in four different Saccharomyces cerevisiae strains and profiled ectopic growth as a proxy for kinase activity across 33 conditions. More than half of the kinases showed an activity-dependent phenotype across many conditions and in more than one strain. We then employed the kinase array to identify the kinase(s) that can modulate protein-protein-interactions (PPIs). Two characterized, phosphorylation-dependent PPIs with unknown kinase-substrate relationships were analyzed in a phospho-yeast two-hybrid assay. CK21 and SGK2 kinases can abrogate the interaction between the spliceosomal proteins AAR2 and PRPF8 and NEK6 kinase was found to mediate the estrogen receptor (ER) interaction with 14-3-3 proteins. The human kinase yeast array can thus be used for a variety of kinase activity-dependent readouts.

systems biology↗

bioRxiv2020

RUNX1 controls the dynamics of cell cycle entry of naive resting B cells by regulating expression of cell cycle and immunomodulatory genes in response to BCR stimulation

RUNX1 is a transcription factor that plays key roles in haematopoietic development and in adult haematopoiesis and lymphopoiesis. Here we report that RUNX1 is also involved in controlling the dynamics of cell cycle entry of naive resting B cells in response to stimulation of the B cell receptor (BCR). Conditional knockout of Runx1 in mouse resting B cells resulted in accelerated entry of the cells into S-phase following BCR engagement. Our results indicate that Runx1 regulates the cyclin D2 (Ccnd2) gene, the immediate early genes, Fosl2, Atf3 and Egr2, and the Notch effector Rbpj, in B cells, reducing the rate at which transcription of these genes increases following BCR stimulation. RUNX1 interacts with the chromatin remodeller SRCAP, recruiting it to promoter and enhancer regions of the Ccnd2 gene. BCR-mediated activation triggers switching between binding of RUNX1 and its paralog RUNX3 and between SRCAP and the SWI/SNF remodelling complex member BRG1. We also find that RUNX1 regulates expression of a number of immunomodulatory genes in resting B cells. These include the interferon receptor subunit gene Ifnar1, which is upregulated in B cells from lupus patients, the Ptpn22 gene, which has been identified as a major lupus risk allele, and the Lrrk2 gene, which is mutated in familial Parkinsons disease. The hyperresponsiveness of the Runx1 knockout B cells to antigen stimulation and its role in regulating a suite of genes that are known to be associated with autoimmune disease suggest that RUNX1 is a major regulator of B cell tolerance and autoimmunity.

immunology↗

bioRxiv2019

Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets

Identifying cellular functions dysregulated by disease associated variants could implicate novel pathways for drug targeting or modulation in cell therapies. Variants associated with immune diseases point towards the role of CD4+ regulatory T cells (Tregs), cell type critical for immune homeostasis. To translate the effects of immune disease alleles on Treg function we mapped genetic regulation (QTL) of gene expression and chromatin activity in Tregs. We identified 123 loci where Treg QTLs colocalized with immune disease variants. These colocalizations indicated that dysregulation of key Treg pathways, including cell activation via CD28 and IL-2 signalling mediated by STAT5A contribute to the shared pathobiology of immune diseases. Finally, using disease GWAS signals colocalizing with Treg QTLs, we identified 34 known drug targets and 270 targets with drug tractability evidence. Our study is the first in-depth characterization of immune disease variant effects on Treg gene expression modulation and dysregulation of Treg function.

genetics↗

bioRxiv2017

A Balance Between Regulatory Constraints And Pathogen Pressure Shapes The Evolution Of Innate Immunity

As the first line of defence against pathogens, cells mount an innate immune response, which is highly variable from cell to cell. The response must be potent yet carefully controlled to avoid self-damage. How these constraints have shaped the evolution of innate immunity remains poorly understood. Here, we characterise this programmes transcriptional divergence between species and expression variability across cells. Using bulk and single-cell transcriptomics in primate and rodent fibroblasts challenged with an immune stimulus, we reveal a striking architecture of the innate immune response. Rapidly diverging genes, including cytokines and chemokines, also vary across cells and have distinct promoter structures. Conversely, genes involved in response regulation, such as transcription factors and kinases, are conserved between species and display low cell-to-cell variability. We suggest that this unique expression pattern, observed across species and conditions, has evolved as a mechanism for fine-tuned regulation, to achieve an effective but balanced response.

evolutionary biology↗