Biology subjects

Shakir, D.

Publications and source records attributed to Shakir, D..

4 recordsLinked to original sources

bioRxiv2026

KDM2B controls HIF levels and activity through its JmjC and CxxC domains

Hypoxia-inducible factors (HIFs) are key regulators of cellular responses to low oxygen (hypoxia), controlling the expression of genes required for survival and adaptation. KDM2B, a chromatin-modifying enzyme, is a direct target of HIF-1, but its precise role in regulating HIF and the hypoxia response remains unclear. Here, we investigated the role of KDM2B in the response to hypoxia in a variety of cell lines. Our analysis reveals that KDM2B depletion regulates HIF activity in a cell type-dependent manner, with KDM2B depletion decreasing HIF activity in U2OS and MDA-MB-231 cells and increasing HIF activity in HeLa cells. We show that KDM2B depletion also reduces HIF-1 protein and RNA expression and reduces HIF-1 binding at hypoxia-response elements of its target genes in U2OS and MDA-MB-231 cells. Conversely, overexpression of KDM2B enhances HIF activity and HIF-1 levels in both U2OS and HEK293 cells. Mechanistically, we find that KDM2B requires its JmjC demethylase and CxxC DNA-binding domains for HIF regulation. Furthermore, we demonstrate that KDM2B is required for RNA Pol II recruitment to the promoter of HIF1A. At the cellular level, KDM2B supports cell proliferation, with its depletion impairing proliferation and reducing cell numbers under hypoxic conditions. Our work highlights a new function of KDM2B as a key regulator of HIF-1 expression, acting through its demethylase and DNA-binding functions. Our data indicate that KDM2B is essential for cellular adaptation to hypoxia, impacting both HIF-dependent gene expression and cell survival, and has important implications for our understanding of HIF regulation.

molecular biology↗

bioRxiv2025

PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression

Prolyl-hydroxylases (PHDs) are oxygen sensing enzymes that mediate the hydroxylation of proline residues. In mammals, three PHD isoforms (PHD1-3) are responsible for proline hydroxylation of Hypoxia Inducible Factor (HIF) alpha, a key regulator of the hypoxia response. In the accompanying paper (Jiang et. al., 2025) we report development of a mass spectrometry-based method to reliably identify proline hydroxylation (OH-Pro) sites on proteins and use this to identify a PHD-dependent OH-Pro modification at Pro604 on the protein RepoMan (CDCA2), a regulatory subunit for protein phosphatase PP1{gamma}, with important roles in mitotic progression and cell viability. Here, we investigate the functional significance of hydroxylation of RepoMan at P604. During M phase, the PP1-RepoMan complex dephosphorylates Thr3 of Histone H3 (H3T3) on chromosomes arms to ensure the correct localisation of the chromosomal passenger complex (CPC) at centromeres. We show that siRNA depletion of PHD1, but not PHD2, increases H3T3 phosphorylation in prometaphase-arrested cells. In cells depleted of endogenous RepoMan, exogenous expression of wild type RepoMan, but not a RepoMan P604A mutant, restored normal H3T3 phosphorylation localisation in prometaphase arrested cells. RepoMan P604 is located proximal to the Short Linear Motifs (SLiMs) that function as binding sites for the serine/threonine Protein Phosphatase 2A (PP2A). The interaction of RepoMan and PP2A-B56{gamma} is reduced in cells expressing RepoMan P604A. Moreover, analyses in both fixed and live cells released from a prometaphase arrest, show that expression of the RepoMan P604A mutant delays completion of mitosis, results in defects in chromosome alignment and segregation and increases levels of cell death. These data support a role for PHD1-mediated prolyl hydroxylation in controlling progression through mitosis, acting, at least in part, via hydroxylation of RepoMan at P604 regulating the interaction of RepoMan with PP2A during chromosome alignment and thereby controlling the levels of Histone H3 phosphorylation at Thr3.

cell biology↗

bioRxiv2025

NF-κB is a Central Regulator of Hypoxia-Induced Gene Expression

Hypoxia is both a physiological and pathological signal in cells. Changes in gene expression play a critical role in the cellular response to hypoxia, enabling cells to adapt to reduced oxygen availability. These changes are primarily mediated by the HIF family of transcription factors, however other transcription factors such as NF-{kappa}B, are also activated by hypoxia. Although NF-{kappa}B is known to be activated by hypoxia, the extent to which NF-{kappa}B contributes to the hypoxic response remains poorly understood. Here, we analysed hypoxia-induced, NF-{kappa}B-dependent gene expression, to define the NF-{kappa}B-dependent hypoxic signature. Our analysis reveals that most genes downregulated by hypoxia require NF-{kappa}B for their repression. We show that although the NF-{kappa}B-mediated hypoxic response may vary between cell types, a core subset of hypoxia-inducible genes requires NF-{kappa}B across multiple cell backgrounds. We demonstrate that NF-{kappa}B is critical for reactive oxygen species (ROS) generation and regulation of genes involved in oxidative phosphorylation under hypoxia. This work highlights NF-{kappa}Bs central role in the hypoxia response and offering new insights into gene expression regulation by hypoxia and NF-{kappa}B.

molecular biology↗

bioRxiv2022

Regulation of Chromatin Accessibility by hypoxia and HIF

Reduced oxygen availability (hypoxia) can act as a signalling cue in physiological processes such as development, but also in pathological conditions such as cancer or ischaemic disease. As such, understanding how cells and organisms respond to hypoxia is of great importance. The family of transcription factors called Hypoxia Inducible Factors (HIFs) coordinate a transcriptional programme required for survival and adaptation to hypoxia. The effects of hypoxia and HIF on the chromatin accessibility landscape are still unclear. Here, using genome wide mapping of chromatin accessibility via ATAC-seq, we find hypoxia induces loci specific changes in chromatin accessibility enriched at hypoxia transcriptionally responsive genes. These changes are predominantly HIF dependent, reversible upon reoxygenation and partially mimicked by chemical HIF stabilisation independent of molecular dioxygenase inhibition. This work demonstrates that indeed, HIF stabilisation is necessary and sufficient to alter chromatin accessibility in hypoxia, with implications for our understanding of gene expression regulation by hypoxia and HIF.

molecular biology↗