Biology subjects

Christophorou, M. A.

Publications and source records attributed to Christophorou, M. A..

5 recordsLinked to original sources

bioRxiv2025

The KRAB-Zinc Finger protein ZKSCAN3 represses enhancers via embedded retrotransposons

Gene cis-regulatory sequences are increasingly recognised as containing "domesticated" transposable elements that impact their function. The KRAB Zinc Finger Protein (KZFP) family of transcription factors is typically associated with transposable element silencing through establishment of heterochromatin. Here, using acute protein depletion in embryonic stem cells, we reveal that the KZFP ZKSCAN3 represses enhancer activity through targeting enhancer-embedded retrotransposons and that ZKSCAN3-mediated repression does not rely on the induction of heterochromatin. ZKSCAN3, which exhibits strong genetic association with the neurodevelopmental disorder schizophrenia, operates during neural differentiation and is necessary for proper cell specification and expression of genes that regulate axon guidance, neuronal motility and pathfinding. These findings define ZKSCAN3 as an enhancer regulator and uncover a heterochromatin-independent KZFP. Additionally, they exemplify how a KZFP epigenetically regulates enhancers in a native setting and highlight how transposable elements and their KZFP binders have shaped gene expression networks.

molecular biology↗

bioRxiv2023

A cyclic peptide toolkit reveals mechanistic principles of peptidylarginine deiminase IV (PADI4) regulation

Peptidylarginine deiminase IV (PADI4) deregulation promotes the development of autoimmunity, cancer, atherosclerosis and age-related tissue fibrosis. Genetic or pharmacological PADI4 inhibition is therapeutically efficacious in mice, but no clinically relevant inhibitors currently exist. PADI4 additionally mediates immune responses and cellular reprogramming, although the full extent of its physiological roles is unexplored. Despite detailed molecular knowledge of PADI4 activation in vitro, we lack understanding of its regulation within cells, largely due to lack of appropriate systems and tools. Here, we developed and applied a set of potent and selective PADI4 modulators. Using the mRNA- display-based RaPID system, we screened >1012 cyclic peptides for high-affinity, conformation-selective binders. We report PADI4_3, an inhibitor specific for the active conformation of PADI4; PADI4_7, an inert binder, which we functionalised for the isolation and study of cellular PADI4; and PADI4_11, a first-in-class activator. Using a newly developed method for the quantification of cellular PADI4 activity, we show that PADI4_3 and PADI4_11 are effective in cells. Structural studies with PADI4_11 reveal an allosteric binding mode that may reflect the mechanism that promotes cellular PADI4 activation. This work offers new understanding of PADI4 regulation and a toolkit for the study and modulation of PADI4 across physiological and pathophysiological contexts.

biochemistry↗

bioRxiv2022

A quantitative and site-specific atlas of the in vivo citrullinome reveals widespread existence of citrullination

Citrullination is the conversion of peptidyl-arginine into the non-coded amino acid citrulline. Despite its importance in physiology and disease, global identification of citrullinated proteins and precise modification sites has remained challenging. Here, we employed quantitative mass spectrometry-based proteomics to generate a comprehensive atlas of citrullination sites in a physiologically relevant cell type. Collectively, we identified 14.056 citrullination sites within 4.008 proteins and quantified their regulation upon inhibition of the citrullinating enzyme PADI4. Using this rich dataset, we uncover general mechanistic and cell biological principles of citrullination function, while providing site-specific and quantitative information on thousands of PAD4 substrates within cells. Our findings include signature histone marks and numerous modifications on transcriptional regulators and chromatin-related signaling effectors. Additionally, we identify precise citrullination sites on an extensive list of known autoantigens. Collectively, we describe systems attributes of the human citrullinome and provide a resource framework for understanding citrullinaiton at the mechanistic level.

molecular biology↗

bioRxiv2021

Peptidylarginine deiminase IV (PADI4) is not essential for cell-autonomous HSC maintenance and normal haematopoiesis

Peptidylarginine deiminases (PADIs, or PADs) are emerging as key regulators of human physiology and pathophysiology. The nuclear deiminase PADI4 regulates embryonic stem cell pluripotency, however its role in adult stem cells is unknown. PADI4 is expressed most highly in the bone marrow (BM), where it is found as part of a self-renewal-associated gene signature and shown to modulate the function of critical transcriptional regulators such as Tal1 and c-Myc, suggesting that it regulates haematopoietic development or regeneration. We investigated the functional significance of PADI4 in haematopoietic stem cell (HSC) biology and normal haematopoiesis. We employed two conditional mouse models of tissue-specific Padi4 ablation, where Padi4 was completely deleted either after the emergence of HSCs, or acutely in the BM of adult mice. We found that loss of PADI4 does not significantly affect HSC self-renewal or differentiation potential upon injury or serial transplantation, nor does it lead to exhaustion or premature ageing of HSCs. Thus, surprisingly, PADI4 is dispensable for cell-autonomous HSC maintenance, differentiation and haematopoietic regeneration. This work has important implications for the clinical use of PADI4 inhibitors as therapeutic agents in autoimmunity and cancer. Key PointsO_LIPADI4 is dispensable for steady-state and post-transplantation haematopoiesis C_LIO_LIHSCs do not require intrinsic PADI4 activity to respond to haematopoietic injury C_LIO_LIPADI4 deficiency does not lead to premature HSC ageing or exhaustion C_LI

developmental biology↗

bioRxiv2020

Protein citrullination was introduced into animals by horizontal gene transfer from cyanobacteria

Protein post-translational modifications (PTMs) add an enormous amount of sophistication to biological systems but their origins are largely unexplored. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is particularly enigmatic in an evolutionary context. The citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates but absent from yeast, worms and flies. Here, we map the surprising evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADIs share unique, functionally relevant synapomorphies that are absent from all other homologues. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be approximately 1 billion years old, far younger than the 3.35-4.52 billion years known to separate bacterial and eukaryotic lineages. Under an assumption of vertical descent, PADI sequence change is anachronistically slow during this evolutionary time frame, even when compared to mitochondrial proteins, products of likely endosymbiont gene transfer and some of the most highly conserved proteins in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial protein is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification with clear relevance in human physiology and disease.

evolutionary biology↗