Biology subjects

Padeken, J.

Publications and source records attributed to Padeken, J..

6 recordsLinked to original sources

bioRxiv2026

Attenuating LRRK2 activity ameliorates progerin-induced aging phenotypes in HGPS models and during physiological aging

Hutchinson-Gilford progeria syndrome (HGPS) is an ultra-rare premature aging disorder caused by progerin, a truncated lamin A variant generated by a silent de novo mutation activating a cryptic splice site in LMNA. The resulting morphological, epigenetic, genomic, and proteostasic defects closely recapitulate some hallmarks of cellular aging. Here, we identify the Parkinsons disease-associated kinase LRRK2 as a critical regulator of HGPS pathology and physiological aging. Rab29-mediated LRRK2 hyperactivation exacerbates progerin-induced cellular aging, whereas LRRK2 knockdown or overexpression of its opposing phosphatase, PPM1H, ameliorates progerin-induced defects. Progerin-expressing cells exhibit altered intracellular trafficking, which is regulated by LRRK2 and links diverse aging hallmarks. Consistent with these findings, reducing LRRK2 levels mitigates cellular aging phenotypes in physiologically aged cells, and loss of the C. elegans ortholog lrk-1 preserves aging-associated loss of motility and extends organismal lifespan. Together, our findings establish LRRK2 as a central node in cellular aging and position it as a potential therapeutic target for aging-related defects in both HGPS and physiological aging.

cell biology↗

bioRxiv2026

Correcting Preprocessing Bias in Sparse Chromatin Contact Data Enables Physically Interpretable Reconstruction of Genome Architecture

DNA is the largest biopolymer in nature, and chromatin contact maps are widely interpreted as quantitative readouts of its three-dimensional organization. However, the validity of such interpretations critically depends on how these maps are processed. Here, we identify a previously overlooked but fundamental source of bias in chromatin contact data analysis. We demonstrate that a widely adopted preprocessing convention, namely whole-matrix percentile clipping, systematically distorts sparse contact maps by collapsing their dynamic range. This effect is strongest in near-diagonal interactions, precisely the regime encoding chromatin domains and looping structures, thereby compromising quantitative interpretation while preserving superficial structural features. We show that this distortion represents a sparsity-dependent failure mode of current preprocessing standards and affects the comparability of datasets and computational methods across technologies and sequencing depths. To address this, we introduce a statistically consistent preprocessing framework based on nonzero-percentile clipping and log-space normalization, which preserves the intrinsic dynamic range of observed contacts. Building on this foundation, we present CCUT, a modular deep learning framework for chromatin contact map reconstruction. Under corrected preprocessing, reconstructed maps recover domain organization, contact decay, and scaling behavior consistent with polymer physics. Importantly, we demonstrate quantitative agreement between reconstructed maps and simulated contact patterns derived from a kinetic Monte Carlo loop extrusion model, enabling direct comparison between experimental data and physical models. Together, our results establish preprocessing as a decisive determinant of the physical interpretability of chromatin contact maps and provide a principled framework for robust and comparable analysis across chromatin conformation capture technologies.

biophysics↗

bioRxiv2024

DNMT/G9a Complex Inhibition Uncovers Epigenetic Vulnerabilities and Induces IFN-Response in Acute Myeloid Leukemia

Epigenetic dysregulation is a hallmark of Acute Myeloid Leukemia (AML), with mutations in DNA Methyltransferases (e.g., DNMT3A) being frequent and promising therapeutic targets. DNMTs form complexes with Histone Methyltransferases (HMTs), driving gene silencing loop via chromatin methylation crosstalk. However, potential connections between this DNMTs/HMTs cooperative activity and oncogenic requirements across the AML mutational spectrum remain poorly understood. Here, we demonstrate that AMLs carrying DNMT3A and Nucleophosmin (NPM1) mutations exhibit a specific epigenetic vulnerability toward a complex formed by DNMTs and G9a, a specific histone H3 Lysine 9 Methyltransferase (H3K9-HMT). Dual inhibition of DNMT/G9a restores differentiation, reduces tumor growth, and spares healthy progenitors compared to standard hypomethylating agents. Mechanistically, DNMT/G9a regulates NPM1 stability, inhibits HOXA9/MEIS1 activity, and triggers interferons (IFN) response via viral mimicry pathways by modulating hypermethylated retrotransposons. Collectively, our data unravel specific epigenetic vulnerabilities within the complex AML mutational landscape and provide a compelling rationale for the design of personalized epigenetic therapies with enhanced efficacy and safer clinical outcomes.

cancer biology↗

bioRxiv2024

H3K9 methylation-independent activity for HPL-2/HP1 in heterochromatin foci, gene repression, and organogenesis

In differentiated cells, genome segregation into heterochromatin and euchromatin is mediated by modified histones, which recruit so-called reader proteins. Surprisingly, many histone modifiers remain functional in the absence of catalytic activity, but the underlying mechanism remains unclear. To explore this puzzle, we examined the relationship between C. elegans MET-2/SETDB1, a histone H3 lysine (H3K9me) methyltransferase that also has non-catalytic roles, and the canonical H3K9me reader HPL-2 (HP1). We show that HPL-2 represses transcription and supports organogenesis independently of H3K9me binding, whereas complete loss of met-2 and hpl-2 causes severe transcriptional and developmental defects. MET-2 and HPL-2 rely on different binding partners - the disordered protein LIN-65/ATF7IP and the multi-zinc finger protein LIN-13, respectively - for localization and function. The results suggest that HPL-2 can operate through alternative protein interactions, and that HPL-2 and MET-2 function in parallel, H3K9me-independent pathways, with H3K9me acting as a reinforcing but non-essential contributor to these processes.

molecular biology↗

bioRxiv2024

Conditions for the co-existence of promoter and gene-body condensates

In cells, transcription is tightly regulated on multiple layers. The condensation of the transcription machinery into distinct phases is hypothesised to spatio-temporally fine tune RNA polymerase II behaviour during two key stages, transcription initiation and the elongation of the nascent RNA transcripts. However, it has remained unclear whether these phases would mix when present at the same time or remain distinct chemical environments; either as multi-phase condensates or by forming entirely separate condensates. Here we combine particle-based multi-scale simulations and experiments in the model organism C. elegans to characterise the biophysical properties of RNA polymerase II condensates. Both simulations and the in vivo work describe a lower critical solution temperature (LCST) behaviour of RNA Polymerase II, with condensates dissolving at lower temperatures whereas higher temperatures promote condensate stability. Importantly this gradual change in temperature correlates with an incremental transcriptional response to temperature, but is largely uncoupled from the classical stress response. The LCST behaviour of CTD also highlights that these condensates are physio-chemically distinct from heterochromatin condensates. Expanding the simulations we model how the degree of phosphorylation of the disordered C-terminal domain of RNA polymerase II (CTD), which is characteristic for each step of transcription, controls demixing of CTD and pCTD in line with phase separation experiments. We show that the two phases putatively underpinning the initiation of transcription and transcription elongation constitute distinct chemical environments and are in agreement with RNA polymerase II condensates observed in C. elegans embryos by super resolution microscopy. Our analysis reveals how depending on its post-translational modifications and its interaction partners a single protein can adopt multiple morphologies and how partially engulfed condensates promote the selective recruitment of additional factors to the different phases.

biophysics↗

bioRxiv2019

LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay

In fission yeast and plants, RNA-processing pathways contribute to constitutive and facultative heterochromatin silencing, complementing well-characterized pathways of transcriptional repression. However, it was unclear whether this additional level of regulation occurs in metazoans. Here we describe a pathway of silencing in C. elegans somatic cells, in which the highly conserved, RNA binding complex LSM2-8 selectively silences heterochromatic reporters and endogenous genes bearing the Polycomb mark H3K27me3. Importantly, the LSM2-8 complex works cooperatively with XRN-2, a 5-3 exoribonuclease, and disruption of the pathway leads to mRNA stabilization. This selective LSM2-8-mediated RNA degradation does not target nor depend on H3K9me2/me3, unlike previously described pathways of heterochromatic RNA degradation. Intriguingly, the loss of LSM2-8 coincides with a localized drop in H3K27me3 levels on lsm-8-sensitive loci only. Together this defines a mechanism of RNA degradation that selectively targets a subset of H3K27me3-marked genes, revealing an unrecognized layer of regulation for facultative heterochromatin in animals.

molecular biology↗