Biology subjects

Meister, P.

Publications and source records attributed to Meister, P..

11 recordsLinked to original sources

bioRxiv2026

Mitochondrial stress signaling shapes the nuclear response to loss of the chromatin reader MRG-1

Perinuclear sequestration of heterochromatin is a major conserved feature of nuclear architecture. In Caenorhabditis elegans, the euchromatic reader MRG-1 was previously shown to promote peripheral localization of heterochromatin through an indirect mechanism that remained largely unknown. Here, we show that loss of MRG-1 activates a mitochondrial stress response. Genetic ablation of the PMK-3/MAPK mitochondrial stress regulator CBP-3 reveals that this pathway contributes to both detachment of a heterochromatic reporter from the nuclear periphery and approximately one-third of the transcriptional changes induced by mrg-1 depletion. Strikingly, loss of cbp-3 in MRG-1-deficient animals exacerbates mitochondrial dysfunction, fertility defects and embryonic lethality, indicating that part of the nuclear response induced by MRG-1 loss contributes to adaptation to mitochondrial stress rather than constituting a defect in heterochromatin 3D organization as previously thought. Together, our findings identify mitochondrial stress signaling as an unexpected mediator of the nuclear response to MRG-1 loss, demonstrating its contribution to gene regulation while supporting the idea that stress-induced changes in cellular physiology can also shape nuclear organization.

cell biology↗

bioRxiv2026

Proximity labeling at H3K9me3 reveals VRK-1 regulate global chromatin distribution in C. elegans

Heterochromatin marked by histone H3 lysine 9 di- or trimethylation (H3K9me2/3) underpins transcriptional silencing and nuclear organization, yet its full complement of associated proteins remains incompletely defined. Here, we apply ChromID proximity labelling with the mouse HP1{beta} chromodomains to map the H3K9me3-proximal proteome in Caenorhabditis elegans, recovering known heterochromatin factors alongside previously uncharacterized candidates. We pursued one such candidate, the vaccinia-related kinase VRK-1, because of its established but poorly understood links to chromatin organization. Intriguingly, VRK-1 dynamically relocates from a broad nuclear distribution to the nuclear periphery upon azide or heat stress. Following these stresses, bulk chromatin exhibits similarly increased peripheral enrichment and apparent compaction, as assessed by radial fluorescence profiles. Although VRK-1 is not necessary for stress-induced chromatin reorganization, decompaction and repositioning of chromatin away from the nuclear envelope during recovery requires VRK-1. VRK-1 depletion leads to persistent perinuclear chromatin retention and compromises post-stress survival. Furthermore, loss of VRK-1 catalytic activity results in over-retention of chromatin at the nuclear periphery under normal growth conditions; this phenotype can be reversed by depletion of a key VRK-1 substrate at the nuclear envelope BAF-1. Our findings identify VRK-1 as a key regulator that controls the interaction of chromatin with the nuclear lamina through regulation of BAF-1.

cell biology↗

bioRxiv2026

Structural Basis of Condensin Recruitment for X Chromosome Repression

In Caenorhabditis elegans, the condensin IDC complex represses transcription from both X chromosomes in hermaphrodites to achieve dosage compensation. How condensin IDC is specifically recruited to the X chromosomes in coordination with sex determination and dosage compensation (SDC) proteins and how it modulates gene expression have, however, remained unresolved. Here, we identify SDC-3 as the key adaptor that directly binds the elbow coiled-coil domain of the condensin IDC-specific SMC subunit DPY-27. Using cryo-electron microscopy, we determine the structure of the SDC-3 adaptor domain bound to an auto-inhibited condensin IDC holoenzyme. Disrupting this interaction compromises dosage compensation and diminishes condensin IDC enrichment on the X chromosomes. Upon overcoming auto-inhibition, condensin IDC exhibits robust DNA loop-extrusion activity comparable to that of canonical condensin. We propose that SDC-3-anchored condensin IDC exploits loop-extrusion to reorganize X-chromosome chromatin and mediate chromosome-wide transcriptional repression.

biochemistry↗

bioRxiv2025

The chromatin remodeler LET-418/Mi-2 regulates the intracellular pathogen response in the C. elegans intestine

Chromatin remodeling provides essential transcriptional regulation for all biological processes. In Caenorhabditis elegans, the chromatin remodeler LET-418, a homolog of the human Mi-2{beta} protein, plays a critical role in regulating development, organogenesis, tissue maintenance, stress resistance and lifespan. LET-418 is part of several chromatin remodeling complexes and contributes significantly to the balance between growth and defense mechanisms, yet its target genes remain unclear. Using DNA methylation profiling, we identified genomic binding sites and associated target genes of LET-418 and its MEC-complex-specific interactor MEP-1 in the intestine. Consistent with their presence in the same complex, the two proteins shared more than half of their target genes. Functional analysis revealed that LET-418 and MEP-1 target genes are highly active in the intestine and are involved in repressing innate immune responses, including the intracellular pathogen response (IPR). Consistently, in let-418 mutants, IPR-induced genes, such as pals-5 or pals-2 are strongly upregulated, in a manner dependent on ZIP-1, a major transcription factor for IPR. Additionally, we found pathogen levels of the natural intracellular intestinal pathogen Nematocida parisii significantly reduced in let-418 mutants, supporting the observation of increased IPR in this mutant. Altogether, these findings reveal a crucial role for LET-418 as a modulator of the IPR, aligning with its role in maintaining the balance between development and defense.

genomics↗

bioRxiv2023

Cohesin forms fountains at active enhancers in C. elegans

Transcriptional enhancers must locate their target genes with both precision and efficiency. In mammals, this specificity is facilitated by topologically associated domains (TADs), which restrict the enhancer search space through three-dimensional genome organization. In contrast, the nematode genome lacks such TAD-based segmentation despite harboring over 30000 sequences with chromatin signature characteristic of enhancers, thereby raising the question of how enhancer-promoter specificity is achieved. Using high-resolution Hi-C in C. elegans, we identify distinct 3D chromatin structures surrounding active enhancers, which we term fountains. These structures span 38 kb in average, are unique to active enhancers, and are enriched for the major somatic cohesin complex. Fountains collapse upon in vivo cohesin cleavage, indicating their cohesin dependency. Notably, fountains accumulate topological stress, as evidenced by the enrichment of topoisomerases and the psoralen-binding signature of negatively-supercoiled DNA. Functionally, fountain disassembly correlates with transcriptional upregulation of active enhancer-proximal genes, suggesting that fountains act as spatial repressors of enhancer activity. This repression is particularly pronounced for neuronal genes, including the skn-1/Nrf gene, which becomes upregulated, switches isoform and transcription start site upon cohesin loss in a pair of head neurons. Behaviorally, cohesin cleavage alters nematode movement and foraging behavior, linking enhancer-driven transcriptional changes to neural circuit function and organismal phenotypes, reminiscent of pathologies caused by cohesin mutations in humans. Together, our findings uncover fountains as a novel 3D chromatin feature that modulates enhancer activity in a TAD-less genome, establishing a mechanistic link between genome architecture, gene regulation and behavior.

genomics↗

bioRxiv2023

Caltubin regulates microtubule stability via Ca2+-dependent mechanisms favouring neurite regrowth

Microtubule regulation is highly controlled in nerve regeneration. Caltubin, a novel Lymnaea stagnalis protein, contains putative EF-hand calcium-binding motifs and promotes neuronal outgrowth in Lymnaea and mouse. Here, we generated cell-permeable caltubin proteins to investigate mechanisms underlying this effect. We observed increased neurite extension and outgrowth following injury in caltubin-treated mouse neurons compared to vehicle controls. Purified caltubin bound -tubulin between its L391-V405 amino acids and promoted microtubule assembly. Caltubin competitively inhibited binding of tubulin tyrosine ligase, which catalyzes tubulin retyrosination, and increased the ratio of detyrosinated to tyrosinated tubulin. Our crystal structure analysis confirmed that caltubin has four Ca2+-binding EF-hand motifs, like calmodulin but has distinct peptide binding domains. Our work suggests a unique Ca2+-dependent regulatory mechanism of microtubule assembly by caltubin. This may represent an essential mechanism of axonal regulation, which may optimize its activity in response to various calcium states, both physiological and following injury.

cell biology↗

bioRxiv2022

Condensin I folds the C. elegans genome

The Structural Maintenance of Chromosomes (SMC) complexes, cohesin and condensins, are named for their roles in separating and compacting chromosomes during meiosis and mitosis. Recent data from mammalian cells have revealed additional functions for cohesin, including folding the interphase genome into loops and domains. However, it remains unclear what determines genome folding in holocentric species. To address this question, we systematically and acutely inactivated each SMC complex. Surprisingly, we found that, in contrast to mammals, condensin I is the major long-range genome loop extruder, while cohesin only creates small loops. Specifically, loss of condensin I led to genome-wide decompaction, chromosome mixing, and the disappearance of topologically associating domain (TAD) structures, while reinforcing fine-scale epigenomic compartments. Strikingly, inactivating condensin I and its X-specific variant condensin IDC from the X chromosomes revealed the existence of a third compartment that groups together a subset of previously characterized loading sites for condensin IDC and binding sites for the X-targeting complex SDC. Although the inactivation of cohesin, condensin II, and condensin I/IDC led to minor transcriptional changes for all autosomes, removing condensin I/IDC from the X chromosome resulted in the up-regulation of X-linked genes. In conclusion, our findings describe a novel function for C. elegans condensin I/IDC in organizing holocentric interphase chromosomes, which substitutes for the role played by cohesin in mammals.

molecular biology↗

bioRxiv2022

3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion

MotivationRecent studies suggest that the loop extrusion activity of Structural Maintenance of Chromosomes complexes is central to proper organization of genomes in vivo. Polymer physics-based modeling of chromosome structure has been instrumental to assess which structures such extrusion can create. Only few laboratories however have the technical and computational expertise to create in silico models combining dynamic features of chromatin and loop extruders. ResultsHere we present 3DPolyS-LE, a self-contained, easy to use modeling and simulation framework allowing non-specialists to ask how specific properties of loop extruders and boundary elements impact on 3D chromosome structure. 3DPolyS-LE also provides algorithms to compare predictions with experimental Hi-C data. Availability and implementationSoftware available at https://gitlab.com/togop/3DPolyS-LE ; implemented in Python and Fortran 2003 and supported on any Unix-based operating system (Linux, Mac OS). Contactpeter.meister@unibe.ch and daniel.jost@ens-lyon.fr Supplementary InformationSupplemental data are available at Bioinformatics online

biophysics↗

bioRxiv2021

Nonlinear control of transcription through enhancer-promoter interactions

Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated interactions and topologically associating domains (TADs)1-4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. To address this question we use a novel assay to position an enhancer at a large number of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. Quantitative analysis of hundreds of cell lines reveal that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a non-linear relationship. Mathematical modeling and validation against experimental data further provide evidence that nonlinearity arises from transient enhancer-promoter interactions being memorized into longer-lived promoter states in individual cells, thus uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism for how enhancers control transcription across large genomic distances despite rarely meeting their target promoters, and for how TAD boundaries can block distal enhancers. We finally show that enhancer strength additionally determines not only absolute transcription levels, but also the sensitivity of a promoter to CTCF-mediated functional insulation. Our unbiased, systematic and quantitative measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.

molecular biology↗

bioRxiv2020

Novel roles for BicD in pronuclear fusion and meiosis II progression via localization of the CHC/TACC/Msps complex to MII spindles

Drosophila Clathrin heavy chain (Chc) is transported by the dynein/dynactin microtubule motor through its interaction with the adaptor protein Bicaudal-D (BicD). Here we show that Drosophila BicD and Chc localize to centrosomes and spindles during mitosis and to the tandem spindles during female meiosis II. Reducing the activity of BicD::GFP specifically in freshly laid eggs revealed that BicD is essential for the production of normal female meiosis II products and for pronuclear fusion. Chc interacts with BicD and D-TACC, and BicD is needed to correctly localize the microtubule-stabilizing factors D-TACC, clathrin, and Msps to the meiosis II spindles, suggesting that BicD acts by localizing these proteins. In unfertilized eggs, reduced BicD levels cause the female meiotic products to re-enter the cell cycle. As BicD is required to localize the spindle assembly checkpoint (SAC) components Mad2 and BubR1 to the female meiotic products, it appears that BicD functions to localize them to control metaphase arrest of polar bodies. Finally, Drosophila and C. elegans orthologs of BicD and tacc are also needed for pronuclear fusion.

developmental biology↗

bioRxiv2020

Tissue-specific transcription footprinting using RNA PoI DamID (RAPID) in C. elegans

Differential gene expression across cell types underlies the development and cell physiology in multicellular organisms. C. elegans is a powerful, extensively used model to address these biological questions. A remaining bottleneck relates, however, to the difficulty to obtain comprehensive tissue-specific gene transcription data, since available methods are still challenging to execute and/or require large worm populations. Here, we introduce the RNA PoI DamID (RAPID) approach, in which the Dam methyltransferase is fused to a ubiquitous RNA polymerase subunit in order to create transcriptional footprints via methyl marks on the DNA of transcribed genes. To validate the method, we determined the polymerase footprints in whole animals, sorted embryonic blastomeres and in different tissues from intact young adults by driving Dam fusion expression tissue-specifically. We obtained meaningful transcriptional footprints in line with RNA-seq studies in whole animals or specific tissues. To challenge the sensitivity of RAPID and demonstrate its utility to determine novel tissue-specific transcriptional profiles, we determined the transcriptional footprints of the pair of XXX neuroendocrine cells, representing 0.2% of the somatic cell content of the animals. We identified 2362 candidate genes with putatively active transcription in XXX cells, among which the few known markers for these cells. Using transcriptional reporters for a subset of new hits, we confirmed that the majority of them were expressed in XXX and identified novel XXX-specific markers. Taken together, our work establishes RAPID as a valid method for the determination of polymerase footprints in specific tissues of C. elegans without the need for cell sorting or RNA tagging. Article summaryGene expression is a major determinant of cell fate and physiology, yet it is notoriously difficult to characterize in individual cell types for the widely used model system C. elegans. Here, we introduce a method based on the in vivo covalent modification of DNA by transcribing RNA polymerases to determine genome-wide transcription patterns in single tissues of embryos or young adult animals. We show that the method is able to identify actively transcribed genes in tissues representing down to 0.2% of the somatic cells in adult animals. Additionally, this method can be fully performed in a single laboratory by using third generation sequencing methods (ONT).

genetics↗