Biology subjects

Erhardt, S.

Publications and source records attributed to Erhardt, S..

9 recordsLinked to original sources

bioRxiv2026

Mitotic centromeres organize in repeat-subunits with specialized histone landscape and multi-domain architecture as revealed by expansion microscopy

Centromeres ensure faithful chromosome segregation during cell division, yet their underlying architecture and spatial arrangement of centromeric proteins remain incompletely resolved. Here, we apply Ten-fold Robust Expansion Microscopy (TREx) to human diploid hTERT RPE-1 cells to visualize mitotic centromeres at nanoscale resolution. We find that the centromeric histone variant CENP-A and the kinetochore protein KNL1 form discontinuous, repeating substructures. We further resolve centromeric chromatin into four spatially distinct domains: an inner kinetochore domain marked by CENP-A, a mantle domain marked by RAD21, an outer core domain marked by CENP-B, and a distinct, RAD21-associated inner centromere domain. Core and pericentromeric regions share a specialized chromatin landscape, extending the concept of centrochromatin, with enrichment of H3S10ph and H3K9me3, depletion of H3K27me3, and low-level enrichment of the euchromatic marks H3K4me3 and H3K36me3. Together, we uncover a discontinuous repeat-subunit organization and multidomain architecture of the human centromere that combines euchromatic and heterochromatic modifications.

cell biology↗

bioRxiv2025

Structural dynamics in the CENP-A nucleosome impacted by protein-protein interactions with centromere protein N

Noncanonical nucleosomes at the centromere contain the histone variant CENP-A, playing a crucial role in chromosome segregation. CENP-A is highly regulated and its centromeric organization is partially regulated by the centromere protein N (CENP-N). Despite its importance, the protein-protein interactions within the complex formed between CENP-A nucleosomes and CENP-N remain poorly understood at a molecular level. Here, we employ the SIRAH coarse-grained molecular dynamics (MD) simulations to investigate the binding interface and structural rearrangements of proteins in the CENP-A nucleosome complexed with CENP-N. We aim to assess the stability of the CENP-A nucleosome and the change in its plasticity upon the CENP-N binding. By the set of {micro}s-long MDs, we reveal enhanced flexibility in the N-terminal region of CENP-A and stabilization of its RG loop in the complex with CENP-N. This is demonstrated to have rather minor effects on the overall stability of the nucleosome and changing its compactness. Nevertheless, the data suggest the binding of CENP-N allosterically changes the conformational states of CENP-A and impacts its interactions with other proteins in the histone core. A distance-based contact map analysis further elucidates key residues mediating the interaction between CENP-A and CENP-N, while umbrella sampling simulations quantify their binding free energy, which remains challenging to measure experimentally.

biophysics↗

bioRxiv2025

Thalamic Nuclei Volumes Across Psychiatric and Neurological Disorders: A Multi-Site Magnetic Resonance Imaging Study

The human thalamus is an integrative hub for multiple cortical and subcortical circuits involved in sensory processing and higher cognitive functions. Thalamic volume differences have been reported across multiple psychiatric and neurological disorders, but previous studies have typically relied on small samples, focused on one or a limited number of disorders, or investigated the thalamus as a whole without considering its functional subdivisions. In this multi-site study, we compared thalamic nuclei volumes across mild cognitive impairment (MCI), dementia (DEM), major depressive disorder, schizophrenia spectrum disorder (SCZ), clinical high risk for schizophrenia, bipolar spectrum disorder, autism spectrum disorder, attention-deficit/hyperactivity disorder, Parkinsons disease, multiple sclerosis (MS), and healthy controls (N > 8 000). Using structural MRI, we segmented 25 bilateral thalamic nuclei, corresponding to six anatomical groups. Linear models revealed that anterior, medial and lateral regions of the thalamus were significantly smaller in several conditions, with largest effects observed for MCI, DEM, SCZ and MS. In contrast, the ventral and intralaminar groups were relatively normal. This pattern of effects largely corresponds to the canonical functional subdivision of the thalamus into higher-order and sensory regions. At the level of individual nuclei, the clinical conditions were associated with distinct patterns of alterations, while left and right lateral geniculate nuclei were implicated in six of the disorders, suggesting a possible relation with circadian and sleep disturbances. Together, the results highlight a role for the higher-order thalamus in common brain disorders and a differential involvement at the nuclei level, refining our understanding of thalamic pathology across common brain disorders.

neuroscience↗

bioRxiv2023

Kynurenic acid promotes activity-dependent synaptic pruning in schizophrenia

Schizophrenia is a neurodevelopmental disorder characterized by an excessive loss of synapses. Recent data suggest that this is due to increased microglia-mediated synaptic pruning. Here, we utilize human induced pluripotent stem cell-derived models to show that kynurenic acid (KYNA), an endogenous NMDA-receptor antagonist observed to be increased in the brains of individuals with schizophrenia, reduces neuronal activity and promote microglial uptake of synapses. In a human brain organoid model, we confirm reduced microglia-mediated synaptic pruning upon inhibiting the endogenous KYNA production. To verify our experimental data in a clinical context, we integrate large-scale transcriptomic and genetic datasets and show that KYNA-producing kynurenine aminotransferases (KATs) enrich for genes governing synaptic activity and genetic risk variants for schizophrenia. Together, these results link genetic risk variants for schizophrenia to elevated production of KYNA and excessive activity-dependent synaptic pruning, while implicating pharmacological inhibition of KATs as a strategy to avoid synapse loss in schizophrenia.

neuroscience↗

bioRxiv2023

Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation

Spatiotemporal organization of transcription is essential for organism development. Most eukaryotic genes are transcribed by RNA polymerase II (Pol II). In stem cells, Pol II forms prominent clusters, which gradually disappear during differentiation, such that only smaller clusters remain. Here, we ask whether the formation and loss of large Pol II clusters is a stereotypical process explicable by changes in the Pol II transcriptional state during differentiation. We assess clusters by super-resolution microscopy in differentiating mouse embryonic stem cells, sperm precursor formation in fruit flies, and germ layer induction in zebrafish. In all cases, Pol II clusters first become larger and rounder, then unfold, and finally disperse into small clusters. These shape changes are accompanied by initial increase in recruited Pol II, subsequent transition into transcript elongation, and finally reduction of active enhancers. We reproduce these observations using a biophysical surface condensation model, where enhancers support Pol II cluster formation, and transcriptional activity unfolds clusters. Our work indicates that changes in enhancer marks and transcriptional activity during differentiation define a stereotyped trajectory through a generally applicable space of cluster shapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/547621v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1fb769borg.highwire.dtl.DTLVardef@27f6a0org.highwire.dtl.DTLVardef@1b0ab7corg.highwire.dtl.DTLVardef@1ca932d_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

The bromodomain inhibitor JQ1 is a molecular glue targeting centromeres

Centromeres are the position on each chromosome that orchestrates the accurate partitioning of the genome during cell division. Centromere-dependent cell-cycle checkpoints are maintained by cancer cells to prevent catastrophic chromosome segregation defects in dividing cells1, 2, making centromeric chromatin a valuable target for anti-cancer therapeutics. However, no compounds have been identified that specifically target centromeric chromatin using standard drug discovery approaches. Here we develop a big-data approach to identify the protein composition of repetitive DNA loci, including centromeres, and screen candidate small molecules that act on centromeric chromatin composition. We discover that the BET bromodomain protein BRD4 localises to centromeres and regulates centromeric cohesion. We further show that the bromodomain inhibitor JQ1 affects centromeric BRD4 by stabilising a direct interaction between BRD4 and Centromere Protein B (CENP-B), acting as a molecular-glue that promotes centromere cohesion in a CENP-B-dependent manner. Strikingly, CENP-B transitions from a non-essential protein in JQ1-sensitive cells to the most significant determinant of cell-proliferation in JQ1-resistant cells. Our observations demonstrate a completely overlooked role for BRD4 and JQ1 in directly targeting the centromere, with important consequences for JQ1-derivatives currently entering clinical use3.

molecular biology↗

bioRxiv2022

A centromeric RNA-associated protein complex affects germ line development in Drosophila melanogaster.

In many metazoans, centromeres are embedded in large blocks of highly repetitive (peri-) centromeric heterochromatin from which non-coding RNAs emanate that have been assigned diverse functions in different species. However, little is known about their functional details or regulation. The pericentromere of the X chromosome in Drosophila melanogaster contains a multi mega-base array of the 359 bp satellite repeats from the 1.688 family, which is transcribed into a lncRNA (SAT III RNA). We performed a SAT III RNA pulldown assay and identified a SAT III RNA-associated complex of four previously uncharacterized proteins and show that they affect germline development. These factors not only interact with each other and with SAT III RNA but also co-regulate each other. RNAi depletion of any of the factors leads to severe defects in the developing germline and sterility. Moreover, we show that the complex plays a crucial role in SAT III RNA repression, as RNAi depletion of the factors leads to a drastic increase of SAT III RNA levels. Importantly, genetic reduction of SAT III RNA level in the RNAi-depleted flies partially rescued the germ line defects and infertility phenotype. Based on our results we hypothesize that the identified complex functions in the germline to regulate SAT III RNA levels, possibly to offset effects of chromatin remodelling taking place in the developing germline.

cell biology↗

bioRxiv2021

Genome-wide prediction and integrative functional characterization of Alzheimer's disease-associated genes

The mechanism of Alzheimers disease (AD) remains elusive, partly due to the incomplete identification of risk genes. We developed an approach to predict AD-associated genes by learning the functional pattern of curated AD-associated genes from brain gene networks. We created a pipeline to evaluate disease-gene association by interrogating heterogeneous biological networks at different molecular levels. Our analysis showed that top-ranked genes were functionally related to AD. We identified gene modules associated with AD pathways, and found that top-ranked genes were correlated with both neuropathological and clinical phenotypes of AD on independent datasets. We also identified potential causal variants for genes such as FYN and PRKAR1A by integrating brain eQTL and ATAC-seq data. Lastly, we created the ALZLINK web interface, enabling users to exploit the functional relevance of predicted genes to AD. The predictions and pipeline could become a valuable resource to advance the identification of therapeutic targets for AD.

bioinformatics↗

bioRxiv2018

Centromeric CENP-A loading requires accurate mitotic timing, which is linked to checkpoint proteins

A defining feature of centromeres is the presence of the histone H3 variant CENP-A that replaces H3 in a subset of centromeric nucleosomes. In Drosophila cultured cells CENP-A deposition at centromeres takes place during the metaphase stage of the cell cycle and strictly depends on the presence of its specific chaperone CAL1. How CENP-A loading is restricted to mitosis is unknown. We found that CAL1 interacts with the spindle assembly checkpoint protein and RZZ complex component Zw10 and thus constitutes the anchor for the recruitment of RZZ. We identify Zw10 as determinant of a mitotic duration and show that it is inversely correlated with CENP-A levels at centromeres. Moreover, overexpression of CAL1 is associated with increased CENP-A levels at centromeres and completely uncouples CENP-A loading from mitosis. Therefore CAL1 controls CENP-A incorporation at centromeres both quantitatively and temporally, connecting it to the spindle assembly checkpoint to further ensure mitotic fidelity.

cell biology↗