Biology subjects

Baumgartner, L.

Publications and source records attributed to Baumgartner, L..

7 recordsLinked to original sources

bioRxiv2026

RNAi-based discrimination of exogenous DNA by mitotic heterochromatin in fission yeast

Various mechanisms protect prokaryotic cells from invasive exogenous (exo)DNA. However, these are rarely conserved in eukaryotes, where the existence of such processes remains elusive. Here, we uncover how fission yeast eliminates exoDNA through unequal partitioning. We show that intrinsic transcriptional features of plasmidial exoDNA produce small interfering (si)RNAs that recruit heterochromatin onto the plasmid. An active, heterochromatin-dependent clustering mechanism then causes its asymmetric partitioning during mitosis. The mitotic kinase Aurora B, which dissociates heterochromatin on segregating chromosomes, is distinctively hypoactive on plasmidial DNA, facilitating its unequal partitioning and, ultimately, elimination from the cell population. Thus, an interplay between RNAi-mediated exoDNA heterochromatinization and chromosomal phosphorylation enables fission yeast to discriminate self-from non-self-DNA, uncovering a hitherto undescribed cell-autonomous immune process in eukaryotic cells.

cell biology↗

bioRxiv2024

Parallel networks to predict TIMP and protease cell activity of Nucleus Pulposus cells exposed and not exposed to pro-inflammatory cytokines

BackgroundIntervertebral disc (IVD) degeneration is characterized by a disruption of the balance between anabolic and catabolic cellular processes. Within the Nucleus Pulposus (NP), this involves increased levels of the pro-inflammatory cytokines Interleukin 1beta (IL1B) and Tumor Necrosis Factor (TNF) and an upregulation of the protease families MMP and ADAMTS. Primary inhibitors of those proteases are the tissue inhibitors of matrix metalloproteinases (TIMP). This work aims at contributing to a better understanding of the dynamics among proteases, TIMP and proinflammatory cytokines within the complex, multifactorial environment of the NP. MethodsThe Parallel Network (PN)-Methodology was used to estimate relative mRNA expressions of TIMP1-3, MMP3 and ADAMTS4 for five simulated human activities; walking, sitting, jogging, hiking with 20 kg extra weight, and exposure to high vibration. Simulations were executed for nutrient conditions in non- and early-degenerated IVD approximations. To estimate the impact of cytokines, the PN-Methodology inferred relative protein levels for IL1B and TNF, re-integrated as secondary stimuli into the network. ResultsTIMP1 and TIMP2 expression were found to be overall lower than TIMP3 exp. In absence of pro-inflammatory cytokines, MMP3 and/or ADAMTS4 expression were strongly downregulated in all conditions but vibration and hiking with extra weight. Pro-inflammatory cytokine exposure resulted in an impaired inhibition of MMP3, rather than of ADAMTS4, progressively rising with increasing nutrient deprivation. TNF mRNA was less expressed than IL1B. However, at the protein level, TNF was mainly responsible for the catabolic shift in the simulated pro-inflammatory environment. Overall, results agreed with previous experimental findings. ConclusionsThe PN-Methodology successfully allowed the exploration of the relative dynamics of TIMP and protease regulations in different mechanical, nutritional, and inflammatory environments, in the NP. It shall stand for a comprehensive tool to integrate in vitro model results in IVD research and approximate NP cell activities in complex multifactorial environments.

systems biology↗

bioRxiv2023

Evolutionary adaptation of the chromodomain of the HP1-protein Rhino allows the integration of chromatin and DNA sequence signals

Members of the diverse heterochromatin protein 1 (HP1) family play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin binding patterns, likely due to interactions with various specificity factors. Here, we elucidate the molecular basis of the interaction between the HP1 protein Rhino, a crucial factor of the Drosophila piRNA pathway, and Kipferl, a DNA sequence-specific C2H2 zinc finger protein and Rhino guidance factor. Through phylogenetic analyses, structure prediction, and in vivo genetics, we identify a single amino acid change within Rhinos chromodomain, G31D, that does not affect H3K9me2/3 binding but disrupts the interaction between Rhino and Kipferl. Flies carrying the rhinoG31Dmutation phenocopy kipferl mutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile of rhinoG31D flies. Thus, Rhinos chromodomain functions as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.

genetics↗

bioRxiv2022

The PNt-Methodology: a top-down network modelling approach to estimate dose-and time-dependent cell responses to complex multifactorial environments

BackgroundNetwork models are convenient to represent in a mechanistic way the complexity of cell biological activity. Dynamic simulations of such networks might require approximations of equation parameters through reverse engineering, numerous and costly experimental research, and/or have limited capacity to explore cell responses to chronic, dose-dependent stimulus exposure. Here we present a mechanistic methodology allowing the simulation of interrelated cell responses of multicellular systems to multifactorial stimuli with dose-and time dependent network links. Methodsa mathematical framework to approach systems biology research questions is presented, the Parallel Networks (PN)-Methodology. It consists of a novel concept, where multicellular systems are described as many relatively small feed-forward networks acting in parallel. Each parallel network is calculated through a specifically designed ordinary differential equation (ODE). Through a unique approach to feed the ODE with interrelated parameters, a system of decoupled, analytically resolvable ODE was obtained. ResultsApplied to intervertebral disc multicellular systems, virtual environments of multifactorial stimuli and multiple cell responses simulating daily moving activities, and to microgravity could successfully be created. ConclusionsThe PN-Methodology stands for a one-of-a-kind mathematical methodology to approximate dynamics of complex multicellular systems over long periods of time at low computational costs.

systems biology↗

bioRxiv2022

The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters

RNA interference systems depend on the synthesis of small RNA precursors whose sequences define the target spectrum of these silencing pathways. The Drosophila Heterochromatin Protein 1 (HP1) variant Rhino permits transcription of PIWI-interacting RNA (piRNA) precursors within transposon-rich heterochromatic loci in germline cells. Current models propose that Rhinos specific chromatin occupancy at piRNA source loci is determined by histone marks and maternally inherited piRNAs, but also imply the existence of other, undiscovered specificity cues. Here, we identify a member of the diverse family of zinc finger associated domain (ZAD)-C2H2 proteins, Kipferl, as critical Rhino cofactor in ovaries. By binding to guanosine-rich DNA motifs and interacting with the Rhino chromodomain, Kipferl recruits Rhino to specific loci and stabilizes it on chromatin. In kipferl mutant flies, Rhino is lost from most of its target chromatin loci and instead accumulates on pericentromeric satellite arrays, resulting in decreased levels of transposon targeting piRNAs and impaired fertility. Our findings reveal that DNA sequence, in addition to the H3K9me3 mark, determines the identity of piRNA source loci and provide insight into how Rhino might be caught in the crossfire of genetic conflicts.

genetics↗

bioRxiv2021

A SUMO-dependent regulatory switch connects the piRNA pathway to the heterochromatin machinery in Drosophila

Nuclear Argonaute proteins, guided by small RNAs, mediate sequence-specific heterochromatin formation. The molecular principles that link Argonaute-small RNA complexes to cellular heterochromatin effectors upon binding to nascent target RNAs are poorly understood. Here, we elucidate the mechanism by which the PIWI interacting RNA (piRNA) pathway connects to the heterochromatin machinery in Drosophila. Piwi-mediated stabilization of the corepressor complex SFiNX on chromatin leads to SUMOylation of its subunit Panoramix. SUMOylation, together with an amphipathic LxxLL motif in Panoramixs intrinsically disordered repressor domain, are necessary and sufficient to recruit small ovary (Sov), a multi-zinc finger protein essential for general heterochromatin formation and viability. Structure-guided mutations that abrogate the Panoramix-Sov interaction or that prevent SUMOylation of Panoramix uncouple Sov from the piRNA pathway, resulting in viable but sterile flies in which Piwi-targeted transposons are derepressed. Thus, by coupling recruitment of a corepressor to nascent transcripts with its SUMOylation, Piwi engages the heterochromatin machinery specifically at transposon loci.

molecular biology↗

bioRxiv2019

Simulating intervertebral disc cell behavior within 3D multifactorial environments

MotivationLow back pain is responsible for more global disability than any other condition. Its incidence is closely related to intervertebral disc (IVD) failure, which is likely caused by an accumulation of microtrauma within the IVD. Crucial factors in microtrauma development are not entirely known yet, probably because their exploration in vivo or in vitro remains tremendously challenging. In-silico modelling is, therefore, definitively appealing, and shall include approaches to integrate influences of multiple cell stimuli at the microscale. Accordingly, this study introduces a hybrid Agent-based (AB) model in IVD research and exploits network modelling solutions in systems biology to mimic the cellular behavior of Nucleus Pulposus cells exposed to a 3D multifactorial biochemical environment, based on mathematical integrations of existing experimental knowledge. Cellular activity reflected by mRNA expression of Aggrecan, Collagen type I, Collagen type II, MMP-3 and ADAMTS were calculated for inflamed and non-inflamed cells. mRNA expression over long periods of time is additionally determined including cell viability estimations. Model predictions were eventually validated with independent experimental data. ResultsAs it combines experimental data to simulate cell behavior exposed to a multifactorial environment, the present methodology was able to reproduce cell death within 3 days under glucose deprivation and a 50% decrease in cell viability after 7 days in an acidic environment. Cellular mRNA expression under non-inflamed conditions simulated a quantifiable catabolic shift under an adverse cell environment, and model predictions of mRNA expression of inflamed cells provide new explanation possibilities for unexpected results achieved in experimental research. Contactlaura.baumgartner@upf.edu

systems biology↗