Biology subjects

Lemaire, L.

Publications and source records attributed to Lemaire, L..

5 recordsLinked to original sources

bioRxiv2025

NRDE2 Interacts with an Early Transcription Elongation Complex and Widely Impacts Gene Expression

NRDE2 is a highly conserved protein implicated in post-transcriptional gene silencing in Schizosaccharomyces pombe and Caenorhabditis elegans and has been shown to modulate splicing in mammals. To explore whether NRDE2 participates in additional processes in human cells, we performed tandem affinity purification followed by proteomic analysis of NRDE2 from nuclear extracts of HEK293T and HeLa cells. Our analysis confirmed the interaction of NRDE2 with its well-characterized partner, the MTR4 helicase (MTREX), as well as with multiple splicing factors. Notably, we also identified interactions with chromatin-associated proteins involved in transcription, including the Polymerase-Associated Factor 1 (PAF1) complex and elongating forms of RNA polymerase II (RNAPII). To further investigate NRDE2 function, we conducted RNA-seq following its transient depletion. Differential expression analysis revealed that loss of NRDE2 alters the expression of thousands of genes. Consistent with earlier reports, we observed splicing defects, particularly intron retention; however, our results indicate that the impact of NRDE2 on intron retention is more extensive than previously recognized. Moreover, intron retention was frequently associated with reduced mRNA expression. Together, these findings suggest that NRDE2 associates with both the transcriptional and splicing machineries and plays a broader role in RNA processing than previously appreciated.

molecular biology↗

bioRxiv2025

Integrate-and-fire neurons with potassium dynamics that capture switches in neuronal excitability class and firing regime

In conductance-based models, spiking-induced ion concentration fluctuations can alter the excitability of single neurons. In particular, in class I models, variations in potassium concentration can induce qualitative changes in the dynamics through a codimension-2 bifurcation known as the saddle-node-loop (SNL). Investigating the implications of such effects at the level of neuronal networks will require computationally efficient single neuron models that still capture ion concentration dynamics realistically. To this end, we propose a method to derive a phenomenological model capturing the coupled extracellular potassium and voltage dynamics of a given class I conductance-based model. Rather than fitting voltage traces, we calibrate a canonical reduced model to the two-parameter bifurcation structure of the target model, with input current and a physiological parameter as coordinates. This preserves the location and type of dynamical transitions as the physiological parameter varies, allowing a single reduced model to capture neuronal dynamics across qualitatively different regimes. The resulting model is an extension of the quadratic integrate-and-fire model, in which extracellular potassium accumulation alters voltage dynamics by increasing the reset voltage. We apply our systematic reduction procedure to the Wang-Buzsaki model. Its phenomenological version exhibits quantitatively comparable dynamics and replicates the reshaping of the phase-response curve associated with the transition from SNIC to HOM spikes at elevated potassium. To illustrate the derived model's applicability, we perform a preliminary investigation of how changes in potassium concentration influence synchronization in networks.

neuroscience↗

bioRxiv2022

Cereblon controls the timing of muscle differentiation in Ciona embryos

Thalidomide has a dark history as a teratogen, but in recent years it has been shown to function as a chemotherapeutic agent. Thalidomide binds cereblon, a component of E3 ubiquitin ligase complex and modifies its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ the simple proto-vertebrate model, Ciona intestinalis, to address this question. We observed a "hotspot" of Crbn expression in the developing tail muscles and identify its enhancer containing both Myod activator sites and a Snail repressive element. Overexpression of Crbn in tail muscles decreases expression of contractility genes. We suggest that this reduction is due to premature degradation of Tbx6. Drug inhibition studies using lenalidomide, a derivative of thalidomide, lead to a striking increase of Crbn expression. This autofeedback regulation could be induced by neomorphic degradation of Snail, contributing to the efficacy of lenalidomide in treating metastatic melanoma. In summary, our analysis of Crbn suggests that its normal function in Ciona is to time expression of contractility genes during muscle differentiation thereby ensuring coordination of tail morphogenesis and hatching of swimming tadpoles.

developmental biology↗

bioRxiv2020

The impact of plasma membrane lipid composition on flagella-mediated adhesion of enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is a major cause of foodborne gastrointestinal illness. The adhesion of EHEC on host tissues is the first step enabling bacterial colonization. Adhesins like fimbriae and flagella mediate this mechanism. Here, we studied the interaction of the bacterial flagellum with the host cell’s plasma membrane using Giant Unilamellar Vesicles (GUVs) as a biologically relevant model. Cultured cell lines contain many different molecular components including proteins and glycoproteins. In contrast, with GUVs we can characterize the bacterial mode of interaction solely with a defined lipid part of the cell membrane. Bacterial adhesion on GUVs was dependent on the presence of the flagellar filament and its motility. By testing different phospholipid head groups, the nature of the fatty acid chains or the liposome curvature, we found that lipid packing is a key parameter to enable bacterial adhesion. Using HT-29 cells grown in the presence of polyunsaturated fatty acid (α-linolenic acid) or saturated fatty acid (palmitic acid), we found that α-linolenic acid reduced adhesion of wild type EHEC but not of a non-flagellated mutant. Finally, our results reveal that the presence of flagella is advantageous for the bacteria to bind to lipid rafts. We speculate that polyunsaturated fatty acids prevent flagellar adhesion on membrane bilayers and play a clear role for optimal host colonization. Flagella-mediated adhesion to plasma membranes has broad implications to host-pathogen interactions.Importance Bacterial adhesion is a crucial step to allow bacteria to colonize their hosts, invade tissues and form biofilm. Enterohemorrhagic E. coli O157:H7 is a human pathogen and the causative agent of diarrhea and hemorrhagic colitis. Here, we use biomimetic membrane models and cell lines to decipher the impact of lipid content of the plasma membrane on enterohemorrhagic E. coli flagella-mediated adhesion. Our findings provide evidence that polyunsaturated fatty acid (α-linolenic acid) inhibits E. coli flagella adhesion to the plasma membrane in a mechanism separate from its antimicrobial and anti-inflammatory functions. In addition, we confirm that cholesterol-enriched lipid microdomains, often called lipid rafts are important in bacterial adhesion. These findings significantly strengthen plasma membrane adhesion via bacterial flagella in an important human pathogen. This mechanism represents a promising target for the development of novel anti-adhesion therapies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

bioRxiv2020

GABAergic neurons and Nav1.1 channel hyperactivity: a novel neocortex-specific mechanism of cortical spreading depression.

Cortical spreading depression (CSD) is a pathologic mechanism of migraine. We have identified a novel neocortex-specific mechanism of CSD initiation and a novel pathological role of GABAergic neurons. Mutations of the NaV1.1 sodium channel (the SCN1A gene), which is particularly important for GABAergic neurons excitability, cause Familial Hemiplegic Migraine type-3 (FHM3), a subtype of migraine with aura. They induce gain-of-function of NaV1.1 and hyperexcitability of GABAergic interneurons in culture. However, the mechanism linking these dysfunctions to CSD and FHM3 has not been elucidated. Here, we show that NaV1.1 gain-of-function, induced by the specific activator Hm1a, or mimicked by optogenetic-induced hyperactivity of cortical GABAergic neurons, is sufficient to ignite CSD by spiking-generated extracellular K+ build-up. This mechanism is neocortex specific because, with these approaches, CSD was not generated in other brain areas. GABAergic and glutamatergic synaptic transmission is not required for optogenetic CSD initiation, but glutamatergic transmission is implicated in CSD propagation. Thus, our results reveal the key role of hyper-activation of Nav1.1 and GABAergic neurons in a novel mechanism of CSD initiation, which is relevant for FHM3 and possibly also for other types of migraine.

neuroscience↗