Biology subjects

Coulon, A.

Publications and source records attributed to Coulon, A..

15 recordsLinked to original sources

bioRxiv2026

The Alzheimer's disease-associated rs28834970 variant in PTK2B impairs electrical activity and regulates Tau phosphorylation and APP processing in human neuronal cultures

Background: Genome-wide association studies have identified the PTK2B gene, which encodes Proline-rich tyrosine kinase 2 (PYK2), as a genetic risk factor for Alzheimer's disease (AD). However, its role in AD aetiology remains to be understood, as a complex contribution to amyloid {beta} (A{beta}) toxicity, tauopathy and neuronal dysfunction is suggested by contradictory evidence. Determining how the causal variant among AD-associated PTK2B variants impairs PYK2 function to trigger AD hallmarks could bring clarification. Methods: We combined in silico prediction tools with luciferase reporter assays in neuroblastoma cells to prioritize potential AD-associated PTK2B functional variants. We generated isogenic KOLF2.1J induced pluripotent stem cells (iPSCs) carrying the most relevant functional variant using CRISPR-Cas9 and differentiated them into human neuronal cultures (hNCs). We assessed PYK2 expression via immunoblotting, performed transcriptomic profiling using RNA-sequencing, analyzed neuronal network activity via multielectrode array (MEA) recordings, quantified synaptic density through immunocytochemistry in microfluidic devices, and assessed Tau phosphorylation and amyloid-precursor protein (APP) metabolism. Results: The rs28834970 regulatory variant was identified as the most functionally relevant in our model, with the C risk allele promoting transcription factor C/EBP{beta} binding within a cis-regulatory element. In hNCs, the homozygous rs28834970 CC genotype reduced total PYK2 levels by more than 80%, while increasing the proportion of phosphorylated (activated) PYK2. Transcriptomic analysis revealed 724 downregulated and 113 upregulated gene sets, with altered expression of genes involved in extracellular matrix organization, cytoplasmic translation and neurotransmitter secretion. MEA recordings showed reduced network recruitment and altered burst organization. Immunocytochemistry in microfluidic devices consistently revealed that rs28834970 impacts dendritic development and postsynaptic maturation. The risk genotype significantly elevated Tau phosphorylation at pathological sites (Thr181, Thr217, Thr231, Ser202-Thr205, Ser396-Ser404), and enhanced APP processing, resulting in decreased levels of APP and CTF but increased levels of sAPP, sAPP{beta} and A{beta}. Conclusion: The rs28834970 C risk allele mechanistically links AD susceptibility to downregulation of PTK2B/PYK2 expression and to the increase in Tau pathology and A{beta} levels while compromising synaptic structure and function.

genetics↗

bioRxiv2026

Rearrangement of chromosome spatial organization in mouse zygotes using optical tweezers does not affect preimplantation development

The spatial arrangement of chromosomes is thought to influence key processes such as gene expression or chromosome segregation. However, the contribution of chromosome spatial organization in physiological contexts remains disputed. Here, we use optical tweezers to displace nucleoli and physically rearrange the nuclear contents of mouse zygotes. Monitoring the preimplantation development of zygotes with physically shuffled nuclei reveals that cell dynamics, gene expression and overall blastocyst formation are not affected. This suggests that in mouse zygotes, the spatial organisation of chromosomes is not critical for blastocyst development.

developmental biology↗

bioRxiv2025

From Field to FASTA: Onsite DNA Barcoding the Mushrooms of the 2024 NAMA Foray

Mushroom forays present unparalleled opportunities to record macrofungal biodiversity in a place and time. The 2024 NAMA annual foray at the Cispus Center near Randle, Washington was the first mass barcoding activity performed by the NAMA DNA Sequencing Committee (DNAMA). The workflows and methods utilized are presented along with planned improvements. Ultimately, 803 ITS barcodes were generated (83.7% of those attempted) for 513 unique taxa belonging to 209 Genera. Of these, 18 novel putative species-level operational taxonomic units (OTUs) were discovered as well as 28 new distribution reports at state level or above. Methods and suggestions for replicating and improving mass barcoding at forays are discussed.

genetics↗

bioRxiv2025

Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy

Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend to show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, where transcription occurs in sporadic bursts, transcriptional coordination has been observed between proximal genes, but how the local folding of mammalian chromosomes influences gene coregulation in cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent transcription from three adjacent genes located around a strong contact insulation site at the FOS locus, during the estrogen response in human breast cancer cells. To interpret this data, we developed two new analysis approaches to dissect the sources of (co)variation in gene activities: one to separate allele-extrinsic, allele-intrinsic, and gene-autonomous components; and another one to quantify the contributions of burst co-occurrence and burst size correlations. We find that transcriptional variability is largely gene-autonomous, yet correlations between genes display distinct patterns and occur almost exclusively in cis. Correlations are stronger between proximal and less insulated genes. However, unexpectedly, substantial correlations also occur across the strong insulation site and, under certain conditions, two proximal genes on the same side can exhibit uncorrelated burst occurrences. By disentangling burst co-occurrence from burst size correlations, we reveal transcriptional patterns suggesting two distinct coregulatory mechanisms influenced by local chromosome folding.

biophysics↗

bioRxiv2024

Neuronal downregulation of PLCG2 impairs synaptic function and elicits Alzheimer disease hallmarks

We developed a high content screening to investigate how Alzheimer disease (AD) genetic risk factors may affect synaptic mechanisms in rat primary neuronal cultures. Out of the target genes identified, we found that Plcg2 downregulation in mouse dentate gyrus neurons consistently disrupted dendritic morphology and synaptic function. In human neuronal cultures (hNCs), PLCG2 downregulation also impaired synaptic function and increased A{beta} levels and Tau phosphorylation. Very rare PLCG2 loss-of-function (LoF) variants were associated with a 10-fold increased AD risk. PLCG2 LoF carriers exhibit low mRNA/protein PLCG2/PLC{gamma}2 levels and the R953* LoF mutation compromised synaptic function and increased AD hallmarks in hNCs. Single nuclei RNAseq analyses confirmed that the downregulation of PLCG2 impacted pathways related to synaptic and neuronal functions, potentially through neurexin in neurons. In conclusion, PLC{gamma}2 downregulation could increase AD risk by impairing synaptic functions and increasing the A{beta} levels and Tau phosphorylation in neurons.

neuroscience↗

bioRxiv2023

Scale-free models of chromosome structure, dynamics, and mechanics

The nucleus of a cell contains its genetic information in the form of chromatin: polymers of DNA and associated proteins. The physical nature of this polymer system is yet to be understood. Orthogonal experimental approaches probing chromosome structure, dynamics, and mechanics typically suggest the existence of scaling relationships, leading to the widespread use of scale-free, or fractal, models to represent interphase chromosomes. However, currently, there is no single physical model consistent with all reported scaling exponents. Here, we consider the space of possible scale-free models of chromosome structure, dynamics, and mechanics, and examine the fundamental connections between these physical properties. We demonstrate the existence of two algebraic relationships between the scaling exponents---connecting structure with dynamics, and dynamics with mechanics, respectively---outlining the necessary physical conditions for a model to match specific exponent values. Applied to values reported in metazoans, our theory identifies the family of models consistent with all observed scalings, which notably excludes the classical Rouse, Zimm, and fractal globule polymer models. Our theory highlights dynamic correlations between distal genomic loci as necessary to reconnect seemingly contra-dictory measurements. Consequently, we propose new experiments to narrow down the space of possible models. We expect this framework to serve as a guide for understanding past and future measurements, and for building new physical models of interphase chromosomes.

biophysics↗

bioRxiv2023

Reproductive tactics, birth timing and the trade-off between risk avoidance and foraging in an income breeder

The behavioural trade-off between foraging and risk avoidance is expected to be particularly acute during gestation and lactation, when the energetic demands of reproduction peak. We investigated how female roe deer, an income breeding ungulate, adjust their management of this trade-off during the birth period in terms of foraging activity and habitat use. We showed that activity levels of reproductive females more than doubled immediately following parturition, when energy demand is highest. Moreover, reproductive females increased their use of open habitat during daytime and ranged closer to roads, but slightly further from refuge woodland, compared to non-reproductive females. However, these post-partum modifications in behaviour were particularly pronounced in late-parturient females who adopted a more risk prone tactic, presumably to compensate for the fitness handicap of their late-born offspring. In income breeders, individuals that give birth late may be forced to trade risk avoidance for resource acquisition during peak allocation to reproduction, likely with significant fitness consequences.

animal behavior and cognition↗

bioRxiv2023

Using accelerometers to infer behaviour of cryptic species in the wild

Accelerometery is revolutionising the field of behavioural ecology through its capacity to detect the fine-scale movements of animals resulting from their behaviour. Because it is often difficult to infer the behaviour of wildlife on a continuous basis, particularly for cryptic species, accelerometers potentially provide powerful tools for remote monitoring of their behavioural responses to the environment. The goal of this study was to provide a detailed, calibrated methodology, including practical guidelines, to infer the behaviour of free-ranging animals from acceleration data. This approach can be employed to reliably infer the time budget of species that are difficult to observe in certain environments or at certain times of the day. To this end, we trained several behavioural classification algorithms with accelerometer data obtained on captive roe deer, then validated these algorithms with data obtained on free-ranging roe deer, and finally predicted the time-budgets of a substantial sample of unobserved free-ranging roe deer in a human-dominated landscape. The best classification algorithm was the Random Forest which predicted five behavioural classes with a high overall level of accuracy ({approx} 90%). Except for grooming (34-38%), we were able to predict the behaviour of free-ranging roe deer over the course of a day with high accuracy, in particular, foraging head down, running, walking and immobile (68-94%). Applied to free-ranging individuals, the classification allowed us to estimate, for example, that roe deer spent about twice as much time foraging head-down, walking or running during dawn and dusk than during daylight or night-time. By integrating step by step calibration and validation of accelerometer data prior to application in the wild, our approach is transferable to other free-ranging animals for predicting key behaviours in cryptic species.

animal behavior and cognition↗

bioRxiv2023

Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration

Seasonal migrations are central ecological processes connecting populations, species and ecosystems in time and space. Land migrations, such as those of ungulates, are particularly threatened by habitat transformations and fragmentation, climate change and other environmental changes caused by anthropogenic activities. Mountain ungulate migrations are neglected because they are relatively short, although traversing highly heterogeneous altitudinal gradients particularly exposed to anthropogenic threats. Detecting migration routes of these species and understanding their drivers is therefore of primary importance to predict connectivity and preserve ecosystem functions and services. The populations of Alpine ibex Capra ibex, an iconic species endemic to the Alps, have all been reintroduced from the last remnant source population. Because of their biology and conservation history, Alpine ibex populations are mostly disconnected. Hence, despite a general increase in abundance and overall distribution range, their conservation is strictly linked to the interplay between external threats and related behavioral responses, including space use and migration. By using 337 migratory tracks from 425 GPS-collared individuals from 15 Alpine ibex populations distributed across their entire range, we (i) identified the environmental drivers of movement corridors in both spring and autumn and (ii) compared the abilities of three modeling approaches to predict migratory movements between seasonal ranges of the 15 populations. Trade-offs between energy expenditure, food, and cover seemed to be the major driver of migration routes: steep south-facing snow-free slopes were selected while high elevation changes were avoided. This revealed the importance of favorable resources and an attempt to limit energy expenditures and perceived predation risk. Based on these findings, we provided efficient connectivity models to inform conservation of Alpine ibex and its habitats, and a framework for future research investigating connectivity in migratory species.

ecology↗

bioRxiv2022

Regulation of replicative histone RNA metabolism by the histone chaperone ASF1

In S phase, duplication and assembly of the whole genome into chromatin requires upregulation of replicative histone gene expression. Here, we explored a potential role of histone chaperones in this process thereby linking chromatin assembly with histone production in human cells. Depletion of the ASF1 chaperone specifically decreased the pool of replicative histones both at the levels of soluble protein and total RNA, while depletion of CAF-1 did not. Most replicative histone genes decreased in their overall expression as revealed by total RNA-seq. In contrast, both their newly synthesized RNAs and nascent RNAs at transcription sites increased as shown by 4sU-labeled RNA-seq and single-molecule RNA FISH, respectively. Further inspection of the sequences corresponding to replicative histone RNAs showed a 3 processing defect, leading to unprocessed transcripts usually targeted for degradation. We discuss how this regulation of replicative histone RNA metabolism by ASF1 fine-tunes the histone dosage to avoid unbalanced situations deleterious for cell survival.

molecular biology↗

bioRxiv2021

Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics

Our understanding of the physical principles organizing the genome in the nucleus is limited by the lack of tools to directly exert and measure forces on interphase chromosomes in vivo and probe their material nature. Here, we present a novel approach to actively manipulate a genomic locus using controlled magnetic forces inside the nucleus of a living human cell. We observe viscoelastic displacements over microns within minutes in response to near-picoNewton forces, which are well captured by a Rouse polymer model. Our results highlight the fluidity of chromatin, with a moderate contribution of the surrounding material, revealing the minor role of crosslinks and topological effects and challenging the view that interphase chromatin is a gel-like material. Our new technology opens avenues for future research, from chromosome mechanics to genome functions.

biophysics↗

bioRxiv2020

Influence of local landscape and time of year on bat-road collision risks

Roads impact bat populations through habitat loss and collisions. High quality habitats particularly increase bat mortalities on roads, yet many questions remain concerning how local landscape features may influence bat behaviour and lead to high collision risks (e.g. influence of distance to trees, or of vegetation density). When comparing the potential danger of different road sections, the most popular method today is the use of simple bat detectors to assess the local densities of current populations at road sites. Yet, it is not known to which extent bat behaviour influences collisions (i.e. bats flying at vehicle height or on the side or above, co-occurrence of bats and vehicles). Behaviour is very rarely taken into account in practice, and this might lead to hazardous site selections for mitigation. Our goals were thus (i) to estimate how local landscape characteristics affect each of the conditional events leading to collisions (i.e. bat presence, flight in the zone at collision risk and bat-vehicle co-occurrence), and (ii) to determine which of the conditional events most contributed to collisions risks. In this study, we recorded bat activity and characterised flight behaviour with three variables: position at collision risk, bat-vehicle co-occurrence, and flight path orientation, using acoustic flight path tracking at 66 study sites in the Mediterranean region for two to five full nights. We modelled the effect of the local landscape, i.e. in a radius of 30 m around the road (vegetation height, distance, density and orientation), road features (road width, traffic volume) and the time of year on eleven species or species groups. We built models for each conditional probability of the road collision risk (i.e. species density, presence in the zone at risk, bat-vehicle co-occurrence) and multiplied their estimates to calculate the overall collision risk. Our results show that the local landscape had different effects on bat density and presence in the zone at collision risk. Increasing distance to trees and decreasing tree height were associated with a decrease in bat density at roads. Forests were the local landscapes where bats flew more often in the zone at collision risk. The overall collision risk was higher either in forests or at tree rows perpendicular to the road depending on species. Contrary to common preconceptions, mid-range echolocators seemed to be generally more at risk of collision than short-range or long-range echolocators. In addition, collision risk was greatest in summer or autumn for most species. Finally, bats mainly followed the road axis regardless of the type of landscape. Our results contribute to a better understanding of bat movements in different local environments at the scale where they directly sense their surroundings with echolocation calls. Disentangling bat density from flight behaviour allowed us to better understand the temporal and spatial contributors of roadkills, and to provide guidance for road impact assessment studies.

ecology↗

bioRxiv2019

Two distinct HIRA-dependent pathways handle H3.3 de novo deposition and recycling during transcription

The packaging of DNA into nucleosomes represents a challenge for transcription. Nucleosome disruption and histone eviction enables RNA Polymerase II progression through DNA, a process that compromises chromatin integrity and the maintenance of epigenetic information. Here, we used the imaging SNAP-tag system to distinguish new and old histones and monitor chromatin re-assembly coupled to transcription in cells. First, we uncovered a loss of both old variants H3.1 and H3.3 that depends on transcriptional activity, with a major effect on H3.3. Focusing on transcriptionally active domains, we revealed a local enrichment in H3.3 with dynamics involving both new H3.3 incorporation and old H3.3 retention. Mechanistically, we demonstrate that the HIRA chaperone is critical to handle both new and old H3.3, and showed that this implicates different pathways. The de novo H3.3 deposition depends strictly on HIRA trimerization as well as its partner UBN1 while ASF1 interaction with HIRA can be bypassed. In contrast, the recycling of H3.3 requires HIRA but proceeds independently of UBN1 or HIRA trimerization and shows an absolute dependency on ASF1-HIRA interaction. Therefore, we propose a model where HIRA can coordinate these distinct pathways for old H3.3 recycling and new H3.3 deposition during transcription to fine-tune chromatin states.

cell biology↗

bioRxiv2019

Molecular basis of CTCF binding polarity in genome folding

Current models propose that boundaries of mammalian topologically associating domains (TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by cohesin proteins (Merkenschlager & Nora, 2016; Fudenberg, Abdennur, Imakaev, Goloborodko, & Mirny, 2017). While the orientation of CTCF motifs determines which pairs of CTCF sites preferentially stabilize DNA loops (de Wit et al., 2015; Guo et al., 2015; Rao et al., 2014; Vietri Rudan et al., 2015), the molecular basis of this polarity remains mysterious. Here we report that CTCF positions cohesin but does not control its overall binding or dynamics on chromatin by single molecule live imaging. Using an inducible complementation system, we found that CTCF mutants lacking the N-terminus cannot insulate TADs properly, despite normal binding. Cohesin remained at CTCF sites in this mutant, albeit with reduced enrichment. Given that the orientation of the CTCF motif presents the CTCF N-terminus towards cohesin as it translocates from the interior of TADs, these observations provide a molecular explanation for how the polarity of CTCF binding sites determines the genomic distribution of chromatin loops.

molecular biology↗

bioRxiv2019

Alzheimer’s genetic risk factor FERMT2 (Kindlin-2) is regulated by risk allele-binding of miR-4504 and leads to synaptic dysfunction in an APP-dependent manner

Although APP metabolism is being intensively investigated, a large fraction of its modulators are yet to be characterized. In this context, we combined two genome-wide high-content screenings to assess the functional impact of miRNAs and genes on APP metabolism and the signaling pathways involved. This approach highlighted the involvement of FERMT2 (or Kindlin-2), a genetic risk factor of Alzheimers disease (AD), as a potential key modulator of axon guidance; a neuronal process that depends on the regulation of APP metabolism. We found that FERMT2 directly interacts with APP to modulate its metabolism and that FERMT2 under-expression impacts axonal growth, synaptic connectivity and long-term potentiation in an APP-dependent manner. Lastly, the rs7143400-T allele, which is associated with an increased AD risk and localized within the 3UTR of FERMT2, induced a down-regulation of FERMT2 expression through binding of miR-4504 among others. This miRNA is mainly expressed in neurons and significantly overexpressed in AD brains compared to controls. Altogether, our data provide strong evidence for a detrimental effect of FERMT2 under-expression in neurons and insight on how this may influence AD pathogenesis.

pathology↗