Genetic assimilation describes the evolutionary process during which an environmentally-induced (conditional) phenotype becomes a genetically controlled (constitutive) phenotype. This important concept remains controversial because the molecular mechanisms of genetic assimilation are rarely understood. Our project seeks to characterize the molecular genetic underpinnings of genetic assimilation in nematode egg retention. This conditional phenotype depends on the environmental modulation of egg-laying behaviour through neuromodulatory changes in the underlying neural circuit. Our past collaborative research has established that natural and experimental populations of the nematode Caenorhabditis elegans show great variation in the environmental sensitivity of egg-laying behaviour, and in extreme cases, display genetic assimilation in egg retention. The existence of this natural variation represents a uniquely well-suited experimental paradigm to characterize the molecular basis of genetic assimilation. Leveraging natural diversity by employing a powerful multi-parental experimental mapping population and a global panel of wild strains, we will conduct unbiased whole-genome screens to uncover the molecular mechanisms governing genetic assimilation. Our first aim involves conducting genome-wide association (GWA) mapping to identify the Quantitative Trait Loci (QTL) that modulate environmental sensitivity of egg retention and thought to underlie genetic assimilation. Our second aim will employ CRISPR-Cas9 gene editing to pinpoint the molecular nature of QTL and explore its functional consequences on egg retention and environmental sensitivity in egg-laying behaviour. In our third final aim, we will evaluate the significance of molecularly validated QTL during the process of genetic assimilation across 100 generations of experimental evolution. Through the integration of these complementary approaches, we will contribute to a deeper understanding of the molecular architecture of genetic assimilation and generate fundamental insights into how environmental and genetic information can act interchangeably to regulate gene activity and phenotype expression. This project is based on extensive past research, novel unpublished data and unique resources developed by the consortium, uniting two project partners with highly complementary expertise in molecular, developmental and evolutionary quantitative genetics.

Mammalian genomes are divided into Topologically Associated Domains (TADs) that restrict the formation of Enhancer-Promoter loops and other biological processes. TADs are formed by a process of Cohesin-mediated loop extrusion, which is subsequently blocked at defined TAD boundaries. Most TAD boundaries bind the CTCF insulator protein, but features like G-quadruplexes (G4s) and transcriptional start sites are enriched as well. We recently reported that CTCF binding is clustered at most TAD boundaries, both at the level of ChIP-seq peaks and of DNA binding motifs within peaks. Clustering of binding motifs within peaks was particularly beneficial for CTCF binding at lower affinity motifs, suggesting that this local clustering may create binding synergies. Using Nano-C, a new multi-contact 3C assay, we showed that TAD boundaries are not impermeable and that CTCF binding peaks contributed individually (but incompletely) to the blocking of loop extrusion. Clustering of peaks thereby improved the overall capacity for loop extrusion blocking, thereby enhancing the separation between TADs. We hypothesize that loop extrusion blocking at TAD boundaries can be defined by their grammar of CTCF binding (‘Insulator Grammar'), with chromatin features like nucleosome positioning, transcription and G4s having a further impact. This DNA-encoded grammar provides a flexible means for the regulation of TAD boundary permeability, thereby allowing the fine-tuning of enhancer-promoter loop formation and gene regulation. Our InsulatorGrammar project aims to systematically dissect how the CTCF grammar can be used to regulate Cohesin-mediated loop extrusion, thereby allowing the modulation of enhancer-promoter loop formation. To address this aim, we will determine how the DNA-encoded local clustering of CTCF binding motifs, in combination with other chromatin features, creates favorable chromatin environments for CTCF binding, and how this synergy affects loop extrusion and enhancer blocking. First, we will first use cells that permit a timed degradation and reestablishment of the CTCF protein to determine, genome-wide, how the CTCF binding grammar (number, orientation and affinity of motifs) and other chromatin features reciprocally influence CTCF binding. Next, we will use a newly developed reporter system for enhancer-promoter looping to integrate 50 synthetic ‘designer’ insulator elements that vary for the number, orientation and affinity of CTCF motifs, and in the presence or absence of nearby transcription and G4s. For all lines, the influence of the CTCF grammar on CTCF binding and enhancer blocking will be determined. Moreover, one-third of these lines will be analyzed using a strategy that combines in-depth multi-omics with biophysical modeling to unravel underlying characteristics of chromatin organization. These studies will reveal how the CTCF grammar and the surrounding chromatin features reciprocally affect the DNA binding of CTCF, the positioning of nucleosomes and the formation of G4s. These structural insights will subsequently be linked to the functional impact on loop extrusion blocking, enhancer-promoter looping and TAD organization. Our multi-disciplinary InsulatorGrammar project will generate an unprecedented view of how clustering of CTCF binding sites can synergize with other chromatin features to create a DNA-encoded means for the fine-tuning of enhancer-promoter looping and gene regulation. The results will help to explain how more subtle changes in gene activity can be introduced, with relevance for development, evolution and disease.

Information processing is realised by neurons and astroglia in tandem. However, the modalities of local neuroglial interactions are still poorly understood. In contrast to neurons, astrocytes are thought to be electrically silent. Yet, the study of astrocytic activity has been focused in rodents and limited to their soma, which is not proximate to synapses nor rich in channels, in contrast to their numerous nanoscopic perisynaptic processes (PAP). In addition, human astrocytes, in comparison to rodent astrocytes, have more processes, interact with more synapses and show conductive membrane properties. Although ideally positioned and equipped to sense and regulate synapses, PAP have nevertheless never been recorded electrically due to their small size, making regular electrophysiology of PAP impossible. Promisingly, we recently found that there are several voltage gated ion channels enriched in PAP compared to astrocyte soma, and that astrocyte fine processes display local spontaneous electrical activity, that we succeeded to identify for the first time via electrophysiological recordings with nanopipettes. Thus, we propose to reveal the previously inaccessible electrical activity of PAP by studying them directly in mice and humans using a unique multidisciplinary approach combining cutting-edge nanopipette electrophysiology, superresolution imaging and electrodiffusion modelling. With this strategy, we propose to characterise 1) PAP electrical activity patterns, 2) their molecular basis and 3) their impact on physiological and pathological neurotransmission in healthy and epileptic brain tissues. The proposed research should thus uncover the intimate astrocyte-synapse electrical dialogue at the nanoscopic level, and its role in synaptic information processing and epileptiform activity.

Superfluorescence (SF) refers to a well-known phenomenon in atomic physics in which emitters can synchronously emit photons through their long-range interaction, resulting in accelerated and bright coherent emission. The SF process should be theoretically efficient by combining similar emitters with large dipole moment within a superlattice, but experimentally strong limitations arise from their organization within an assembly, due to the difficulties of obtaining spectrally identical individual emitters with high densities and identical dipole orientations. The control of the inter-emitter distance is also a key parameter, with a trade-off between the necessary electromagnetic coupling and the detrimental electronic coupling. That is why in solid-state physics, SF has been demonstrated in very limited systems. Recently, perovskite nanocrystal (pNC) superlattices have joined this shortlist, thanks to their optimal optical and structural properties. Nevertheless, a critical frontier remains unexplored: the demonstration of cavity-enhanced SF of pNC superlattices coupled to a photonic structure. To tackle this challenge, CSUPER2 aims to integrate pNC superlattices into an open fibered-microcavity specially designed for solution-processed individual nanoemitters. This integration would advance the field of cooperative light-matter interactions in pNCs by unlocking cavity-enhanced SF, which is expected to exhibit higher brightness at lower excitation fluences, improved coherence properties, and even SF lasing effects. Overall, CSUPER2 aims to achieve 3 main objectives: (1) to synthesize cubic-shaped pNCs with narrow size-distribution through soft chemistry and ligand-engineering in order to assemble the pNCs into controlled long-range ordered superlattices; (2) to demonstrate SF in the resulting pNC superlattices and investigate in detail the SF fundamental optical properties, such as the spectral signatures, the ultrafast dynamics, the coherence and the photon statistics, using steady-state and time-resolved spectroscopy as well as quantum optics experiments at room and low temperature. The effect of disorder will be precisely analysed in order to assess the number of coherently coupled pNCs contributing to the SF signal; (3) to investigate unexplored areas of cavity-enhanced SF from pNC superlattices, by using a tunable fibered microcavity in order to modify and tune the key element responsible for SF emission, i.e. the dipole-dipole coupling mediated by the vacuum fluctuation of the electromagnetic field. The cavity will thus constitute a new knob to explore the rich physics of SF, and ultimately explore the transition from conventional to SF lasing. To fully exploit the experimental results, the CSUPER2 project will benefit from a strong theoretical support on collective light matter effect. The theoretical studies of the collective emission properties in pNCs superlattices will be done by considering precisely the effect of disorder, along with the effect of the cavity coupling.

The temporal perception of visual events is not simply delayed relative to physical time. Sensory signals are consolidated in temporal integration windows before a perceptual decision is reached. The existence of these windows is often acknowledged but their role in visual perception is rarely studied. We focus here on three sets of issues that we believe are fundamental for time perception: (1) how adaptive are the windows to different contexts, (2) when are events perceived within a window, and (3) what are the consequences of the integration windows on the perceived identity and location of objects? We believe that addressing these issues will help us explain basic and puzzling phenomena in time perception such as the Fröhlich effect, the flash-lag and the flash-drag effects, and the late cue reportability effect. Because these effects are strongly phenomenological, our method of choice is the design of new carefully controlled psychophysical experiments. The project involves three researchers from two laboratories, the “Laboratoire des Systèmes Perceptifs” (LSP, CNRS/ENS) and the “Integrative Neuroscience & Cognition Center” (INCC, CNRS/Univ. Paris).