Biology subjects

Pekowska, A.

Publications and source records attributed to Pekowska, A..

7 recordsLinked to original sources

bioRxiv2026

Evolutionary diversification of lipid logistics shapes synaptic maturation in primates

The prolonged developmental trajectory of the human brain (neoteny) is a defining feature of human evolution. Yet, the cellular mechanisms underlying this delay remain poorly understood. Here, comparing human and chimpanzee induced neurons and cerebral organoids, we we show that human neurons form fewer excitatory synapses and synchronize network activity later. Electron microscopy further revealed reduced synaptic vesicle docking and clustering near release sites, identifying altered presynaptic assembly as a prominent feature of human neuronal development. Unexpectedly, human neurons accumulate more, not less, membrane lipids, revealing a dissociation between lipid abundance and synaptic maturation. Transcriptomics and synaptosome proteomics resolve this paradox: chimpanzee neurons preferentially engage lipid metabolism and synaptic-maturation programs, whereas human neurons upregulate intracellular lipid transport and trafficking pathways. Together, our findings identify membrane organization as a previously unrecognized regulatory layer that controls neuronal neoteny. These results also suggest that evolutionary divergence can arise through changes in the spatial deployment of membrane lipids rather than their abundance, providing a molecular framework for understanding the evolution of human brain neoteny.

evolutionary biology↗

bioRxiv2026

Primate Astrocyte Evolution Controls the Tempo of Neuronal Development

Prolonged neuronal maturation, also referred to as neoteny, constitutes a hallmark of human brain evolution. Yet, the mechanisms controlling neotenic brain development remain poorly understood, and have been defined as neuron-intrinsic. Astrocytes shape synapse formation, activity, and elimination, and have changed substantially between humans and other species. Yet, whether the evolutionary divergence in astrocytes shapes the timing of neuronal maturation is unknown. Here, we show that astrocytes from humans and their closest living relatives, chimpanzees, exert contrasting effects on neuronal maturation: chimpanzee astrocytes accelerate it, whereas human astrocytes delay it, without affecting neuronal survival. Through comparative transcriptomics and epigenomics, we find that evolutionarily reduced APOE expression in human astrocytes underlies the observed delay in neuronal maturation: restoring APOE levels in human astrocytes accelerates neuronal development. We further establish that the Hippo-TEAD signaling represses APOE expression in human astrocytes, revealing a link between the enhanced morphological complexity of human astrocytes and the observed reduced tempo of neuronal development in their presence. Strikingly, neuronal genes differentially impacted by human and chimpanzee astrocytes are associated with schizophrenia, Alzheimers disease, and epilepsy, linking astrocyte evolution to disease vulnerability. Altogether, these findings establish that brain neoteny is partly a glial phenomenon, revealing that understanding the pace of human brain development requires understanding how astrocytes, not only neurons, have evolved.

neuroscience↗

bioRxiv2026

Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis

Advances in single-cell RNA sequencing (scRNA-seq) and high-resolution imaging techniques, such as single-molecule tracking (SMT) of RNA and transcription factors, allow researchers to quantitatively explore dynamics and variation but have never been integrated into a single coherent model. In this study, we propose a kinetic model that intakes multiple data types, including steady-state and time-resolved datasets, to simulate and fit stochastic models of gene transcription to experimental data. We find that 3-state models provide an essential improvement over the widely used 2-state model for most genes and have the property of kinetic proofreading, which we argue is advantageous in the cellular context. We further identify two dimensionless quantities derived from the rate equations which are broadly conserved across genes. Finally, we extend this model to scRNA-seq datasets to infer kinetic rates under defined perturbations and reveal biochemical insight into the mechanism of action of transcription factors.

bioinformatics↗

bioRxiv2023

Molecular signature of primate astrocytes reveals pathways and regulatory changes contributing to the human brain evolution

Astrocytes contribute to the development and regulation of the higher-level functions of the brain, the critical targets of evolution. However, the molecular signature of foetal astrocyte evolution in primates is unknown. Here, to address this question, we use human, chimpanzee, and macaque induced pluripotent stem cell-derived foetal astrocytes (iAstrocytes). Human iAstrocytes are bigger and more complex than the non-human primate iAstrocytes. We find loci related to the regulation of cell size with increased expression in the human lineage. Likewise, we uncover that genes and mechanisms implicated in long-range intercellular signalling are activated in the human iAstrocytes. Strikingly, loci downregulated in the human lineage frequently relate to intellectual disability raising new questions on the trade-offs associated with the evolution of the human mind. Using our system, through a multilevel regulome analysis and machine learning, we uncover that functional activation of enhancers coincides with a previously unappreciated, pervasive gain of binding sites of stripe transcription factors. In summary, we shed new light on a mechanism driving the acquisition of the regulatory potential of enhancers.

neuroscience↗

bioRxiv2022

Remodeling of Il4-Il13-Il5 locus underlies selective gene expression

The type 2 cytokines, interleukin (IL)-4, IL-5 and IL-13 reside within a tandem multi-gene cluster in mammals. These cytokines represent the hallmark of type 2 immune responses controlling parasites, promoting tissue repair as well as causing allergic diseases. Both innate and adaptive lymphocytes secrete type 2 cytokines with discordant production spectra. We took a holistic structural and functional view of the type 2 cytokine locus before and after activation, comparing innate (ILC2) and adaptive (Th2) lymphocytes to understand mechanisms underlying their distinctive programs. Rapid induction of IL-5 dominates in ILC2, whereas IL-4 does so in Th2 cells. Using high-resolution chromatin conformation capture we found that global cellular chromatin architecture remained constant, whereas the type 2 cytokine locus rapidly remodeled. In ILC2, Il13 and Il5 loci were aligned in proximity whereas Il4 locus was insulated. In Th2 cells, Il4 and Il13 positioned in proximity while the Il5 locus remained distal. Select REs were separately deleted in mice to confirm cell-type specific and activation-dependent roles in type 2 responses in vivo. Thus, contrary to the premise that chromatin architecture plays a minimal role in steady-state gene induction, signal-dependent remodeling of 3D configuration underlies the discordant cytokine outputs in ILC2s versus Th2 cells.

immunology↗

bioRxiv2018

Condensin II inactivation in interphase does not affect chromatin folding or gene expression

Condensin complexes have been proposed to play a prominent role in interphase chromatin organization and control of gene expression. Here, we report that the deletion of the central condensin II kleisin subunit Ncaph2 in differentiated mouse hepatocytes does not lead to significant changes in chromosome organization or in gene expression. Both observations challenge current views that implicate condensin in interphase chromosomal domain formation and in enhancer-promoter interactions. Instead, we suggest that the previously reported effects of condensin perturbation may result from their structural role during mitosis, which might indirectly impact the re-establishment of interphase chromosomal architecture after cell division.

genomics↗

bioRxiv2016

Two independent modes of chromosome organization are revealed by cohesin removal

The three-dimensional organization of chromosomes is tightly related to their biological function 1. Both imaging and chromosome conformation capture studies have revealed several layers of organization 2-4: segregation into active and inactive compartments at the megabase scale 5, and partitioning into domains (TADs) 6,7 and associated loops 8 at the sub-megabase scale. Yet, it remains unclear how these layers of genome organization form, interact with one another, and contribute to or result from genome activities. TADs seem to have critical roles in regulating gene expression by promoting or preventing interactions between promoters and distant cis-acting regulatory elements 9-14, and different architectural proteins, including cohesin, have been proposed to play central roles in their formation 15,16. However, experimental depletions of these proteins have resulted in marginal changes in chromosome organization 17-19. Here, we show that deletion of the cohesin-loading factor, Nipbl, leads to loss of chromosome-associated cohesin and results in dramatic genome reorganization. TADs and associated loops vanish globally, even in the absence of transcriptional changes. In contrast, segregation into compartments is preserved and even reinforced. Strikingly, the disappearance of TADs unmasks a finer compartment structure that accurately reflects the underlying epigenetic landscape. These observations demonstrate that the 3D organization of the genome results from the independent action of two distinct mechanisms: 1) cohesin-independent segregation of the genome into fine-scale compartment regions, defined by the underlying chromatin state; and 2) cohes-dependent formation of TADs possibly by the recently proposed loop extrusion mechanism 20,21, enabling long-range and target-specific activity of promiscuous enhancers. The interplay between these mechanisms creates an architecture that is more complex than a simple hierarchy of layers and can be central to guiding normal development.

genomics↗