Biology subjects

Butt, U. J.

Publications and source records attributed to Butt, U. J..

6 recordsLinked to original sources

bioRxiv2026

A single-nucleus regulatory atlas links transposable elements to adult hippocampal neurogenesis

Adult hippocampal neurogenesis can be enhanced or even triggered by extrinsic stimuli, but the lineage-specific regulatory changes that accompany a stimulated neurogenic response remain undefined. We used recombinant human erythropoietin (rhEPO), a defined influencing factor that enriches newly formed pyramidal neurons by ~2 fold in this paradigm, to profile ~35,000 nuclei by single-nucleus ATAC sequencing (snATAC-seq) from rhEPO- and placebo-treated adult mouse hippocampi and to integrate them with matched single-nucleus RNA sequencing (snRNA-seq) of ~120,000 nuclei. Thirty-five accessibility-defined clusters resolved 11 major lineages. Of 39,404 differentially accessible regions (DARs), more than half arose in pyramidal neurons, whereas dentate gyrus granule neurons and interneurons showed predominantly reduced accessibility; within the pyramidal lineage, remodelling was predominant in newly-formed rather than mature neurons. About 20% of hippocampal candidate cis-regulatory elements (cCREs) overlapped transposable elements (TEs) at baseline, rising to about 50% among regions that gained accessibility upon stimulation, and multiple families were significantly bound above the expected threshold by neurogenic transcription factors, whereby the many neighbouring genes have established roles for neuronal differentiation and synapse formation. These data define TE-derived sequences as candidate components of stimulus-responsive neurogenic regulatory networks and provide a cell-type-specific chromatin resource for the adult hippocampus at single-nucleus resolution.

neuroscience↗

bioRxiv2025

Transposable Element-Mediated Epigenomic Remodeling Drives Erythropoietin-Induced Neurogenesis in the Adult Hippocampus

Understanding the molecular mechanisms by which erythropoietin (EPO) acts as neurotrophic factor that enhances hippocampal function and learning is essential to harness its therapeutic potential. Here, we employ single-nucleus ATAC-seq and RNA-seq to map the epigenomic and transcriptional landscapes of adult mouse hippocampus under recombinant human EPO (rhEPO) treatment. We discover significant lineage-specific chromatin remodeling predominantly in newly formed and immature excitatory neurons, highlighting a robust EPO-driven neurogenic response as the first direct evidence that an extrinsic factor can induce adult hippocampal neurogenesis. Notably, many EPO-induced accessible regions overlap ancient transposable elements, particularly ancient LINEs and SINEs, that are bound by key neurogenic transcription factors such as NEUROD1/2, NEUROG2, FOXG1, and ASCL1 and are linked to nearby genes governing neuronal differentiation and synaptic plasticity. Our findings uncover a previously unrecognized transposon-mediated mechanism underlying EPO-induced neurogenesis, highlighting an underappreciated role for TE-derived sequences in this process, and establish a publicly available single-nucleus multiomic atlas as a resource for understanding cell-type-specific gene regulation and neuroplasticity in the adult brain.

neuroscience↗

bioRxiv2025

Transcriptional dynamics of the oligodendrocyte lineageand its regulation by the brain erythropoietin system

Oligodendrocytes differentiate from oligodendrocyte progenitor cells (OPC) in early postnatal development, but some oligodendrogenesis is maintained throughout adulthood, where oligodendrocyte lineage dynamics may contribute to neuroplasticity, adaptive myelination, and myelin repair. Here, we studied the effect of erythropoietin (EPO) and its receptor (EPOR) on oligodendrocyte lineage dynamics employing murine hippocampus and its myelinated fibers as model region. Using multiple stage-specific markers and single-nuclei-RNA-seq data, we find that EPO stimulates all oligodendroglial lineage cells directly, driving differentiation/maturation. Differential gene expression analysis reveals multiple EPO-regulated mRNAs, including downregulated transcripts for GABA-A receptors, fitting the known inhibition of oligodendrocyte maturation by GABA. Importantly, analogous oligodendrocyte responses are seen when endogenous EPO expression in brain is stimulated by hypoxia. Mice lacking EPOR from mature oligodendrocytes show subtle deficiencies of adult myelination in hippocampal fimbria and mild working memory deficits. These gain- and loss-of-function experiments may further suggest EPO as clinically safe treatment for remyelination therapies.

neuroscience↗

bioRxiv2025

Erythropoietin alleviates intellectual disability and autism-like behavior of mice caused by Zbtb20 haploinsufficiency, a construct-valid model of Primrose syndrome

Among the known genetic causes of syndromic autism spectrum disorders (ASD) are transcription factor deficiencies. In this regard, haploinsufficiency of the zinc finger and broad complex, tramtrack, bric and brac domain-containing protein 20 (ZBTB20) leads to a prototypical clinical picture, referred to as Primrose syndrome, comprising severe ASD symptoms together with intellectual disability. Here, we present a comprehensive behavioral and phenotypical characterization of Zbtb20+/- mice, a construct valid model of this thus far untreatable human condition. Zbtb20+/- mice exhibit diminished sociability, reduced vocalization, distinct repetitive behaviors, impaired cognitive flexibility, hyperactivity and hypoalgesia. Magnetic resonance imaging reveals increased volumes of hippocampus, cerebellum, brain matter, and whole brain, confirmed by postmortem brain weight measurements. Due to our previous observation of enhanced ZBTB20 expression in CA1 pyramidal neurons upon recombinant human erythropoietin (rhEPO) injections, we anticipated a mitigating effect through rhEPO treatment of Zbtb20 deficiency/Primrose syndrome. Indeed, after three weeks of alternate-day rhEPO injections, a remarkable improvement in the behavioral phenotype was observed. Our results highlight rhEPO as a first promising treatment for Primrose syndrome.

neuroscience↗

bioRxiv2025

Forebrain-specific loss of erythropoietin provokes compensatory upregulation of different EPO receptors

The procognitive growth factor erythropoietin (EPO) and its canonical receptor, EPOR, have long been recognized to be expressed by most cell types in the brain. Cognitive domains, improved by injections of exogenous EPO or by endogenous, hypoxia-stimulated EPO, include important forebrain functions, namely attention, working memory, drive, and executive performance. To gain mechanistic insight into the involvement of forebrain-expressed EPO, we deleted EPO in mice using as specific cre-driver Emx1. Here, we report that these mutant mice act comparably to their wildtype littermates in a comprehensive behavioral test battery. Importantly, we find that the transcripts of both EPOR and a novel, brain-expressed EPO receptor, EphB4, respond to EPO deletion with compensatory upregulation. EphB4 expression in brain and its increase upon forebrain erasure of EPOR are confirmed by in situ hybridization and immunohistochemistry. The augmented expression of both EPOR and EphB4 and their regulatory intercorrelation may explain why EmxEPO mutants show an even superior performance in the most challenging working memory task. Using the previously published single-nuclei-RNA-seq dataset, we further confirm the suggested compensatory mechanism, wherein EPO loss or reduction drives elevated EPOR expression, adding another layer to the intricate regulation of EPO signaling in hippocampal pyramidal neurons. Collectively, these data may explain the lack of behavioral and negative cognitive consequences upon forebrain-wide EPO elimination.

neuroscience↗

bioRxiv2024

IntelliR: A comprehensive and standardized pipeline for automated profiling of higher cognition in mice

In the rapidly evolving field of rodent behavior research, observer-independent methods facilitate data collection within a social, stress-reduced, and thus more natural environment. A prevalent system in this research area is the IntelliCage, which empowers experimenters to design individual tasks and higher cognitive challenges for mice, driven by their motivation to access reward. The extensive amount and diversity of data provided by the IntelliCage system explains the growing demand for automated analysis among users. Here, we introduce IntelliR, a standardized pipeline for analyzing raw data generated by the IntelliCage software, as well as novel parameters including the cognition index, which enables comparison of performance across various challenges. With IntelliR, we provide the tools to implement and automatically analyze 3 challenges that we designed, encompassing spatial, episodic-like, and working memory with their respective reversal tests. Using results from 3 independent control cohorts of adult female wildtype mice, we demonstrate their ability to comprehend and learn the tasks, thereby improving their proficiency over time. To validate the sensitivity of our approach for detecting cognitive impairment, we used adult female NexCreERT2xRosa26-eGFP-DTA mice after tamoxifen induced diphtheria toxin-mediated ablation of pyramidal neurons in cortex and hippocampus. We observed deterioration in learning capabilities and cognition index across several tests. IntelliR can be readily integrated into and adapted for individual research, thereby improving time management and reproducibility of data analysis. HIGHLIGHTSO_LIIntelliR is a standardized pipeline for analyzing raw data of IntelliCage software. C_LIO_LIDomains include spatial, episodic-like, and working memory with reversals. C_LIO_LIWT mice (3 cohorts) comprehend, learn and improve proficiency over time. C_LIO_LICognition index permits comparison of performance across cognitive domains. C_LIO_LIMice with ablation of pyramidal neurons decline mainly in working memory. C_LI

animal behavior and cognition↗