Biology subjects

Mann, R.

Publications and source records attributed to Mann, R..

16 recordsLinked to original sources

bioRxiv2026

Enhancers require an active resetting phase after transcriptional activation

Signal-responsive enhancers must activate transcription and then return to a competent but inactive state, yet whether this transition is passive or actively driven has remained unresolved. We define this process as enhancer resetting and identify the androgen receptor (AR) as the factor that executes it as an endogenous response to estrogen signaling, independent of exogenous androgen. As estrogen receptor- (ER) undergoes ligand-induced proteasomal degradation during late-phase signaling, AR progressively accumulates in the nucleus and preferentially occupies highly active, persistent ER enhancers in a transcriptionally silent manner. This late-phase AR binding evicts the pioneer factor FOXA1 from chromatin while preserving baseline accessibility, a handoff mechanism that decouples chromatin openness from active transcription. Conversely, augmenting AR activity by DHT treatment or AR overexpression accelerates FOXA1 eviction, while disrupting AR chromatin binding, either by AR knockdown or a DNA-binding-deficient mutant, prevents it, leaving enhancers in an aberrantly permissive state that drives amplified ER rebinding and transcriptional hyperactivation upon subsequent estrogen stimulation. These findings establish active enhancer resetting as a mechanism safeguarding the fidelity of repeated transcriptional responses. Failure of this mechanism may underlie the transcriptional dysregulation that drives tumor progression and endocrine therapy resistance in ER-positive breast cancer, where estrogen signaling is chronic and cyclic.

molecular biology↗

bioRxiv2026

Multimodal characterization of variation in neuronal types in the mouse basal ganglia

AbstractThe basal ganglia (BG) are a set of topographically organized, interconnected structures that are pivotal for regulating volitional movement and other aspects of cognitive, motivational, and affective behavior. Recently generated taxonomies of transcriptomically-defined cell types (T-types) have revealed both fine-grained distinctions in gene expression between neurons in these structures as well as continuous transcriptomic variation across similar T-types1-9, which are both related to location within a structure. However, it remains unclear to what extent these and other cellular properties co-vary with each other. Therefore, we performed Patch-seq experiments10,11 on over 900 neurons in mouse brain slices from BG to provide an integrated view of the co-variation between gene expression, location, physiology, and morphology measured from the same neurons. Medium spiny neurons (MSNs) from both the direct and indirect pathways across the dorsal and ventral striatum follow a gene expression gradient that varies in a dorsolateral to ventromedial direction; we find that this gradient also corresponds with systematic differences in action potential kinetics and dendritic arborization. Our analysis also characterizes additional multimodal dimensions of MSN variation, such as those between direct and indirect pathway neurons and between matrix and striosome neurons. Furthermore, through comparison with Patch-seq data from macaque, we demonstrate that the relationship between the transcriptomic/spatial gradient and electrophysiological and morphological properties is conserved across these two species. We also find that properties of striatal interneurons, such as action potential kinetics, vary across the striatum in a manner consistent with the MSN gradient. Outside the striatum, our multimodal Patch-seq dataset from the globus pallidus, subthalamic nucleus, and substantia nigra enabled us to characterize transcriptomically-defined types and link them to prior descriptions of cell types in these structures. Finally, we examined to what extent the MSN transcriptomic/spatial gradient persisted across different stages of the BG circuit by comparing Patch-seq neurons to reconstructed whole-neuron morphologies and the topography of their interareal projections, finding that the gradient is better preserved in GPe and GPi compared to SNr. Our study links transcriptomic variation across T-types in mouse BG to spatial localization and phenotypic differences at the level of individual cells, improving our understanding of cell type architecture in topographically organized circuits of the brain.

neuroscience↗

bioRxiv2025

Decoding neuronal wiring by joint inference of cell identity and synaptic connectivity

Animal behaviors are executed by motor neurons (MNs), which receive information from complex pre-motor neuron (preMN) circuits and output commands to muscles. How motor circuits are established during development remains an important unsolved problem in neuroscience. Here we focus on the development of the motor circuits that control the movements of the adult legs in Drosophila melanogaster. After generating single-cell RNA sequencing (scRNAseq) datasets for leg MNs at multiple time points, we describe the time course of gene expression for multiple gene families. This analysis reveals that transcription factors (TFs) and cell adhesion molecules (CAMs) appear to drive the molecular diversity between individual MNs. In parallel, we introduce ConnectionMiner, a novel computational tool that integrates scRNAseq data with electron microscopy-derived connectomes. ConnectionMiner probabilistically refines ambiguous cell type annotations by leveraging neural wiring patterns, and, in turn, it identifies combinatorial gene expression signatures that correlate with synaptic connectivity strength. Applied to the Drosophila leg motor system, ConnectionMiner yields a comprehensive transcriptional annotation of both MNs and preMNs and uncovers candidate effector gene combinations that likely orchestrate the assembly of neural circuits from preMNs to MNs and ultimately to muscles.

neuroscience↗

bioRxiv2025

Nuclear myosin I mediates genomic clustering of estrogen receptor-α without affecting ligand-induced transcriptional robustness

Ligand-induced transcriptional responses are rapid and robust. Estrogen, one such ligand, exerts its rapid effects through the steroid hormone receptor estrogen receptor-alpha (ER). Upon stimulation, ER binds to clustered enhancers to drive target gene expression. Here, we identify nuclear myosin 1 (NM1/Myo1c) as a positive regulator of ER clustering on enhancers, promoting condensate formation on chromatin. NM1 is enriched on chromatin at the peak of the signaling response, and its depletion leads to a genome-wide reduction in ER occupancy and condensates. Surprisingly, these alterations in chromatin occupancy of ER have minimal impact on estrogen-regulated gene expression, suggesting that transcriptional output remains robust despite disruptions in transcription factor clustering. This study reveals a regulatory axis between Myo1c and ER clustering, offering fresh insights into the intricacies of transcriptional regulation.

molecular biology↗

bioRxiv2025

Molecular evolution of silver nanoparticle resistance in a bacterial pathogen and a unique adaptation response to ionic silver

This research explores the adaptive defense mechanisms of a nanosilver-resistant pathogen (NAgR) to protect and fight off the complex antimicrobial targeting of silver nanoparticles. The Gram-negative bacterium Acinetobacter baumannii upregulated expression of outer membrane proteins for cell surface defense, as well as membrane and capsule synthesis genes. Increased abundance of surface-attached biofilm colonies in NAgR was linked to the phenotypically indicated increase in membrane integrity, with the bacterium also forming more EPS, the biopolymer matrix that protects the residing colony. In response to the known reactive oxygen species (ROS) toxicity characteristics of the nanoparticle, NAgR upregulated its oxidative stress management system, specifically involving ROS scavenger enzymes and opportunistic metal efflux pumps. Many of these evolved defense mechanisms only manifested in the resistant bacterium, while they were absent in the wild-type strain. This study also details the unique defenses of an ionic silver-adapted A. baumannii variant, having evolved from the same wild-type parental strain as NAgR. Despite similarities in cell surface and biofilm defense trends, the slower-to-kill tolerant strain (AgT) exclusively upregulated multidrug efflux systems and respiratory chain enzymes, thought to maintain enhanced respiration activity, a known tolerant characteristic. Identification of these stable defense mechanisms can recommend strategies for molecular targeting to overcome the adaptation phenomena.

microbiology↗

bioRxiv2024

Paused Polymerase synergises with transcription factors and RNA to enhance the transcriptional potential of promoters

Regulated pausing of RNA polymerase II (Pol II) is essential for enabling rapid and coordinated transcriptional responses to signalling cues. Pausing also contributes to the formation of nucleosome-free regions with the help of chromatin remodellers. However, if these nucleosome-free regions engage with transcription factors to stimulate the transcription potential of paused promoters is not known. In this study, we demonstrate that ligand-induced estrogen receptor-alpha (ER) binding is stabilized at Pol II-paused sites. This stabilization results from an increased dwell time of ER on chromatin, as revealed by single molecule tracking (SMT) experiments. Notably, short chromatin-associated RNAs generated by the paused Pol II contribute to enhancing ER binding at paused promoters. We also observe that pausing increases histone H3K27 acetylation (H3K27ac) levels, which primes paused promoters for robust transcriptional activation upon release. Collectively, these findings suggest that paused Pol II plays a central role in enhancing transcription factor binding through an RNA-dependent mechanism. This, in turn, results in a more vigorous transcriptional response following pausing release, thus contributing to the fine-tuning of ER-mediated gene regulation.

molecular biology↗

bioRxiv2023

Connecting single neuron transcriptomes to the projectome in mouse visual cortex

The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neurons role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morphoelectric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.

neuroscience↗

bioRxiv2023

RNA binding limits the ligand induced transcriptional potential of estrogen receptor-alpha

Transcription factors (TFs) primarily regulate gene expression by binding to DNA through their DNA binding domains (DBD). Additionally, approximately half of these TFs also interact with RNA. However, the role of RNA in enabling TF binding on chromatin and subsequent transcription is poorly understood. Estrogen receptor- (ER) is one such TF that activates genes in response to estrogen stimulation. Here, we report that ER interacts with various types of RNAs in ligand dependent manner via its RNA binding motif in hinge region. RNA binding defects lead to a global loss of ER binding in the genome, particularly at weaker ER motifs. In the absence of RNA binding, the ER exhibits dynamic behavior in the nucleus and unexpectedly, the dynamic binding coincides with robust polymerase loading on ER bound chromatin regions. The higher occupancy of PolII was recapitulated by robust ligand induced transcription of ER-regulated genes. Collectively, our results suggest that RNA interactions strengthen ER binding to chromatin limiting the ligand-dependent transcriptional upregulation of estrogen-induced genes.

molecular biology↗

bioRxiv2022

Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

Human cortical interneurons have been challenging to study due to high diversity and lack of mature brain tissue platforms and genetic targeting tools. We employed rapid GABAergic neuron viral labeling plus unbiased Patch-seq sampling in brain slices to define the signature morpho-electric properties of GABAergic neurons in the human neocortex. Viral targeting greatly facilitated sampling of the SST subclass, including primate specialized double bouquet cells which mapped to two SST transcriptomic types. Multimodal analysis uncovered an SST neuron type with properties inconsistent with original subclass assignment; we instead propose reclassification into PVALB subclass. Our findings provide novel insights about functional properties of human cortical GABAergic neuron subclasses and types and highlight the essential role of multimodal annotation for refinement of emerging transcriptomic cell type taxonomies. One Sentence SummaryViral genetic labeling of GABAergic neurons in human ex vivo brain slices paired with Patch-seq recording yields an in-depth functional annotation of human cortical interneuron subclasses and types and highlights the essential role of multimodal functional annotation for refinement of emerging transcriptomic cell type taxonomies.

neuroscience↗

bioRxiv2022

Morpho-electric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Neocortical layer 1 (L1) is a site of convergence between pyramidal neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by distinctive pyramidal neuron types with extensive branching in L1, but whether L1 interneurons are similarly diverse is underexplored. Using patch-seq recordings from human neurosurgically resected tissues, we identified four transcriptomically defined subclasses, unique subtypes within those subclasses and additional types with no mouse L1 homologue. Compared with mouse, human subclasses were more strongly distinct from each other across all modalities. Accompanied by higher neuron density and more variable cell sizes compared with mouse, these findings suggest L1 is an evolutionary hotspot, reflecting the increasing demands of regulating the expanding human neocortical circuit. One Sentence SummaryUsing transcriptomics and morpho-electric analyses, we describe innovations in human neocortical layer 1 interneurons.

neuroscience↗

bioRxiv2021

Models of increased latent HIV reservoir turnover prior to cART initiation imply novel clearance strategies

CD4+ T cells with a naive or memory phenotype carrying a replication-competent HIV provirus are recognized as the major component of the persistent HIV reservoir. These cells only minimally express viral protein, reducing viral cytotoxicity effects and making them difficult targets for immune responses as well as every available antiretroviral drug. In patients on suppressive antiretroviral therapy, the half-life of these cells is approximately 4-5 years, balanced by clonal expansion of the cells resulting in an overall reservoir half-life in excess of 40 years. A recent study has shown that prior to the initiation of antiretroviral therapy, the half-life of these cells is instead on the order of two weeks. We present two models explaining the wide disparity in the on- and off-treatment half-lives of the quiescent infected T cells. In the first model, generalized (antigen non-specific) immune activation due to the high HIV viral loads explains the high latent reservoir turnover rates in the absence of treatment. If this mechanism dominates, we demonstrate that reduction of the latent reservoir size is possible, either through the administration of exogenous antigen or through the use of timed treatment interruptions. In the second model, direct killing of reservoir cells by HIV drives the increased turnover off-treatment. If this mechanism dominates, modulation of the reservoir size is not possible by the methods described above. Previously published models of the immune response to HIV show the possibility of inducing post-treatment control by reducing the latent reservoir size; by incorporating the same immune response dynamics in our first model, it is shown that it may be possible to induce post-treatment control using either exogenous antigen administration or timed treatment interruptions.

systems biology↗

bioRxiv2020

High fidelity electrophysiological, morphological, and transcriptomic cell characterization using a refined Patch-seq protocol

The Patch-seq approach is a powerful variation of the standard patch clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at a scale and quality that can be integrated with high-throughput dissociated cell transcriptomic data, we have optimized the technique by identifying and refining key factors that contribute to the efficient collection of high-quality data. To rapidly generate high-quality electrophysiology data, we developed patch clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized a substantial improvement in transcriptomic data quality when the nucleus was extracted following the recording. For morphology success, the importance of maximizing the neurons membrane integrity during the extraction of the nucleus was much more critical to success than varying the duration of the electrophysiology recording. We compiled the lab protocol with the analysis and acquisition software at https://github.com/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate Patch-seq data across diverse mammalian species and that is compatible with recent large-scale publicly available Allen Institute Patch-seq datasets.

neuroscience↗

bioRxiv2020

Multi-modal characterization and simulation of human epileptic circuitry

Temporal lobe epilepsy is the fourth most common neurological disorder with about 40% of patients not responding to pharmacological treatment. Increased cellular loss in the hippocampus is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions such as temporal lobe resection, the impact of the disease at the cellular level remains unclear in humans. Here we show that properties of hippocampal granule cells change with disease progression as measured in living, resected hippocampal tissue excised from epilepsy patients. We show that granule cells increase excitability and shorten response latency while also enlarging in cellular volume, surface area and spine density. Single-cell RNA sequencing combined with simulations ascribe the observed electrophysiological changes to gradual modification in three key ion channel conductances: BK, Cav2.2 and Kir2.1. In a bio-realistic computational network model, we show that the changes related to disease progression bring the circuit into a more excitable state. In turn, we observe that by reversing these changes in the three key conductances produces a less excitable, "early disease-like" state. These results provide mechanistic understanding of epilepsy in humans and will inform future therapies such as viral gene delivery to reverse the course of the disorder.

neuroscience↗

bioRxiv2019

A size principle for leg motor control in Drosophila

To move the body, the brain must precisely coordinate patterns of activity among diverse populations of motor neurons. In many species, including vertebrates, the motor neurons innervating a given muscle fire in a specific order that is determined by a gradient of cellular size and electrical excitability. This hierarchy allows premotor circuits to recruit motor neurons of increasing force capacity in a task-dependent manner. However, it remains unclear whether such a size principle also applies to species with more compact motor systems, such as the fruit fly, Drosophila melanogaster, which has just 53 motor neurons per leg. Using in vivo calcium imaging and electrophysiology, we found that genetically-identified motor neurons controlling flexion of the fly tibia exhibit a gradient of anatomical, physiological, and functional properties consistent with the size principle. Large, fast motor neurons control high force, ballistic movements while small, slow motor neurons control low force, postural movements. Intermediate neurons fall between these two extremes. In behaving flies, motor neurons are recruited in order from slow to fast. This hierarchical organization suggests that slow and fast motor neurons control distinct motor regimes. Indeed, we find that optogenetic manipulation of each motor neuron type has distinct effects on the behavior of walking flies.

neuroscience↗

bioRxiv2019

Ligand dependent gene regulation by transient ER clustered enhancers

Unliganded nuclear receptors have been implicated in ligand-dependent gene regulation. However, the underlying mechanisms are not fully understood. Here we demonstrate that unliganded ER binds to specific sites in the genome thereby pre-marking them as future functional enhancers. Upon ligand exposure, ER binds to several EREs relatively proximal to the pre-marked, or persistent, ER-bound sites. Interestingly, the persistent sites interact extensively, via chromatin looping, with the proximal transiently bound sites forming ER clustered enhancers in 3D. CRISPR-based deletion of TFF1 persistent site disrupts the formation of its clustered enhancer resulting in the loss of E2-dependent induced expression of TFF1 and its neighboring genes within the same cluster. The clustered enhancers overlap with nuclear ER puncta that coalesce in a ligand-dependent manner. Furthermore, formation of clustered enhancers, as well as puncta, coincide with the active phase of signaling and their later disappearance results in the loss of gene expression even though persistent sites remain bound by ER. Our results establish the role of persistent unliganded ER binding in priming enhancer clusters in 3D that drive transient, but robust, gene expression in a ligand-dependent fashion.

molecular biology↗

bioRxiv2017

A Systematic Nomenclature for the Drosophila Ventral Nervous System

The fruit fly, Drosophila melanogaster, is an established and powerful model system for neuroscience research with wide relevance in biology and medicine. Until recently, research on the Drosophila brain was hindered by the lack of a complete and uniform nomenclature. Recognising this problem, the Insect Brain Name Working Group produced an authoritative hierarchical nomenclature system for the adult insect brain, using Drosophila melanogaster as the reference framework, with other taxa considered to ensure greater consistency and expandability (Ito et al., 2014). Here, we extend this nomenclature system to the sub-gnathal regions of the adult Drosophila nervous system, thus providing a systematic anatomical description of the ventral nervous system (VNS). This portion of the nervous system includes the thoracic and abdominal neuromeres that were not included in the original work and contains the motor circuits that play essential roles in most fly behaviours.

neuroscience↗