scholarly journals Spatial organization of the transcriptome in individual neurons

2020 ◽  
Author(s):  
Guiping Wang ◽  
Cheen-Euong Ang ◽  
Jean Fan ◽  
Andrew Wang ◽  
Jeffrey R. Moffitt ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Spatial Clustering ◽  
Super Resolution ◽  
Distribution Patterns ◽  
Synaptic Activity ◽  
Spatial Profiling ◽  
Multiple Length Scales ◽  
Neuronal Functions ◽  
Genome Scale ◽  
Micrometer Scale

AbstractNeurons are highly polarized cells with complex neurite morphology. Spatial organization and local translation of RNAs in dendrites and axons play an important role in many neuronal functions. Here we performed super-resolution spatial profiling of RNAs inside individual neurons at the genome scale using multiplexed error-robust fluorescence in situ hybridization (MERFISH), and mapped the spatial organization of up to ∼4,200 RNA species (genes) across multiple length scales, ranging from sub-micrometer to millimeters. Our data generated a quantitative intra-neuronal atlas of RNAs with distinct transcriptome compositions in somata, dendrites, and axons, and revealed diverse sub-dendritic distribution patterns of RNAs. Moreover, our spatial analysis identified distinct groups of genes exhibiting specific spatial clustering of transcripts at the sub-micrometer scale that were dependent on protein synthesis and differentially dependent on synaptic activity. Overall, these data provide a rich resource for characterizing the subcellular organization of the transcriptome in neurons with high spatial resolution.

scholarly journals Topological demarcation by HMGB2 is disrupted early upon senescence entry across cell types and induces CTCF clustering

2017 ◽  
Author(s):  
Anne Zirkel ◽  
Milos Nikolic ◽  
Konstantinos Sofiadis ◽  
Jan-Philipp Mallm ◽  
Lilija Brant ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Spatial Clustering ◽  
High Mobility ◽  
Super Resolution ◽  
Cell Types ◽  
Cell Nuclei ◽  
Genome Chromosome ◽  
Chromosome Conformation ◽  
Nuclear Factors ◽  
Stochastic Events

AbstractAgeing-relevant processes, like cellular senescence, are characterized by complex, often stochastic, events giving rise to heterogeneous cell populations. We hypothesized that entry into senescence of different primary human cells can be triggered by one early molecular event affecting the spatial organization of chromosomes. To test this, we combined whole-genome chromosome conformation capture, population and single-cell transcriptomics, super-resolution imaging, and functional analyses applied on proliferating and replicatively-senescent populations from three distinct human cell types. We found a number of genes involved in DNA conformation maintenance being suppressed upon senescence across cell types. Of these, the abundant high mobility group (HMG) B1 and B2 nuclear factors are quantitatively removed from cell nuclei before typical senescence markers appear, and mark a subset of topologically-associating domain (TAD) boundaries. Their loss coincides with obvious reorganization of chromatin interactions via the dramatic spatial clustering of CTCF foci. HMGB2 knock-down recapitulates this senescence-induced CTCF clustering, while also affecting insulation at TAD boundaries. We accordingly propose that HMGB-mediated deregulation of chromosome conformation constitutes a primer for the ensuing senescent program across cell types.

scholarly journals A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair

2013 ◽  
Vol 202 (3) ◽  
pp. 579-595 ◽  
Author(s):  
Sébastien Britton ◽  
Julia Coates ◽  
Stephen P. Jackson
Keyword(s):  
High Resolution ◽  
Single Molecule ◽  
Anticancer Agents ◽  
Spatial Organization ◽  
System Development ◽  
Super Resolution ◽  
Strand Break ◽  
Resistance Mechanisms ◽  
Original Method ◽  
Immune System Development

DNA double-strand breaks (DSBs) are the most toxic of all genomic insults, and pathways dealing with their signaling and repair are crucial to prevent cancer and for immune system development. Despite intense investigations, our knowledge of these pathways has been technically limited by our inability to detect the main repair factors at DSBs in cells. In this paper, we present an original method that involves a combination of ribonuclease- and detergent-based preextraction with high-resolution microscopy. This method allows direct visualization of previously hidden repair complexes, including the main DSB sensor Ku, at virtually any type of DSB, including those induced by anticancer agents. We demonstrate its broad range of applications by coupling it to laser microirradiation, super-resolution microscopy, and single-molecule counting to investigate the spatial organization and composition of repair factories. Furthermore, we use our method to monitor DNA repair and identify mechanisms of repair pathway choice, and we show its utility in defining cellular sensitivities and resistance mechanisms to anticancer agents.

scholarly journals Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function

2021 ◽  
Vol 7 (1) ◽  
pp. eabe4310
Author(s):  
Yue Li ◽  
Adam Eshein ◽  
Ranya K.A. Virk ◽  
Aya Eid ◽  
Wenli Wu ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Super Resolution ◽  
Population Level ◽  
Average Diameter ◽  
Live Cells ◽  
Molecular Function ◽  
Label Free ◽  
Multiple Length Scales ◽  
Chromatin Packing ◽  
Analysis Platform

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

scholarly journals Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

Science ◽  
2018 ◽  
Vol 362 (6413) ◽  
pp. eaau1783 ◽  
Author(s):  
Bogdan Bintu ◽  
Leslie J. Mateo ◽  
Jun-Han Su ◽  
Nicholas A. Sinnott-Armstrong ◽  
Mirae Parker ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Single Cells ◽  
Domain Boundary ◽  
Super Resolution ◽  
Chromatin Domain ◽  
Imaging Method ◽  
Imaging Data ◽  
Chromatin Interactions ◽  
Population Average ◽  
Binding Factor

The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish TAD-like structures in single cells but eliminated preferential domain boundary positions. Moreover, we observed widespread, cooperative, multiway chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.

scholarly journals High-throughput super-resolution analysis of influenza virus pleomorphism reveals insights into viral spatial organization

2021 ◽  
Author(s):  
Andrew McMahon ◽  
Rebecca Andrews ◽  
Sohail V Ghani ◽  
Thorben Cordes ◽  
Achillefs N Kapanidis ◽  
...  
Keyword(s):  
Large Scale ◽  
Spatial Organization ◽  
Structural Information ◽  
Virus Assembly ◽  
Super Resolution ◽  
Automated Analysis ◽  
Size Analysis ◽  
Analysis Pipeline ◽  
Single Experiment ◽  
Viral Immunology

Many viruses form highly pleomorphic particles; in influenza, these particles range from spheres of ~ 100 nm in diameter to filaments of several microns in length. Virion structure is of interest, not only in the context of virus assembly, but also because pleomorphic variations may correlate with infectivity and pathogenicity. Detailed images of virus morphology often rely on electron microscopy, which is generally low throughput and limited in molecular identification. We have used fluorescence super-resolution microscopy combined with a rapid automated analysis pipeline to image many thousands of individual influenza virions, gaining information on their size, morphology and the distribution of membrane-embedded and internal proteins. This large-scale analysis revealed that influenza particles can be reliably characterised by length, that no spatial frequency patterning of the surface glycoproteins occurs, and that RNPs are preferentially located towards filament ends within Archetti bodies. Our analysis pipeline is versatile and can be adapted for use on multiple other pathogens, as demonstrated by its application for the size analysis of SARS-CoV-2. The ability to gain nanoscale structural information from many thousands of viruses in just a single experiment is valuable for the study of virus assembly mechanisms, host cell interactions and viral immunology, and should be able to contribute to the development of viral vaccines, anti-viral strategies and diagnostics.

scholarly journals Extended Synaptotagmin is a presynaptic ER Ca2+ sensor that promotes neurotransmission and synaptic growth in Drosophila

2017 ◽  
Author(s):  
Koto Kikuma ◽  
Daniel Kim ◽  
David Sutter ◽  
Xiling Li ◽  
Dion K. Dickman
Keyword(s):  
Plasma Membrane ◽  
Membrane Trafficking ◽  
Synaptic Activity ◽  
Synaptic Growth ◽  
Synaptic Physiology ◽  
Lipid Exchange ◽  
Membrane Tethering ◽  
Conserved Gene ◽  
Neuronal Functions

ABSTRACTThe endoplasmic reticulum (ER) is an extensive presynaptic organelle, exerting important influences at synapses by responding to Ca2+ and modulating transmission, growth, lipid metabolism, and membrane trafficking. Despite intriguing evidence for these crucial functions, how presynaptic ER influences synaptic physiology remains enigmatic. To gain insight into this question, we have generated and characterized mutations in the single Extended Synaptotagmin (Esyt) ortholog in Drosophila. Esyts are evolutionarily conserved ER proteins with Ca2+ sensing domains that have recently been shown to orchestrate membrane tethering and lipid exchange between the ER and plasma membrane. We first demonstrate that Esyt localizes to an extensive ER structure that invades presynaptic terminals at the neuromuscular junction. Next, we show that synaptic growth, structure, function, and plasticity are surprisingly unperturbed at synapses lacking Esyt expression. However, presynaptic overexpression of Esyt leads to enhanced synaptic growth, neurotransmission, and sustainment of the vesicle pool during intense levels of activity, suggesting that elevated Esyt at the ER promotes constitutive membrane trafficking or lipid exchange with the plasma membrane. Finally, we find that Esyt mutants fail to maintain basal neurotransmission and short term plasticity at elevated extracellular Ca2+, consistent with Esyt functioning as an ER Ca2+ sensor that modulates synaptic activity. Thus, we identify Esyt as a presynaptic ER Ca2+ sensor that can promote neurotransmission and synaptic growth, revealing the first in vivo neuronal functions of this conserved gene family.

scholarly journals Single Molecule Localization Microscopy (SMLM) imaging of bacteria: A sample preparation guide

2020 ◽  
Author(s):  
Sachith D. Gunasinghe ◽  
Kirstin D. Elgass ◽  
Toby D. M. Bell ◽  
Trevor Lithgow
Keyword(s):  
Membrane Proteins ◽  
Outer Membrane ◽  
Single Molecule ◽  
Spatial Organization ◽  
Outer Membrane Proteins ◽  
Fluorescent Microscopy ◽  
Super Resolution ◽  
Model Systems ◽  
Invaluable Tool ◽  
Optical Reconstruction

Abstract In recent years Super-resolution microscopy has become an invaluable tool to noninvasively interrogate the membrane architecture of bacteria to study the spatial organization of proteins associated with membranes, which in turn help us to understand how bacteria have evolved to exploit environmental niches. Model systems like Escherichia coli and Caulobacter cresentus have been used to study the spatiotemporal organization of membrane proteins. Like most gram-negative bacteria, the outer membrane of E.coli is populated with β-barrel proteins, which serve as selective channels where exchange of small molecules take place. Surface exposed domains in these channels provide means to fluorescently label and utilise them for fluorescent microscopy studies to investigate their spatial organization at the outer membrane. Here, we describe a methodology to fluorescently label outer membrane proteins in E.coli and study their spatial organization using direct stochastic optical reconstruction microscopy (dSTORM).

Geographical Psychology

2016 ◽  
Vol 25 (6) ◽  
pp. 393-398 ◽  
Author(s):  
Peter J. Rentfrow ◽  
Markus Jokela
Keyword(s):  
Spatial Organization ◽  
Spatial Clustering ◽  
Health Indicators ◽  
Well Being ◽  
Individual Characteristics ◽  
Psychological Characteristics ◽  
Future Research ◽  
Organization Studies ◽  
Psychological Phenomena ◽  
Multilevel Studies

There is geographical variation in the ways in which people think, feel, and behave. How are we to understand the causes and consequences of such variation? Geographical psychology is an emerging subarea of research concerned with the spatial organization of psychological phenomena and how individual characteristics, social entities, and physical features of the environment contribute to their organization. Studies at multiple levels of analysis have indicated that social influence, ecological influence, and selective migration are key mechanisms that contribute to the spatial clustering of psychological characteristics. Investigations in multiple countries have shown that the psychological characteristics common in particular regions are respectively linked to important political, economic, and health indicators. Furthermore, results from large multilevel studies have shown that the psychological characteristics of individuals interact with features of the local environment to impact psychological development and well-being. Future research is needed to better understand the scale and impact of person-environment associations over time.

scholarly journals Spatial Organization of Transcription in E. Coli using Super-Resolution Fluorescence Microscopy

2017 ◽  
Vol 112 (3) ◽  
pp. 212a
Author(s):  
Xiaoli Weng ◽  
Christopher Bohrer ◽  
Arvin Lagda ◽  
Jie Xiao
Keyword(s):  
Fluorescence Microscopy ◽  
Spatial Organization ◽  
Super Resolution ◽  
E Coli

scholarly journals Human autoantibodies to amphiphysin induce defective presynaptic vesicle dynamics and composition

Brain ◽  
2015 ◽  
Vol 139 (2) ◽  
pp. 365-379 ◽  
Author(s):  
Christian Werner ◽  
Martin Pauli ◽  
Sören Doose ◽  
Andreas Weishaupt ◽  
Holger Haselmann ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Ex Vivo ◽  
Super Resolution ◽  
Synaptic Activity ◽  
Stiff Person Syndrome ◽  
Specific Patient ◽  
Presynaptic Boutons ◽  
Presynaptic Vesicle

Abstract See Irani (doi:10.1093/awv364) for a scientific commentary on this article.  Stiff-person syndrome is the prototype of a central nervous system disorder with autoantibodies targeting presynaptic antigens. Patients with paraneoplastic stiff-person syndrome may harbour autoantibodies to the BAR (Bin/Amphiphysin/Rvs) domain protein amphiphysin, which target its SH3 domain. These patients have neurophysiological signs of compromised central inhibition and respond to symptomatic treatment with medication enhancing GABAergic transmission. High frequency neurotransmission as observed in tonic GABAergic interneurons relies on fast exocytosis of neurotransmitters based on compensatory endocytosis. As amphiphysin is involved in clathrin-mediated endocytosis, patient autoantibodies are supposed to interfere with this function, leading to disinhibition by reduction of GABAergic neurotransmission. We here investigated the effects of human anti-amphiphysin autoantibodies on structural components of presynaptic boutons ex vivo and in vitro using electron microscopy and super-resolution direct stochastic optical reconstruction microscopy. Ultrastructural analysis of spinal cord presynaptic boutons was performed after in vivo intrathecal passive transfer of affinity-purified human anti-amphiphysin autoantibodies in rats and revealed signs of markedly disabled clathrin-mediated endocytosis. This was unmasked at high synaptic activity and characterized by a reduction of the presynaptic vesicle pool, clathrin coated intermediates, and endosome-like structures. Super-resolution microscopy of inhibitory GABAergic presynaptic boutons in primary neurons revealed that specific human anti-amphiphysin immunoglobulin G induced an increase of the essential vesicular protein synaptobrevin 2 and a reduction of synaptobrevin 7. This constellation suggests depletion of resting pool vesicles and trapping of releasable pool vesicular proteins at the plasma membrane. Similar effects were found in amphiphysin-deficient neurons from knockout mice. Application of specific patient antibodies did not show additional effects. Blocking alternative pathways of clathrin-independent endocytosis with brefeldin A reversed the autoantibody induced effects on molecular vesicle composition. Endophilin as an interaction partner of amphiphysin showed reduced clustering within presynaptic terminals. Collectively, these results point towards an autoantibody-induced structural disorganization in GABAergic synapses with profound changes in presynaptic vesicle pools, activation of alternative endocytic pathways, and potentially compensatory rearrangement of proteins involved in clathrin-mediated endocytosis. Our findings provide novel insights into synaptic pathomechanisms in a prototypic antibody-mediated central nervous system disease, which may serve as a proof-of-principle example in this evolving group of autoimmune disorders associated with autoantibodies to synaptic antigens.

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