scholarly journals A First-principles Approach to Large-scale Nuclear Architecture

2018 ◽  
Author(s):  
Ankit Agrawal ◽  
Nirmalendu Ganai ◽  
Surajit Sengupta ◽  
Gautam I. Menon
Keyword(s):  
First Principles ◽  
Large Scale ◽  
Transcriptional Activity ◽  
Nuclear Architecture ◽  
Cell Type ◽  
Cell Nuclei ◽  
Differential Positioning ◽  
Cell Type Specific ◽  
Active Processes ◽  
Stochastic Forces

AbstractModel approaches to nuclear architecture have traditionally ignored the biophysical consequences of ATP-fueled active processes acting on chromatin. However, transcription-coupled activity is a source of stochastic forces that are substantially larger than the Brownian forces present at physiological temperatures. Here, we describe a first-principles approach to large-scale nuclear architecture in metazoans that incorporates cell-type-specific active processes. The model predicts the statistics of positional distributions, shapes and overlaps of each chromosome. Our simulations reproduce common organising principles underlying large-scale nuclear architecture across human cell nuclei in interphase. These include the differential positioning of euchromatin and heterochromatin, the territorial organisation of chromosomes including both gene-density-based and size-based chromosome radial positioning schemes, the non-random locations of chromosome territories and the shape statistics of individual chromosomes. We propose that the biophysical consequences of the distribution of transcriptional activity across chromosomes should be central to any chromosome positioning code.

Chromatin as an active polymeric material

2020 ◽  
Vol 4 (2) ◽  
pp. 111-118
Author(s):  
Gautam I. Menon
Keyword(s):  
Large Scale ◽  
Transcriptional Activity ◽  
Spatial Organization ◽  
Nuclear Architecture ◽  
Chromosome Territories ◽  
X Chromosomes ◽  
Equilibrium Processes ◽  
Territorial Organization ◽  
Differential Positioning ◽  
Radial Separation

The patterns of the large-scale spatial organization of chromatin in interphase human somatic cells are not random. Such patterns include the radial separation of euchromatin and heterochromatin, the territorial organization of individual chromosomes, the non-random locations of chromosome territories and the differential positioning of the two X chromosomes in female cells. These features of large-scale nuclear architecture follow naturally from the hypothesis that ATP-consuming non-equilibrium processes associated with highly transcribed regions of chromosomes are a source of ‘active’ forces. These forces are in excess of those that arise from Brownian motion. Simulations of model chromosomes that incorporate such activity recapitulate these features. In addition, they reproduce many other aspects of the spatial organization of chromatin at large scales that are known from experiments. Our results, reviewed here, suggest that the distribution of transcriptional activity across chromosomes underlies many aspects of large-scale nuclear architecture that were hitherto believed to be unrelated.

scholarly journals Quantitative synapse analysis for cell-type specific connectomics

2018 ◽  
Author(s):  
Dika A. Kuljis ◽  
Khaled Zemoura ◽  
Cheryl A. Telmer ◽  
Jiseok Lee ◽  
Eunsol Park ◽  
...  
Keyword(s):  
Large Scale ◽  
Neural Circuit ◽  
Apical Dendrite ◽  
Automated Detection ◽  
Cell Type ◽  
Disease States ◽  
Specific Localization ◽  
Cell Type Specific ◽  
Dendritic Branches ◽  
Circuit Function

AbstractAnatomical methods for determining cell-type specific connectivity are essential to inspire and constrain our understanding of neural circuit function. We developed new genetically-encoded reagents for fluorescence-synapse labeling and connectivity analysis in brain tissue, using a fluorogen-activating protein (FAP)-or YFP-coupled, postsynaptically-localized neuroligin-1 targeting sequence (FAP/YFPpost). Sparse viral expression of FAP/YFPpost with the cell-filling, red fluorophore dTomato (dTom) enabled high-throughput, compartment-specific localization of synapses across diverse neuron types in mouse somatosensory cortex. High-resolution confocal image stacks of virally-transduced neurons were used for 3D reconstructions of postsynaptic cells and automated detection of synaptic puncta. We took advantage of the bright, far-red emission of FAPpost puncta for multichannel fluorescence alignment of dendrites, synapses, and presynaptic neurites to assess subtype-specific inhibitory connectivity onto L2 neocortical pyramidal (Pyr) neurons. Quantitative and compartment-specific comparisons show that PV inputs are the dominant source of inhibition at both the soma and across all dendritic branches examined and were particularly concentrated at the primary apical dendrite, a previously unrecognized compartment of L2 Pyr neurons. Our fluorescence-based synapse labeling reagents will facilitate large-scale and cell-type specific quantitation of changes in synaptic connectivity across development, learning, and disease states.

Canine H(+)-K(+)-ATPase alpha-subunit gene promoter: studies with canine parietal cells in primary culture

1996 ◽  
Vol 271 (6) ◽  
pp. G1104-G1113 ◽  
Author(s):  
A. Muraoka ◽  
M. Kaise ◽  
Y. J. Guo ◽  
J. Yamada ◽  
I. Song ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Primary Culture ◽  
Transcriptional Activity ◽  
Parietal Cells ◽  
Luciferase Reporter ◽  
Cell Type ◽  
High Concentration ◽  
Specific Expression ◽  
Atpase Gene ◽  
Cell Type Specific

H(+)-K(+)-adenosinetriphosphatase (H(+)-K(+)-ATPase) is the principal enzyme responsible for the process of gastric acid secretion. This enzyme is expressed in a cell-type-specific manner in gastric parietal cells. To explore the mechanisms regulating its expression, we transfected differentiated canine parietal cells in primary culture with H(+)-K(+)-ATPase-luciferase reporter genes and assessed transcriptional activities. Deletional analysis of the 5'-flanking region of this gene demonstrated a remarkable increment in transcriptional activity associated with a segment between bases -54 to -45 (5' GCTCCGCCTC 3') relative to the transcriptional initiation site. Gel shift assays with competition and supershift analysis demonstrated that this segment is specifically bound by the transcription factor Sp1. A point mutation, eliminating Sp1 binding, diminished basal transcriptional activity by 80%, indicating that this Sp1 binding site is important for constitutive transcriptional activity. Although these studies indicate that Sp1 is required to maintain a high concentration of the H(+)-K(+)-ATPase gene in the parietal cell, its cell-type-specific expression must rely on other elements because Sp1 is a ubiquitously expressed transcription factor.

scholarly journals ASCOT identifies key regulators of neuronal subtype-specific splicing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan P. Ling ◽  
Christopher Wilks ◽  
Rone Charles ◽  
Patrick J. Leavey ◽  
Devlina Ghosh ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Large Scale ◽  
Splice Variants ◽  
Next Generation Sequencing Data ◽  
Data Sets ◽  
Cell Type ◽  
Sequencing Data ◽  
Large Scale Analysis ◽  
Cell Type Specific ◽  
Public Archives

AbstractPublic archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.

scholarly journals State-dependent control of cortical processing speed via gain modulation

2020 ◽  
Author(s):  
David Wyrick ◽  
Luca Mazzucato
Keyword(s):  
Information Processing ◽  
Processing Speed ◽  
Visual Processing ◽  
Large Scale ◽  
Internal State ◽  
Gain Modulation ◽  
Cell Type ◽  
Information Processing Speed ◽  
Afferent Projections ◽  
Cell Type Specific

AbstractTo thrive in dynamic environments, animals can generate flexible behavior and rapidly adapt responses to a changing context and internal state. Examples of behavioral flexibility include faster stimulus responses when attentive and slower responses when distracted. Contextual modulations may occur early in the cortical hierarchy and may be implemented via afferent projections from top-down pathways or neuromodulation onto sensory cortex. However, the computational mechanisms mediating the effects of such projections are not known. Here, we investigate the effects of afferent projections on the information processing speed of cortical circuits. Using a biologically plausible model based on recurrent networks of excitatory and inhibitory neurons arranged in cluster, we classify the effects of cell-type specific perturbations on the circuit’s stimulus-processing capability. We found that perturbations differentially controlled processing speed, leading to counter-intuitive effects such as improved performance with increased input variance. Our theory explains the effects of all perturbations in terms of gain modulation, which controls the timescale of the circuit dynamics. We tested our model using large-scale electrophysiological recordings from the visual hierarchy in freely running mice, where a decrease in single-cell gain during locomotion explained the observed acceleration of visual processing speed. Our results establish a novel theory of cell-type specific perturbations linking connectivity, dynamics, and information processing via gain modulations.

scholarly journals Selective isolation of mouse glial nuclei optimized for reliable downstream omics analyses

2021 ◽  
Author(s):  
Miguel Angel Pena-Ortiz ◽  
Sarfraz Shafiq ◽  
Megan E Rowland ◽  
Nathalie G Berube
Keyword(s):  
Sample Preparation ◽  
Glial Cell ◽  
Mouse Brain ◽  
Cellular Damage ◽  
Rna Seq ◽  
Cell Type ◽  
Cell Nuclei ◽  
Dapi Staining ◽  
High Quality ◽  
Cell Type Specific

Background: Isolation of cell types of interest from the brain for molecular applications presents several challenges, including cellular damage during tissue dissociation or enrichment procedures, and low cell number in the tissue in some cases. Techniques have been developed to enrich distinct cell populations using immunopanning or fluorescence activated cell/nuclei sorting. However, these techniques often involve fixation, immunolabeling and DNA staining steps, which could potentially influence downstream omics applications. New Method: Taking advantage of readily available genetically modified mice with fluorescent-tagged nuclei, we describe a technique for the purification of cell-type specific brain nuclei, optimized to decrease sample preparation time and to limit potential artefacts for downstream omics applications. We demonstrate the applicability of this approach for the purification of glial cell nuclei and show that the resulting cell-type specific nuclei obtained can be used effectively for omics applications, including ATAC-seq and RNA-seq. Results: We demonstrate excellent enrichment of fluorescently-tagged glial nuclei, yielding high quality RNA and chromatin. We identify several critical steps during nuclei isolation that help limit nuclei rupture and clumping, including quick homogenization, dilution before filtration and loosening of the pellet before resuspension, thus improving yield. Sorting of fluorescent nuclei can be achieved without fixation, antibody labelling, or DAPI staining, reducing potential artifactual results in RNA-seq and ATAC-seq analyses. We show that reproducible glial cell type-specific profiles can be obtained in transcriptomic and chromatin accessibility assays using this rapid protocol. Comparison with existing methods: Our method allows for rapid enrichment of glial nuclei populations from the mouse brain with minimal processing steps, while still providing high quality RNA and chromatin required for reliable omics analyses. Conclusions : We provide a reproducible method to obtain nucleic material from glial cells in the mouse brain with a quick and limited sample preparation.

scholarly journals MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Pavlo Lutsik ◽  
Martin Slawski ◽  
Gilles Gasparoni ◽  
Nikita Vedeneev ◽  
Matthias Hein ◽  
...  
Keyword(s):  
Matrix Factorization ◽  
Exploratory Study ◽  
Large Scale ◽  
Cell Type ◽  
Computational Framework ◽  
Biological Interpretation ◽  
Cell Type Specific ◽  
Latent Components ◽  
Methylation Variation ◽  
Non Negative Matrix Factorization

Abstract It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions. MeDeCom is a new unsupervised tool for the exploratory study of the major sources of methylation variation, which should lead to a deeper understanding and better biological interpretation.

scholarly journals Differential repair of DNA damage in the human metallothionein gene family.

1988 ◽  
Vol 8 (12) ◽  
pp. 5331-5338 ◽  
Author(s):  
S A Leadon ◽  
M M Snowden
Keyword(s):  
Dna Damage ◽  
Gene Family ◽  
Transcriptional Activity ◽  
Initial Rate ◽  
Uv Damage ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Processed Pseudogene ◽  
Cell Type Specific

We studied the repair of UV- and aflatoxin B1 (AFB1)-induced damage in the human metallothionein (hMT) gene family. After exposure to either UV or AFB1, DNA damage was initially repaired faster in the DNA fragments containing the transcribed hMT-IA, hMT-IE, and hMT-IIA genes than in the genome overall. By 6 h posttreatment, there was at least twice as much repair in these genes as in the rest of the genome. Repair of UV damage in the hMT-IB gene, which shows cell-type specific expression, and in the hMT-IIB gene, which is a nontranscribed processed pseudogene, was about the same as in the rest of the genome, whereas repair of AFB1-induced damage was deficient in these two genes. Inducing transcription of the three expressed hMT genes with CdCl2 or of only the hMT-IIA gene with dexamethasone increased the initial rate of repair in the induced genes another twofold over the rate observed when they were transcribed at a basal level. The rates of repair in the hMT-IB and hMT-IIB genes were not altered by these inducing treatments. Transcription of the hMT genes was transiently inhibited after UV irradiation. Inducing transcription of the genes did not shorten this UV-induced delay. Thus, the efficiency of repair of damage in a DNA sequence is dependent on the level of transcriptional activity associated with that sequence. However, an increased efficiency in repair of a gene itself is not necessarily coupled to recovery of its transcription after DNA damage.

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