scholarly journals Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

2020 ◽  
Vol 6 (39) ◽  
pp. eaba8811 ◽  
Author(s):  
Ezequiel Miron ◽  
Roel Oldenkamp ◽  
Jill M. Brown ◽  
David M. S. Pinto ◽  
C. Shan Xu ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Super Resolution ◽  
Functional Modules ◽  
Cell Level ◽  
The Core ◽  
Topologically Associating Domains ◽  
Interchromatin Compartment ◽  
Functional Topography ◽  
Fixed Cell ◽  
Physical Features

Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function; however, many of its physical features at the single-cell level remain underexplored. Here, we use live- and fixed-cell 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify chains of interlinked ~200- to 300-nm-wide chromatin domains (CDs) composed of aggregated nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin compartment. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications toward the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in postreplicative chromatin but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

scholarly journals Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin

2019 ◽  
Author(s):  
Ezequiel Miron ◽  
Roel Oldenkamp ◽  
Jill M. Brown ◽  
David M. S. Pinto ◽  
C. Shan Xu ◽  
...  
Keyword(s):  
Nuclear Organization ◽  
Three Dimensional ◽  
Super Resolution ◽  
Mammalian Genome ◽  
Functional Modules ◽  
Cell Level ◽  
The Core ◽  
Topologically Associating Domains ◽  
Functional Topography ◽  
Physical Features

ABSTRACTThree-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural and functional nuclear organization in somatic cells. We identify linked chromatin domains (CDs) composed of irregular ∼200-300-nm-wide aggregates of nucleosomes that can overlap with individual topologically associating domains and are distinct from a surrounding RNA-populated interchromatin region. High-content mapping uncovers confinement of cohesin and active histone modifications to surfaces and enrichment of repressive modifications towards the core of CDs in both hetero- and euchromatic regions. This nanoscale functional topography is temporarily relaxed in post-replicative chromatin, but remarkably persists after ablation of cohesin. Our findings establish CDs as physical and functional modules of mesoscale genome organization.

scholarly journals Rad21 is the core subunit of the cohesin complex involved in directing genome organization

2021 ◽  
Author(s):  
Yujie Sun ◽  
Yuao Sun ◽  
Xin Xu ◽  
Wenxue Zhao ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Important Determinant ◽  
Genome Structure ◽  
Super Resolution ◽  
Loop Model ◽  
Cohesin Complex ◽  
Aberrant Expression ◽  
The Core ◽  
Topologically Associating Domains ◽  
Resolution Imaging ◽  
Cohesin Subunit

Abstract The ring-shaped cohesin complex is an important factor regulating genome structure. It is thought to mediate the formation of chromatin loops and topologically associating domains (TADs) by loop extrusion. However, the regulation of association between cohesin and chromatin is poorly understood. In this study, we directly visualized cohesin loading after up-regulation of cohesin subunit Rad21 by identifying the formation of vermicelli-like structures via live cell super-resolution imaging. We also reveal that cohesin loading can be promoted by Rad21-loader interactions and accumulated contacts were shown at TAD corners while inter-TAD interactions increased after vermicelli formation, indicating that Rad21 is an important determinant of chromatin structure. Moreover, we find that cohesin saddle on topologically associating domains by FISH assay, which is consistent with the CTCF/cohesin-anchored chromatin loop model. Importantly, expression of Rad21 is strictly controlled, and aberrant expression of Rad21 leads to the formation of Rad21 “beads” in the nucleus. In summary, our observations provided important new biological insights into the mechanism of cohesin loading and its functions.

scholarly journals Three-dimensional super-resolution imaging for fluorescence emission difference microscopy

AIP Advances ◽  
2015 ◽  
Vol 5 (8) ◽  
pp. 084901 ◽  
Author(s):  
Shangting You ◽  
Cuifang Kuang ◽  
Shuai Li ◽  
Xu Liu ◽  
Zhihua Ding
Keyword(s):  
Three Dimensional ◽  
Fluorescence Emission ◽  
Super Resolution ◽  
Resolution Imaging

Super-resolution imaging using a three-dimensional metamaterials nanolens

2010 ◽  
Vol 96 (2) ◽  
pp. 023114 ◽  
Author(s):  
B. D. F. Casse ◽  
W. T. Lu ◽  
Y. J. Huang ◽  
E. Gultepe ◽  
L. Menon ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Super Resolution ◽  
Resolution Imaging

The three-dimensional structure of interleukin-1β

1988 ◽  
Vol 16 (6) ◽  
pp. 949-953 ◽  
Author(s):  
JOHN P. PRIESTLE ◽  
HANS-PETER SCHÄR ◽  
MARKUS G. GRÜTTER
Keyword(s):  
Polypeptide Chain ◽  
Three Dimensional ◽  
Interleukin 1Β ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
R Factor ◽  
The Core ◽  
Internal Sequence ◽  
Network Of Hydrogen Bonds

Summary The three-dimensional structure of human recombinant interleukin-1β has been determined at 0.24 nm resolution by X-ray crystallographic techniques. The partially refined model has a crystallographic R-factor of just under 19%. The structure is composed of 12 β-strands forming a complex network of hydrogen bonds. The core of the structure can best be described as a tetrahedron whose edges are each formed by two antiparallel β-strands. The interior of this structure is filled with hydrophobic side-chains. There is a 3-fold repeat in the folding of the polypeptide chain. Although this folding pattern suggests gene triplication, no significant internal sequence homology between topologically corresponding residues exists. The folding topology of interleukin-1β is very similar to that described by A. D. McLachlan [(1979) J. Mol. Biol. 133, 557–563] for soybean trypsin inhibitor.

SISSI Project: A Feasibility Study for a Super Resolved Compressive Sensing Multispectral Imager in the Medium Infrared

2021 ◽  
Vol 8 (1) ◽  
pp. 28
Author(s):  
Cinzia Lastri ◽  
Gabriele Amato ◽  
Massimo Baldi ◽  
Tiziano Bianchi ◽  
Maria Fabrizia Buongiorno ◽  
...  
Keyword(s):  
Energy Consumption ◽  
Compressive Sensing ◽  
Feasibility Study ◽  
Spatial Resolution ◽  
Spatial Light Modulator ◽  
Super Resolution ◽  
Earth Observation ◽  
Light Modulator ◽  
The Core ◽  
Multispectral Imager

This paper describes the activities related to a feasibility study for an Earth observation optical payload, operating in the medium infrared, based on super-resolution and compressive sensing techniques. The presented activities are running in the framework of the ASI project SISSI, aiming to improve ground spatial resolution and mitigate saturation/blooming effects. The core of the payload is a spatial light modulator (SLM): a bidimensional array of micromirrors electronically actuated. Thanks to compressive sensing approach, the proposed payload eliminates the compression board, saving mass, memory and energy consumption.

A Fast View Synthesis Implementation Method for Light Field Applications

2021 ◽  
Vol 17 (4) ◽  
pp. 1-20
Author(s):  
Wei Gao ◽  
Linjie Zhou ◽  
Lvfang Tao
Keyword(s):  
Neural Networks ◽  
Light Field ◽  
Three Dimensional ◽  
Super Resolution ◽  
View Synthesis ◽  
Compact Representation ◽  
Light Weight ◽  
Computationally Efficient ◽  
Full Resolution ◽  
Time Systems

View synthesis (VS) for light field images is a very time-consuming task due to the great quantity of involved pixels and intensive computations, which may prevent it from the practical three-dimensional real-time systems. In this article, we propose an acceleration approach for deep learning-based light field view synthesis, which can significantly reduce calculations by using compact-resolution (CR) representation and super-resolution (SR) techniques, as well as light-weight neural networks. The proposed architecture has three cascaded neural networks, including a CR network to generate the compact representation for original input views, a VS network to synthesize new views from down-scaled compact views, and a SR network to reconstruct high-quality views with full resolution. All these networks are jointly trained with the integrated losses of CR, VS, and SR networks. Moreover, due to the redundancy of deep neural networks, we use the efficient light-weight strategy to prune filters for simplification and inference acceleration. Experimental results demonstrate that the proposed method can greatly reduce the processing time and become much more computationally efficient with competitive image quality.

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