scholarly journals Chromatin-lamin B1 interaction promotes genomic compartmentalization and constrains chromatin dynamics

2019 ◽  
Author(s):  
Lei Chang ◽  
Mengfan Li ◽  
Shipeng Shao ◽  
Boxin Xue ◽  
Yingping Hou ◽  
...  
Keyword(s):  
Higher Order ◽  
Order Structure ◽  
Chromatin Dynamics ◽  
Lamin B1 ◽  
Structure And Dynamics ◽  
Chromatin Architecture ◽  
Topologically Associating Domains ◽  
Chromosomal Territory ◽  
Molecular Machinery

AbstractThe eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized chromatin architecture and dynamics remains poorly understood. Here by combining imaging and Hi-C sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to chromatin redistribution and decompaction. Consequently, the inter-chromosomal interactions and overlap between chromosome territories are increased. Moreover, Hi-C data revealed that lamin B1 is required for the integrity and segregation of chromatin compartments but not for the topologically associating domains (TADs). We further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nuclear interior. Taken together, our data suggest that chromatin-lamin B1 interactions promote chromosomal territory segregation and genomic compartmentalization, and confine chromatin dynamics, supporting its crucial role in chromatin higher-order structure and dynamics.

scholarly journals Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells

2020 ◽  
Author(s):  
Lei Chang ◽  
Mengfan Li ◽  
Shipeng Shao ◽  
Chen Li ◽  
Shanshan Ai ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Three Dimensional ◽  
Higher Order ◽  
Order Structure ◽  
Chromatin Dynamics ◽  
Lamin B1 ◽  
Chromatin Architecture ◽  
Chromatin Interactions ◽  
Molecular Machinery

Abstract The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome functions. However, the molecular machinery underlying these hierarchically organized three-dimensional (3D) chromatin architecture and dynamics remains poorly understood. Here by combining imaging and sequencing, we studied the role of lamin B1 in chromatin architecture and dynamics. We found that lamin B1 depletion leads to detachment of lamina-associated domains (LADs) from the nuclear periphery accompanied with global chromatin redistribution and decompaction. Consequently, the inter-chromosomal as well as inter-compartment interactions are increased, but the structure of topologically associating domains (TADs) is not affected. Using live-cell genomic loci tracking, we further proved that depletion of lamin B1 leads to increased chromatin dynamics, owing to chromatin decompaction and redistribution toward nucleoplasm. Taken together, our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance, chromatin compaction, genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics, supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.

The role of Bni5 in the regulation of septin higher-order structure formation

2015 ◽  
Vol 396 (12) ◽  
pp. 1325-1337 ◽  
Author(s):  
Csilla Patasi ◽  
Jana Godočíková ◽  
Soňa Michlíková ◽  
Yan Nie ◽  
Radka Káčeriková ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Structural Changes ◽  
Higher Order ◽  
Cytoskeletal Proteins ◽  
Order Structure ◽  
Division Plane ◽  
Cellular Processes ◽  
Order Structures

Abstract Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins.

scholarly journals Investigating Topological and Functional Features of Multimodular Proteins

2009 ◽  
Vol 2009 ◽  
pp. 1-10 ◽  
Author(s):  
Zelmina Lubovac
Keyword(s):  
Higher Order ◽  
Protein Interaction Networks ◽  
Interaction Networks ◽  
Order Structure ◽  
Functional Modules ◽  
Functional Aspect ◽  
Generate Functional ◽  
Functional Features ◽  
Cell Functionality

To generate functional modules as functionally and structurally cohesive formations in protein interaction networks (PINs) constitutes an important step towards understanding how modules communicate on a higher level of the PIN organisation that underlies cell functionality. However, we need to understand how individual modules communicate and are organized into the higher-order structure(s) of the PIN organization that underlies cell functionality. In an attempt to contribute to this understanding, we make an assumption that the proteins reappearing in several modules, termed here as multimodular proteins (MMPs), may be useful in building higher-order structure(s) as they may constitute communication points between different modules. In this paper, we investigate common properties shared by these proteins and compare them with the properties of so-called single-modular proteins (SMPs) by analyzing three aspects: functional aspect, that is, annotation of the proteins, topological aspect that is betweenness centrality of the proteins, and lethality. Furthermore, we investigate the interconnectivity role of some proteins that are identified as functionally and topologically important.

scholarly journals Chromatin Higher-order Structure and Dynamics

2010 ◽  
Vol 2 (5) ◽  
pp. a000596-a000596 ◽  
Author(s):  
C. L. Woodcock ◽  
R. P. Ghosh
Keyword(s):  
Higher Order ◽  
Order Structure ◽  
Structure And Dynamics

Chromatin structure of eukaryotic promoters: a changing perspective

2002 ◽  
Vol 80 (3) ◽  
pp. 295-300 ◽  
Author(s):  
Philippe T Georgel
Keyword(s):  
Transcriptional Activation ◽  
Structural Changes ◽  
Current Knowledge ◽  
Higher Order ◽  
Current View ◽  
Order Structure ◽  
Chromatin Dynamics ◽  
Technical Developments ◽  
Agarose Electrophoresis

Over the past few years, many studies have attempted to determine the role of nucleosomes as both positive and negative transcription regulators. The emphasis has mostly centered on chromatin remodeling activities and histone modifications, leaving the question of the influence of the higher-order structure out of the spotlight. Recent technical developments allowing direct measurements of size and mechanical properties of in vivo assembled chromatin may shed light on this poorly understood area. This article presents a brief summary of the current knowledge on transcription-dependent chromatin dynamics and how a rather simple agarose electrophoresis method may change the current view on structural changes linked to transcriptional activation of chromatin.Key words: chromatin, higher-order structure, quantitative agarose gel electrophoresis.

Sign in / Sign up

Export Citation Format

Share Document