scholarly journals Stress as a Chromatin Landscape Architect

2021 ◽  
Vol 9 ◽  
Author(s):  
Anastassiia Vertii
Keyword(s):  
Cell Fate ◽  
Genome Organization ◽  
Nuclear Bodies ◽  
Chromosome Territories ◽  
Stress Exposure ◽  
Multiple Factors ◽  
Topologically Associated Domains ◽  
Multiple Levels ◽  
Spatial Genome Organization ◽  
Different Levels

The exponential development of methods investigating different levels of spatial genome organization leads to the appreciation of the chromatin landscape's contribution to gene regulation and cell fate. Multiple levels of 3D chromatin organization include chromatin loops and topologically associated domains, followed by euchromatin and heterochromatin compartments, chromatin domains associated with nuclear bodies, and culminate with the chromosome territories. 3D chromatin architecture is exposed to multiple factors such as cell division and stress, including but not limited to mechanical, inflammatory, and environmental challenges. How exactly the stress exposure shapes the chromatin landscape is a new and intriguing area of research. In this mini-review, the developments that motivate the exploration of this field are discussed.

scholarly journals LncRNA:DNA triplex-forming sites are positioned at specific areas of genome organization and are predictors for Topologically Associated Domains

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Benjamin Soibam ◽  
Ayzhamal Zhamangaraeva
Keyword(s):  
Genome Organization ◽  
Chromatin Organization ◽  
Ctcf Binding ◽  
General Mechanism ◽  
Promoter Regions ◽  
Cellular Processes ◽  
A Genome ◽  
Topologically Associated Domains ◽  
Multiple Cell ◽  
Genomic Regions

Abstract Background Chromosomes are organized into units called topologically associated domains (TADs). TADs dictate regulatory landscapes and other DNA-dependent processes. Even though various factors that contribute to the specification of TADs have been proposed, the mechanism is not fully understood. Understanding the process for specification and maintenance of these units is essential in dissecting cellular processes and disease mechanisms. Results In this study, we report a genome-wide study that considers the idea of long noncoding RNAs (lncRNAs) mediating chromatin organization using lncRNA:DNA triplex-forming sites (TFSs). By analyzing the TFSs of expressed lncRNAs in multiple cell lines, we find that they are enriched in TADs, their boundaries, and loop anchors. However, they are evenly distributed across different regions of a TAD showing no preference for any specific portions within TADs. No relationship is observed between the locations of these TFSs and CTCF binding sites. However, TFSs are located not just in promoter regions but also in intronic, intergenic, and 3’UTR regions. We also show these triplex-forming sites can be used as predictors in machine learning models to discriminate TADs from other genomic regions. Finally, we compile a list of important “TAD-lncRNAs” which are top predictors for TADs identification. Conclusions Our observations advocate the idea that lncRNA:DNA TFSs are positioned at specific areas of the genome organization and are important predictors for TADs. LncRNA:DNA triplex formation most likely is a general mechanism of action exhibited by some lncRNAs, not just for direct gene regulation but also to mediate 3D chromatin organization.

scholarly journals Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

Methods ◽  
2017 ◽  
Vol 123 ◽  
pp. 47-55 ◽  
Author(s):  
Elizabeth H. Finn ◽  
Gianluca Pegoraro ◽  
Sigal Shachar ◽  
Tom Misteli
Keyword(s):  
Comparative Analysis ◽  
Genome Organization ◽  
Distance Measurements ◽  
Spatial Genome Organization ◽  
2D And 3D

scholarly journals Understanding Spatial Genome Organization: Methods and Insights

2016 ◽  
Vol 14 (1) ◽  
pp. 7-20 ◽  
Author(s):  
Vijay Ramani ◽  
Jay Shendure ◽  
Zhijun Duan
Keyword(s):  
Genome Organization ◽  
Spatial Genome Organization

The subcellular localization and activity of Drosophila cubitus interruptus are regulated at multiple levels

Development ◽  
1999 ◽  
Vol 126 (22) ◽  
pp. 5097-5106 ◽  
Author(s):  
Q.T. Wang ◽  
R.A. Holmgren
Keyword(s):  
Subcellular Localization ◽  
Nuclear Localization Signal ◽  
Transcriptional Repression ◽  
Target Genes ◽  
Cubitus Interruptus ◽  
Downstream Target ◽  
Localization Signal ◽  
Hh Signaling ◽  
Multiple Levels ◽  
Different Levels

Cubitus interruptus (Ci), a Drosophila transcription factor, mediates Hedgehog (Hh) signaling during the patterning of embryonic epidermis and larval imaginal discs. In the absence of Hh signal, Ci is cleaved to generate a truncated nuclear form capable of transcriptional repression. Hh signaling stabilizes and activates the full-length Ci protein leading to strong activation of downstream target genes including patched and decapentaplegic. A number of molecules have been implicated in the regulation of Ci. Mutations in these molecules lead to changes in Ci protein level, the extent of Ci proteolysis and the expression of Ci target genes. This paper examines the regulation of Ci subcellular localization and activity. We first characterize a bipartite nuclear localization signal (NLS) within Ci. We propose that the subcellular distribution of Ci is affected by two opposing forces, the action of the NLS and that of at least two regions targeting Ci to the cytoplasm. Further our data show that loss of PKA or Costal-2 activity does not fully mimic Hh signaling, demonstrating that Ci proteolysis and Ci activation are two distinct events which are regulated through different paths. Finally, we propose that there are three levels of apparent Ci activity, corresponding to three zones along the AP axis with different sets of gene expression and different levels of Hh signaling.

Unmasking conflict in vertical coopetition

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Anni Rajala ◽  
Annika Tidström
Keyword(s):  
Design Methodology ◽  
Manufacturing Sector ◽  
Single Case ◽  
Content Type ◽  
Multiple Levels ◽  
A Company ◽  
Practical Implications ◽  
Different Levels ◽  
And Task

Purpose The purpose of this study is to increase understanding about vertical coopetition from the perspective of interrelated conflict episodes on multiple levels. Design/methodology/approach The empirical part is based on a qualitative single case study of a coopetitive buyer-supplier relationship in the manufacturing sector. Findings Conflicts in vertical coopetition evolve from being merely functional and task-related to becoming dysfunctional and relationship-related, as the level of competition increases. The nature of conflict episodes influences the development of vertical coopetition, and therefore, the interrelatedness of conflict episodes is important to acknowledge. Practical implications Although a conflict is considered functional within a company, it may still be dysfunctional as far as the coopetitive relationship with the buyer or seller is concerned. Competition may trigger conflicts related to protecting own technology and knowledge, which may lead to termination of the cooperation, therefore coopetition should be managed in a way that balance sharing and protecting important knowledge to get advantages of coopetition. Originality/value The findings enhance prior research on vertical coopetition by offering new perspectives on causes of conflicts, their management, outcomes and types. The value of taking a multilevel approach lies in the ability to show how conflicts occur and influence other conflicts through the interrelatedness of conflict elements on different levels.

scholarly journals Technologies to study spatial genome organization: beyond 3C

2019 ◽  
Author(s):  
Nadine Übelmesser ◽  
Argyris Papantonis
Keyword(s):  
Genome Organization ◽  
Nuclear Organization ◽  
Three Dimensional ◽  
Nuclear Space ◽  
Chromosome Conformation ◽  
Novel Variants ◽  
Cell Processes ◽  
Systematic Biases ◽  
And Function ◽  
Spatial Genome Organization

Abstract The way that chromatin is organized in three-dimensional nuclear space is now acknowledged as a factor critical for the major cell processes, like transcription, replication and cell division. Researchers have been armed with new molecular and imaging technologies to study this structure-to-function link of genomes, spearheaded by the introduction of the ‘chromosome conformation capture’ technology more than a decade ago. However, this technology is not without shortcomings, and novel variants and orthogonal approaches are being developed to overcome these. As a result, the field of nuclear organization is constantly fueled by methods of increasing resolution and/or throughput that strive to eliminate systematic biases and increase precision. In this review, we attempt to highlight the most recent advances in technology that promise to provide novel insights on how chromosomes fold and function.

scholarly journals An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

2016 ◽  
Vol 26 (12) ◽  
pp. 1697-1709 ◽  
Author(s):  
Przemysław Szałaj ◽  
Zhonghui Tang ◽  
Paul Michalski ◽  
Michal J. Pietal ◽  
Oscar J. Luo ◽  
...  
Keyword(s):  
Genome Organization ◽  
Data Driven ◽  
3 Dimensional ◽  
Spatial Genome Organization

Expertise in applied studio teaching: Teachers working with multiple levels of learners

2020 ◽  
Vol 38 (2) ◽  
pp. 283-298
Author(s):  
Jennifer Blackwell
Keyword(s):  
College Students ◽  
Music Education ◽  
Positive Feedback ◽  
Music Teachers ◽  
Applied Music ◽  
Teacher Modeling ◽  
Video Recordings ◽  
Multiple Levels ◽  
Different Levels ◽  
Formal Recognition

One-to-one lessons are ubiquitous in music education, and thus understanding the components of effective teaching in this environment is essential for student learning. This study explored whether the teaching elements identified in previous studies were evident with applied music teachers working with both college and pre-college students, and if those elements differed as a function of the level of the students. In addition, these teachers were asked to provide commentary on what they deemed important to effective studio teaching. I examined video recordings of 18 lessons given by two applied teachers who had received formal recognition for outstanding teaching. Many of the observations in this study were consistent with previous findings; however, higher rates of low magnitude positive feedback and student errors that did not elicit stops were present. One element regarding physical proximity was added. The findings indicate important differences in the way these teachers approach students at different levels, particularly regarding side coaching during performance, teacher modeling, feedback, and correction of errors. Participants also emphasized the importance of rapport and positive relationships.

scholarly journals Genome organization via loop extrusion, insights from polymer physics models

2019 ◽  
Vol 19 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Surya K Ghosh ◽  
Daniel Jost
Keyword(s):  
Genome Organization ◽  
Extrusion Process ◽  
Polymer Physics ◽  
Modern Biology ◽  
Precise Information ◽  
Multi Scale ◽  
Topologically Associated Domains ◽  
Structural Maintenance Of Chromosome ◽  
Smc Proteins

Abstract Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.

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