scholarly journals Three-dimensional nuclear organization in Arabidopsis thaliana

2020 ◽  
Vol 133 (4) ◽  
pp. 479-488 ◽  
Author(s):  
Frédéric Pontvianne ◽  
Stefan Grob
Keyword(s):  
Arabidopsis Thaliana ◽  
Nuclear Organization ◽  
Three Dimensional

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 Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽  
2020 ◽  
Vol 214 (3) ◽  
pp. 651-667 ◽  
Author(s):  
Marco Di Stefano ◽  
Francesca Di Giovanni ◽  
Vasilisa Pozharskaia ◽  
Mercè Gomar-Alba ◽  
Davide Baù ◽  
...  
Keyword(s):  
Gene Expression ◽  
Budding Yeast ◽  
Nuclear Organization ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
3D Genome ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

scholarly journals The role of CTCF in regulating nuclear organization

2008 ◽  
Vol 205 (4) ◽  
pp. 747-750 ◽  
Author(s):  
Adam Williams ◽  
Richard A. Flavell
Keyword(s):  
Long Range ◽  
Dna Sequences ◽  
Spatial Organization ◽  
Zinc Finger Protein ◽  
Nuclear Organization ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Binding Factor ◽  
Long Range Interactions ◽  
Regulatory Functions

The spatial organization of the genome is thought to play an important part in the coordination of gene regulation. New techniques have been used to identify specific long-range interactions between distal DNA sequences, revealing an ever-increasing complexity to nuclear organization. CCCTC-binding factor (CTCF) is a versatile zinc finger protein with diverse regulatory functions. New data now help define how CTCF mediates both long-range intrachromosomal and interchromosomal interactions, and highlight CTCF as an important factor in determining the three-dimensional structure of the genome.

scholarly journals An in-silico study of Polymerase Epsilon catalytic subunit proteins in Arabidopsis thaliana

2020 ◽  
Vol 1 (1) ◽  
pp. 21-36
Author(s):  
Adoum Mahamat Baraka ◽  
Kanita Šabanović ◽  
Mohamed Ragab Abdel Gawwad
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Repair ◽  
Three Dimensional ◽  
Catalytic Subunit ◽  
Dimensional Structure ◽  
Dna Repair Mechanisms ◽  
In Silico Study ◽  
Repair Mechanisms ◽  
Polymerase Epsilon ◽  
Subunit B

Arabidopsis thaliana genome encodes two POLE2 homologs known as polymerase epsilon catalytic subunit A (POLE2A) and polymerase epsilon catalytic subunit B (POLE2B). They play a very important role in DNA repair mechanisms. In this study, bioinformatics tools were used to understand DNA repair mechanisms in A. thaliana in which POLE2A and POLE2B proteins are involved. Through interactome analysis of POLE2A and POLE2B homolog proteins in A. thaliana, their additional roles in DNA repair were explored. The most important proteins that are participating in DNA repairs,  like MSH2, MSH5, PCNA1, PCNA2, PRL, and CDC45 were identified as interactors of both POLE2A and POLE2B. The three-dimensional structure of POLE2 proteins was identified to decipher the complexity of NER, GG-NER, MMR, TFIIH, and TC-NER repair mechanisms through the identification of docking sites. The interaction complex of POLE2A and POLE2B with six proteins was confirmed and found to have a significant role in DNA repair processes and UV-B tolerance. The interactome analysis of POLE2A and POLE2B performed here once again confirms the complexity of the DNA repair mechanism in plants.

scholarly journals A CLEM approach to access to the ultrastructure at the graft interface in Arabidopsis thaliana

2021 ◽  
Author(s):  
Clément Chambaud ◽  
Sarah Jane Cookson ◽  
Nathalie Ollat ◽  
Emmanuelle M. F. Bayer ◽  
Lysiane Brocard
Keyword(s):  
Electron Microscopy ◽  
Arabidopsis Thaliana ◽  
Endoplasmic Reticulum ◽  
Cell Wall ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Cellular Events ◽  
Membrane Tethering ◽  
Secondary Plasmodesmata ◽  
Graft Interface

Despite recent progress in our understanding of the graft union formation, we still know little about the cellular events underlying the grafting process. This is partially due to the difficulty of reliably targeting the graft interface in electron microscopy to study its ultrastructure and three-dimensional architecture. To overcome this technological bottleneck, we developed a correlative light electron microscopy approach (CLEM) to study the graft interface with high ultrastructural resolution. Grafting hypocotyls of Arabidopsis thaliana lines expressing YFP or mRFP in the endoplasmic reticulum allowed the efficient targeting of the grafting interface for under light and electron microscopy. To explore the potential of our method to study sub-cellular events at the graft interface, we focused on the formation of secondary plasmodesmata (PD) between the grafted partners. We showed that 4 classes of PD were formed at the interface and that PD introgression into the call wall was initiated equally by both partners. Moreover, the success of PD formation appeared not systematic with a third of PD not spanning the cell wall entirely. Characterizing the ultrastructural characteristics of these failed PD gives us insights into the process of secondary PD biogenesis. We showed that the thinning of the cell wall and the endoplasmic reticulum-plasma membrane tethering seem to be required for the establishment of symplastic connections between the scion and the rootstock. The resolution reached in this work shows that our CLEM method offer a new scale to the study for biological processes requiring the combination of light and electron microscopy.

An algorithm for estimation of chromosome motion in Four-Dimensional microscopic images

1994 ◽  
Vol 52 ◽  
pp. 930-931
Author(s):  
Wallace Marshall ◽  
David Agard ◽  
John Sedat
Keyword(s):  
Nuclear Organization ◽  
Three Dimensional ◽  
Estimation Algorithm ◽  
Structural Features ◽  
Random Motion ◽  
Structural Representation ◽  
Functional Roles ◽  
The Face ◽  
Chromosome Motion

Analysis of the three-dimensional organization of chromosomes within the nucleus has revealed a number of characteristic structural features. Yet imaging of living nuclei indicate that chromosomes undergo considerable random motion. Maintenance of nuclear organization in the face of such motion is thought to involve the attachment of chromosomes to the nuclear envelope or matrix. Yet while such attachments have been proposed to play a variety of functional roles as well as maintain nuclear organization, direct evidence for the existence of these mechanical interactions in vivo has been lacking. One way to demonstrate such attachment directly would be to estimate the motion of chromosomes and attempt thereby to demonstrate the presence of fixed points, which would indicate attachment of chromatin to some fixed superstructure.We have previously presented a motion estimation algorithm that is designed for tracking the motion of nonrigid and featureless objects such as chromosomes. This algorithm starts with a structural representation for the set of chromosomes at each time point, and then finds a correspondence between elements of the representations at successive time points.

3D Telomeric Profiles of MGUS, MMN and Relapsed MM

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2899-2899
Author(s):  
Ade B Olujohungbe ◽  
Ludger R Klewes ◽  
Morel Rubinger ◽  
Sabine Mai
Keyword(s):  
Bone Marrow ◽  
Cancer Progression ◽  
Plasma Cells ◽  
Conflicts Of Interest ◽  
Nuclear Organization ◽  
Three Dimensional ◽  
Individual Risk ◽  
Cell Cycle Distribution ◽  
Patient Groups ◽  
The Individual

Abstract Abstract 2899 Multiple myeloma (MM) is recognized as the second most common cancer of the blood. It is a malignant disorder of plasma cells and commonly affects adults past the age of 50. Although risk factors have been established, it is currently not possible to assess the individual risk to cancer progression. Moreover, the causes of disease progression from its precursor condition, monoclonal gammopathy of undetermined significance (MGUS), to full-blown MM and its progression to relapsed MM remain elusive. We have performed previous studies on the three-dimensional (3D) nuclear organization of telomeres and found that normal and tumor cells display significant differences in their nuclear organization. These differences were objectively quantified with two software programs, TeloView and TeloScan developed by our group. We now report on a new double blinded preliminary study with 36 patients, including 20 MM, 12 MGUS and 4 relapsed MM. Using blood- and bone marrow-derived plasma cells from the respective patient groups, we have examined 3D nuclear telomeric profiles of the above patients. Plasma cells from MM, MGUS and relapsed MM exhibit specific 3D telomeric signatures. MM have the highest telomere numbers, followed by MGUS, while relapsed MM presents with the lowest numbers of telomeres and the shortest telomeres. Additional telomere parameters, such as cell cycle distribution profiles (a/c ratio), telomere aggregate numbers, distances from nuclear centre and also exhibited significance (p< 0.001). Within the MGUS and MM patient groups we studied are patients whose 3D telomeric profiles indicate the beginning of a new signature that resembles signatures of MM and relapsed MM respectively. Blood and bone marrow gave us comparable results opening the future opportunity to base diagnostics and monitoring on blood samples, sparing the patient form invasive bone marrow sampling with potentially adverse effects. Based on our current preliminary data, we propose the following 3D telomeric criteria that define individual signatures of MGUS and MM and progression within each of the groups: telomere numbers, telomere sizes, presence of telomeric aggregates, telomeres per nuclear volume, and a/c ratios. The clinical significance of these findings is the early identification of individuals with high risk of progression. This opens the possibility for better monitoring and early intervention with newer treatments with an acceptable efficacy and low toxicity ratio. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Mitochondrial Arabidopsis thaliana TRXo Isoforms Bind an Iron–Sulfur Cluster and Reduce NFU Proteins In Vitro

Antioxidants ◽  
2018 ◽  
Vol 7 (10) ◽  
pp. 142 ◽  
Author(s):  
Flavien Zannini ◽  
Thomas Roret ◽  
Jonathan Przybyla-Toscano ◽  
Tiphaine Dhalleine ◽  
Nicolas Rouhier ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Function Analysis ◽  
Active Form ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Regulation Mechanism ◽  
Iron Sulfur Cluster ◽  
Iron Sulfur

In plants, the mitochondrial thioredoxin (TRX) system generally comprises only one or two isoforms belonging to the TRX h or o classes, being less well developed compared to the numerous isoforms found in chloroplasts. Unlike most other plant species, Arabidopsis thaliana possesses two TRXo isoforms whose physiological functions remain unclear. Here, we performed a structure–function analysis to unravel the respective properties of the duplicated TRXo1 and TRXo2 isoforms. Surprisingly, when expressed in Escherichia coli, both recombinant proteins existed in an apo-monomeric form and in a homodimeric iron–sulfur (Fe-S) cluster-bridged form. In TRXo2, the [4Fe-4S] cluster is likely ligated in by the usual catalytic cysteines present in the conserved Trp-Cys-Gly-Pro-Cys signature. Solving the three-dimensional structure of both TRXo apo-forms pointed to marked differences in the surface charge distribution, notably in some area usually participating to protein–protein interactions with partners. However, we could not detect a difference in their capacity to reduce nitrogen-fixation-subunit-U (NFU)-like proteins, NFU4 or NFU5, two proteins participating in the maturation of certain mitochondrial Fe-S proteins and previously isolated as putative TRXo1 partners. Altogether, these results suggest that a novel regulation mechanism may prevail for mitochondrial TRXs o, possibly existing as a redox-inactive Fe-S cluster-bound form that could be rapidly converted in a redox-active form upon cluster degradation in specific physiological conditions.

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