Three-dimensional chromosome organization in flowering plants

2020 ◽  
Vol 19 (2) ◽  
pp. 83-91 ◽  
Author(s):  
Stefan Grob
Keyword(s):  
Plant Species ◽  
De Novo ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Chromosome Organization ◽  
Data Sets ◽  
Comprehensive Overview ◽  
De Novo Genome Assembly ◽  
3D Genome ◽  
Wide Range

Abstract Research on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes reported to be vital for chromosome folding in animals. However, similar 3D structures such as topologically associating domains and chromatin loops were identified. Recent studies in Arabidopsis thaliana revealed how chromosomal regions are positioned within the nucleus by determining their association with both, the nuclear periphery and the nucleolus. Additionally, many plant species exhibit high-frequency interactions among KNOT entangled elements, which are associated with safeguarding the genome from invasive DNA elements. Many of the recently published Hi-C data sets were generated to aid de novo genome assembly and remain to date little explored. These data sets represent a valuable resource for future comparative studies, which may lead to a more profound understanding of the evolution of 3D chromosome organization in plants.

scholarly journals CAMISIM: Simulating metagenomes and microbial communities

2018 ◽  
Author(s):  
Adrian Fritz ◽  
Peter Hofmann ◽  
Stephan Majda ◽  
Eik Dahms ◽  
Johannes Dröge ◽  
...  
Keyword(s):  
Microbial Communities ◽  
De Novo ◽  
Real Data ◽  
Small Data ◽  
Data Sets ◽  
Sequencing Data ◽  
Taxonomic Profiling ◽  
Benchmark Data ◽  
Sequencing Technologies ◽  
Wide Range

Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Here, we describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series and differential abundance studies, includes real and simulated strain-level diversity, and generates second and third generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT and metaSPAdes, on several thousand small data sets generated with CAMISIM. CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with truth standards for method evaluation. All data sets and the software are freely available at: https://github.com/CAMI-challenge/CAMISIM

scholarly journals 3D genome organization during lymphocyte development and activation

2019 ◽  
Vol 19 (2) ◽  
pp. 71-82 ◽  
Author(s):  
Anne van Schoonhoven ◽  
Danny Huylebroeck ◽  
Rudi W Hendriks ◽  
Ralph Stadhouders
Keyword(s):  
Genome Organization ◽  
Transcriptional Control ◽  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Three Dimensional ◽  
Lymphocyte Development ◽  
Control Of Gene Expression ◽  
3D Genome ◽  
Wide Range ◽  
3D Architecture

Abstract Chromosomes have a complex three-dimensional (3D) architecture comprising A/B compartments, topologically associating domains and promoter–enhancer interactions. At all these levels, the 3D genome has functional consequences for gene transcription and therefore for cellular identity. The development and activation of lymphocytes involves strict control of gene expression by transcription factors (TFs) operating in a three-dimensionally organized chromatin landscape. As lymphocytes are indispensable for tissue homeostasis and pathogen defense, and aberrant lymphocyte activity is involved in a wide range of human morbidities, acquiring an in-depth understanding of the molecular mechanisms that control lymphocyte identity is highly relevant. Here we review current knowledge of the interplay between 3D genome organization and transcriptional control during B and T lymphocyte development and antigen-dependent activation, placing special emphasis on the role of TFs.

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 microstructure investigation of plant architecture with X-ray microscopy

2019 ◽  
Author(s):  
Wenting Zhang ◽  
Tao Guo ◽  
Ke Chen ◽  
Ting La ◽  
Philipp Alexander Bastians ◽  
...  
Keyword(s):  
Plant Species ◽  
3D Imaging ◽  
Three Dimensional ◽  
Plant Morphology ◽  
Plant Tissues ◽  
X Ray ◽  
Wide Range ◽  
Observation Method ◽  
Microscopy Techniques ◽  
Non Destructive

ABSTRACTBackgroundIn recent years, the plant morphology has been well studied by multiple approaches at cellular and subcellular levels. Two-dimensional (2D) microscopy techniques offer imaging of plant structures on a wide range of magnifications for researchers. However, subcellular imaging is still challenging in plant tissues like roots and seeds.ResultsHere we use a three-dimensional (3D) imaging technology based on the ZEISS X-ray microscope (XRM) Versa and analyze several plant tissues from different plant species. The XRM provides new insights into plant structures using non-destructive imaging at high-resolution and high contrast. We also developed a workflow aiming to acquire accurate and high-quality images in the context of the whole specimen. Multiple plant samples including rice, tobacco, Arabidopsis and maize were used to display the differences of phenotypes, which indicates that the XRM is a powerful tool to investigate plant microstructure.ConclusionsOur work provides a novel observation method to evaluate and quantify tissue specific differences for a range of plant species. This new tool is suitable for non-destructive seed observation and screening.

scholarly journals Telomeres Cluster De Novo before the Initiation of Synapsis: A Three-dimensional Spatial Analysis of Telomere Positions before and during Meiotic Prophase

1997 ◽  
Vol 137 (1) ◽  
pp. 5-18 ◽  
Author(s):  
Hank W. Bass ◽  
Wallace F. Marshall ◽  
John W. Sedat ◽  
David A. Agard ◽  
W. Zacheus Cande
Keyword(s):  
Zea Mays L ◽  
Chromosome Structure ◽  
De Novo ◽  
Control Point ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Early Event ◽  
Quantitative Measurements ◽  
Telomere Cluster

We have analyzed the progressive changes in the spatial distribution of telomeres during meiosis using three-dimensional, high resolution fluorescence microscopy. Fixed meiotic cells of maize (Zea mays L.) were subjected to in situ hybridization under conditions that preserved chromosome structure, allowing identification of stage-dependent changes in telomere arrangements. We found that nuclei at the last somatic prophase before meiosis exhibit a nonrandom, polarized chromosome organization resulting in a loose grouping of telomeres. Quantitative measurements on the spatial arrangements of telomeres revealed that, as cells passed through premeiotic interphase and into leptotene, there was an increase in the frequency of large telomere-to-telomere distances and a decrease in the bias toward peripheral localization of telomeres. By leptotene, there was no obvious evidence of telomere grouping, and the large, singular nucleolus was internally located, nearly concentric with the nucleus. At the end of leptotene, telomeres clustered de novo at the nuclear periphery, coincident with a displacement of the nucleolus to one side. The telomere cluster persisted throughout zygotene and into early pachytene. The nucleolus was adjacent to the cluster at zygotene. At the pachytene stage, telomeres rearranged again by dispersing throughout the nuclear periphery. The stagedependent changes in telomere arrangements are suggestive of specific, active telomere-associated motility processes with meiotic functions. Thus, the formation of the cluster itself is an early event in the nuclear reorganizations associated with meiosis and may reflect a control point in the initiation of synapsis or crossing over.

scholarly journals Modern Applications of 3D Printing: The Case of an Artificial Ear Splint Model

2021 ◽  
Vol 4 (3) ◽  
pp. 54
Author(s):  
Athanasios Argyropoulos ◽  
Pantelis N. Botsaris
Keyword(s):  
3D Printing ◽  
Three Dimensional ◽  
Shape Preservation ◽  
Patient Specific ◽  
Fused Deposition Modelling ◽  
Comprehensive Overview ◽  
Protruding Ears ◽  
Fused Deposition ◽  
Custom Made ◽  
Wide Range

Three-dimensional (3D) printing is a leading manufacturing technique in the medical field. The constantly improving quality of 3D printers has revolutionized the approach to new challenges in medicine for a wide range of applications including otoplasty, medical devices, and tissue engineering. The aim of this study is to provide a comprehensive overview of an artificial ear splint model applied to the human auricle for the treatment of stick-out protruding ears. The deformity of stick-out protruding ears remains a significant challenge, where the complex and distinctive shape preservation are key factors. To address this challenge, we have developed a protocol that involves photogrammetry techniques, reverse engineering technologies, a smart prototype design, and 3D printing processes. Specifically, we fabricated a 3D printed ear splint model via fused deposition modelling (FDM) technology by testing two materials, a thermoplastic polyester elastomer material (Z-Flex) and polycaprolactone (PCL 100). Our strategy affords a custom-made and patient-specific artificial ear aligner with mechanical properties that ensures sufficient preservation of the auricular shape by applying a force on the helix and antihelix and enables the ears to pin back to the head.

scholarly journals Benchmarking topological accuracy of bacterial phylogenomic workflows using in silico evolution

2021 ◽  
Author(s):  
Boas CL van der Putten ◽  
Niek AH Huijsmans ◽  
Daniel R Mende ◽  
Constance Schultsz
Keyword(s):  
De Novo ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Phylogenetic Reconstruction ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
Relevant Alternatives ◽  
Wide Range ◽  
Similar Accuracy

Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95% average nucleotide identity). We replicated each simulation three times to assess replicability. In total, we benchmarked seventeen distinct phylogenetic workflows using 8 different simulated datasets. We found that recently developed k-mer alignment methods such as kSNP and SKA achieve similar accuracy as reference mapping. The high accuracy of k-mer alignment methods can be explained by the large fractions of genomes these methods can align, relative to other approaches. We also found that the choice of de novo assembly algorithm influences the accuracy of phylogenetic reconstruction, with workflows employing SPAdes or SKESA outperforming those employing Velvet. Finally, we found that the results of phylogenetic benchmarking are highly variable between replicates. We conclude that for phylogenomic reconstruction k-mer alignment methods are relevant alternatives to reference mapping at species level, especially in the absence of suitable reference genomes. We show de novo genome assembly accuracy to be an underappreciated parameter required for accurate phylogenomic reconstruction.

scholarly journals Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Jonas Paulsen ◽  
Monika Sekelja ◽  
Anja R. Oldenburg ◽  
Alice Barateau ◽  
Nolwenn Briand ◽  
...  
Keyword(s):  
Single Cells ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Modeling Framework ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Spatial Features ◽  
Nuclear Lamin ◽  
Topologically Associated Domains ◽  
User Friendly

Abstract Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells. Chrom3D reveals unexpected spatial features of LAD regulation in cells from patients with a laminopathy-causing lamin mutation. Chrom3D is freely available on github.

scholarly journals Volume-CLEM: a method for correlative light and electron microscopy in three dimensions

2019 ◽  
Vol 317 (6) ◽  
pp. L778-L784 ◽  
Author(s):  
Jan Hegermann ◽  
Christoph Wrede ◽  
Susanne Fassbender ◽  
Ronja Schliep ◽  
Matthias Ochs ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Fluorescent Labeling ◽  
Three Dimensions ◽  
Data Sets ◽  
New Approach ◽  
3D Data ◽  
Wide Range ◽  
3D Em

Generation of three-dimensional (3D) data sets from serial sections of tissues imaged by light microscopy (LM) allows identification of rare structures by morphology or fluorescent labeling. Here, we demonstrate a workflow for correlative LM and electron microscopy (EM) from 3D LM to 3D EM, using the same sectioned material for both methods consecutively. The new approach is easy to reproduce in routine EM laboratories and applicable to a wide range of organs and research questions.

Sign in / Sign up

Export Citation Format

Share Document