scholarly journals A Multiplexed DNA FISH strategy for Assessing Genome Architecture in C. elegans

2018 ◽  
Author(s):  
Brandon Fields ◽  
Son C. Nguyen ◽  
Guy Nir ◽  
Scott Kennedy
Keyword(s):  
Genome Organization ◽  
Genomic Organization ◽  
Intact Animal ◽  
Model System ◽  
Genome Architecture ◽  
Synthesis Reaction ◽  
C Elegans ◽  
3D Architecture ◽  
Eukaryotic Dna

AbstractEukaryotic DNA is highly organized within nuclei and this genomic organization is important for genome function. Fluorescent in situ hybridization (FISH) approaches allow the 3D architecture of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entire C. elegans genome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual DNA FISH experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system.

scholarly journals A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Brandon D Fields ◽  
Son C Nguyen ◽  
Guy Nir ◽  
Scott Kennedy
Keyword(s):  
Caenorhabditis Elegans ◽  
Genome Organization ◽  
Fluorescent In Situ Hybridization ◽  
Intact Animal ◽  
Model System ◽  
Genome Architecture ◽  
Synthesis Reaction ◽  
Eukaryotic Dna ◽  
Caenorhabditis Elegans Genome

Eukaryotic DNA is highly organized within nuclei and this organization is important for genome function. Fluorescent in situ hybridization (FISH) approaches allow 3D architectures of genomes to be visualized. Scalable FISH technologies, which can be applied to whole animals, are needed to help unravel how genomic architecture regulates, or is regulated by, gene expression during development, growth, reproduction, and aging. Here, we describe a multiplexed DNA FISH Oligopaint library that targets the entire Caenorhabditis elegans genome at chromosome, three megabase, and 500 kb scales. We describe a hybridization strategy that provides flexibility to DNA FISH experiments by coupling a single primary probe synthesis reaction to dye conjugated detection oligos via bridge oligos, eliminating the time and cost typically associated with labeling probe sets for individual experiments. The approach allows visualization of genome organization at varying scales in all/most cells across all stages of development in an intact animal model system.

scholarly journals Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale

2021 ◽  
Author(s):  
Jian Zhou
Keyword(s):  
Genome Organization ◽  
In Silico ◽  
Genomic Sequence ◽  
Spatial Scales ◽  
Genome Structure ◽  
Genome Architecture ◽  
Transcription Start Sites ◽  
3D Architecture ◽  
Mechanistic Basis ◽  
Genome Interactions

The structural organization of the genome plays an important role in multiple aspects of genome function. Understanding how genomic sequence influences 3D organization can help elucidate their roles in various processes in healthy and disease states. However, the sequence determinants of genome structure across multiple spatial scales are still not well understood. To learn the complex sequence dependencies of multiscale genome architecture, here we developed a sequence-based deep learning approach, Orca, that predicts genome 3D architecture from kilobase to whole-chromosome scale, covering structures including chromatin compartments and topologically associating domains. Orca also makes both intrachromosomal and interchromosomal predictions and captures the sequence dependencies of diverse types of interactions, from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions. Orca enables the interpretation of the effects of any structural variant at any size on multiscale genome organization and provides an in silico model to help study the sequence-dependent mechanistic basis of genome architecture. We show that the models accurately recapitulate effects of experimentally studied structural variants at varying sizes (300bp-80Mb) using only sequence. Furthermore, these sequence models enable in silico virtual screen assays to probe the sequence-basis of genome 3D organization at different scales. At the submegabase scale, the models predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, based on virtual screens of sequence activities, we propose a new model for the sequence basis of chromatin compartments: sequences at active transcription start sites are primarily responsible for establishing the expression-active compartment A, while the inactive compartment B typically requires extended stretches of AT-rich sequences (at least 6-12kb) and can form 'passively' without depending on any particular sequence pattern. Orca thus effectively provides an 'in silico genome observatory' to predict variant effects on genome structure and probe the sequence-based mechanisms of genome organization.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

Rhizobial plasmids — replication, structure and biological role

2012 ◽  
Vol 7 (4) ◽  
pp. 571-586 ◽  
Author(s):  
Andrzej Mazur ◽  
Piotr Koper
Keyword(s):  
Genome Organization ◽  
Soil Bacteria ◽  
Evolutionary History ◽  
Bacterial Genome ◽  
Biological Role ◽  
Genome Architecture ◽  
Genomic Knowledge ◽  
History Of ◽  
Cryptic Plasmids ◽  
Complex Evolutionary History

AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids and the presence of some important (or even essential) genes contribute to the capability of environmental adaptation and competitiveness with other bacteria. On the other hand, their mosaic structure results in the plasticity of the genome and demonstrates a complex evolutionary history of plasmids. In this review, a genomic perspective was employed for discussion of several aspects regarding rhizobial plasmids comprising structure, replication, genetic content, and biological role. A special emphasis was placed on current post-genomic knowledge concerning plasmids, which has enriched the view of the entire bacterial genome organization by the discovery of plasmids with a potential chromosome-like role.

scholarly journals Real-Time in Situ Monitoring of Particle and Structure Evolution in Mechanochemical Synthesis of UiO-66 Metal-Organic Framework

2019 ◽  
Author(s):  
Luzia S. Germann ◽  
Athanassios D. Katsenis ◽  
Igor Huskić ◽  
Patrick A. Julien ◽  
Krunoslav Uzarevic ◽  
...  
Keyword(s):  
Metal Organic Framework ◽  
Model System ◽  
In Situ Monitoring ◽  
Mechanochemical Reaction ◽  
Structure Evolution ◽  
X Ray ◽  
Framework Model ◽  
Metal Organic ◽  
Organic Framework

Manuscript about monitoring the mechanochemical reaction of a metal-organic framework model system by in situ X-ray powder diffraction<br>

scholarly journals Real-Time in Situ Monitoring of Particle and Structure Evolution in Mechanochemical Synthesis of UiO-66 Metal-Organic Framework

2019 ◽  
Author(s):  
Luzia S. Germann ◽  
Athanassios D. Katsenis ◽  
Igor Huskić ◽  
Patrick A. Julien ◽  
Krunoslav Uzarevic ◽  
...  
Keyword(s):  
Metal Organic Framework ◽  
Model System ◽  
In Situ Monitoring ◽  
Mechanochemical Reaction ◽  
Structure Evolution ◽  
X Ray ◽  
Framework Model ◽  
Metal Organic ◽  
Organic Framework

Manuscript about monitoring the mechanochemical reaction of a metal-organic framework model system by in situ X-ray powder diffraction<br>

scholarly journals The TRH Gene Is Regulated by Thyroid Hormone at the Level of Transcription in Vivo

2010 ◽  
Vol 31 (1) ◽  
pp. 136-136
Author(s):  
Michelle L. Sugrue ◽  
Kristen R. Vella ◽  
Crystal Morales ◽  
Marisol E. Lopez ◽  
Anthony N. Hollenberg
Keyword(s):  
Thyroid Hormone ◽  
Genomic Region ◽  
Model System ◽  
Model Systems ◽  
In Vivo Model ◽  
Pituitary Thyroid Axis ◽  
Thyroid Axis ◽  
Normal Production

ABSTRACT The expression of the TRH gene in the paraventricular nucleus (PVH) of the hypothalamus is required for the normal production of thyroid hormone (TH) in rodents and humans. In addition, the regulation of TRH mRNA expression by TH, specifically in the PVH, ensures tight control of the set point of the hypothalamic-pituitary-thyroid axis. Although many studies have assumed that the regulation of TRH expression by TH is at the level of transcription, there is little data available to demonstrate this. We used two in vivo model systems to show this. In the first model system, we developed an in situ hybridization (ISH) assay directed against TRH heteronuclear RNA to measure TRH transcription directly in vivo. We show that in the euthyroid state, TRH transcription is present both in the PVH and anterior/lateral hypothalamus. In the hypothyroid state, transcription is activated in the PVH only and can be shut off within 5 h by TH. In the second model system, we employed transgenic mice that express the Cre recombinase under the control of the genomic region containing the TRH gene. Remarkably, TH regulates Cre expression in these mice in the PVH only. Taken together, these data affirm that TH regulates TRH at the level of transcription in the PVH only and that genomic elements surrounding the TRH gene mediate its regulation by T3. Thus, it should be possible to identify the elements within the TRH locus that mediate its regulation by T3 using in vivo approaches.

scholarly journals Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Olga Raskina
Keyword(s):  
Transposable Elements ◽  
Mobile Element ◽  
Plant Genome ◽  
Aegilops Speltoides ◽  
Genome Architecture ◽  
Different Types ◽  
In The Wild ◽  
Species Specific ◽  
Current Species

Repetitive DNA—specifically, transposable elements (TEs)—is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

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