Ultrastructural Details of Mammalian Chromosome Architecture.
Ontology highlight
ABSTRACT:
SUBMITTER: Krietenstein N
PROVIDER: S-EPMC7222625 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Knowledge of the interactions between nanomaterials and large-size mammalian cells, including cellular uptake, intracellular localization and translocation, has greatly advanced nanomedicine and nanotoxicology. Imaging techniques that can locate nanomaterials within the structures of intact large-size cells at nanoscale resolution play crucial roles in acquiring this knowledge. Here, the quantitative imaging of intracellular nanomaterials in three dimensions was performed by combining dual-energy contrast X-ray microscopy and an iterative tomographic algorithm termed equally sloped tomography (EST). Macrophages with a size of ?20?µm that had been exposed to the potential antitumour agent [Gd@C82(OH)22] n were investigated. Large numbers of nanoparticles (NPs) aggregated within the cell and were mainly located in phagosomes. No NPs were observed in the nucleus. Imaging of the nanomedicine within whole cells advanced the understanding of the high-efficiency antitumour activity and the low toxicity of this agent. This imaging technique can be used to probe nanomaterials within intact large-size cells at nanometre resolution uniformly in three dimensions and may greatly benefit the fields of nanomedicine and nanotoxicology.
| S-EPMC5947718 | biostudies-literature
Project description:Approximately 3,000 cattle bacterial artificial chromosome (BAC)-end sequences were added to the Illinois-Texas 5,000-rad RH (RH, radiation hybrid) map. The BAC-end sequences selected for mapping are approximately 1 Mbp apart on the human chromosomes as determined by blastn analysis. The map has 3,484 ordered markers, of which 3,204 are anchored in the human genome. Two hundred-and-one homologous synteny blocks (HSBs) were identified, of which 27 are previously undiscovered, 79 are extended, 26 were formed by previously unrecognized breakpoints in 18 previously defined HSBs, and 23 are the result of fusions. The comparative coverage relative to the human genome is approximately 91%, or 97% of the theoretical maximum. The positions of 64% of all cattle centromeres and telomeres were reassigned relative to their positions on the previous map, thus facilitating a more detailed comparative analysis of centromere and telomere evolution. As an example of the utility of the high-resolution map, 22 cattle BAC fingerprint contigs were directly anchored to cattle chromosome 19 [Bos taurus, (BTA) 19]. The order of markers on the cattle RH and fingerprint maps of BTA19 and the sequence-based map of human chromosome 17 [Homo sapiens, (HSA) 17] were found to be highly consistent, with only two minor ordering discrepancies between the RH map and fingerprint contigs. The high-resolution Illinois-Texas 5,000-rad RH and comparative maps will facilitate identification of candidate genes for economically important traits, the phylogenomic analysis of mammalian chromosomes, proofing of the BAC fingerprint map and, ultimately, aid the assembly of cattle whole-genome sequence.
| S-EPMC1317968 | biostudies-literature
Project description:This method for plant cuticles was adapted from spores and pollen procedure. It already enabled to prepare ultrathin plant cuticle sections of 60-70 nanometers of thickness, in high numbers as a routine, and allowed statistical measurements as any other macro- and/or micro-features. It provides through transmission electron microscope clean and contrasted observations of layers and sublayers of the cuticle, at a magnification over 100,000 times. It has been used efficiently for taxonomy, signature of environment and evolution topics since the end of the nineties (Gaëtan Guignard, 2019), however it is detailed here step by step for the first time, and illustrated. It can serve in the future for many purposes, like other taxonomical comparisons, palaeoreconstructions and evolutionary considerations. Value of the protocol•This method provides ultrathin plant cuticle sections of 60-70 nanometers of thickness•Details of layers and sublayers of the cuticle are easily observed•High numbers of sections allows statistical measurements as a routine.
| S-EPMC8374509 | biostudies-literature
Project description:In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. We report a theoretical model for chromatin (Minimal Chromatin Model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. First, we trained our energy function using the Hi-C contact map of chromosome 10 from human GM12878 lymphoblastoid cells. Then, we used the model to perform molecular dynamics simulations producing an ensemble of 3D structures for all GM12878 autosomes. Finally, we used these 3D structures to generate contact maps. We found that simulated contact maps closely agree with experimental results for all GM12878 autosomes. The ensemble of structures resulting from these simulations exhibited unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories.
| S-EPMC5087044 | biostudies-literature
Project description:How the same DNA sequences can function in the three-dimensional architecture of interphase nucleus, fold in the very compact structure of metaphase chromosomes and go precisely back to the original interphase architecture in the following cell cycle remains an unresolved question to this day. The strategy used to address this issue was to analyze the correlations between chromosome architecture and the compositional patterns of DNA sequences spanning a size range from a few hundreds to a few thousands Kilobases. This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands. The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm "beads-on-a-string" structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the "mitotic memory" of interphase architecture and the reversibility of the interphase to mitosis process. The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase.
| S-EPMC4664426 | biostudies-literature
Project description:Individual chromosome arms have specific individual telomere lengths (TLs). Past studies within species have shown strong positive correlations between individual chromosome length and TL at that chromosome. While the reasons for these associations are unclear, the strength and consistency of the associations across disparate taxa suggest that this is important to telomere biology and should be explored further. If TL is primarily determined by chromosome length, then chromosome length should be considered and controlled for in cross-species analyses of TL. Here, we employ a cross-species approach to explore whether the chromosome length-TL association observed intraspecifically is a determinant of mean TL across species. Data were compiled from two studies characterizing TL across a range of mammalian taxa and analysed in a phylogenetic framework. We found no significant relationship between TL and chromosome size across mammals or within mammalians orders. The pattern trends in the expected direction and we suggest may be masked by evolutionary lag effects.
| S-EPMC6083700 | biostudies-literature
Project description:Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The 14 conserved 'core' subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 'supernumerary' subunits are unknown. Here we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we considerably advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases.
| S-EPMC4224586 | biostudies-literature
Project description:The spatial organization of chromosomes inside the cell nucleus is still poorly understood. This organization is guided by intra- and interchromosomal contacts and by interactions of specific chromosomal loci with relatively fixed nuclear 'landmarks' such as the nuclear envelope and the nucleolus. Researchers have begun to use new molecular genome-wide mapping techniques to uncover both types of molecular interactions, providing insights into the fundamental principles of interphase chromosome folding.
| S-EPMC3023824 | biostudies-literature
Project description:Tardigrades can cope with adverse environmental conditions by turning into anhydrobiotes with a characteristic tun shape. Tun formation is an essential morphological adaptation for tardigrade entry into the anhydrobiotic state. The tun cell structure and ultrastructure have rarely been explored in tardigrades in general and never in Hypsibius exemplaris. We used transmission electron microscopy to compare cellular organization and ultrastructures between hydrated and anhydrobiotic H. exemplaris. Despite a globally similar cell organelle structure and a number of cells not significantly different between hydrated and desiccated tardigrades, reductions in the sizes of both cells and mitochondria were detected in dehydrated animals. Moreover, in anhydrobiotes, secretory active cells with a dense endoplasmic reticulum network were observed. Interestingly, these anhydrobiote-specific cells are in a close relationship with a specific extracellular structure surrounding each cell. It is possible that this rampart-like extracellular structure resulted from the accumulation of anhydrobiotic-specific material to protect the cells. Interestingly, after five hours of rehydration, the number of secretory cells decreased, and the specific extracellular structure began to disappear. Twenty-four hours after the beginning of rehydration, the cellular structure and ultrastructure were comparable to those observed in hydrated tardigrades.
| S-EPMC7062702 | biostudies-literature
Project description:The second messenger cAMP has been extensively studied for half a century, but the plethora of regulatory mechanisms controlling cAMP synthesis in mammalian cells is just beginning to be revealed. In mammalian cells, cAMP is produced by two evolutionary related families of adenylyl cyclases, soluble adenylyl cyclases (sAC) and transmembrane adenylyl cyclases (tmAC). These two enzyme families serve distinct physiological functions. They share a conserved overall architecture in their catalytic domains and a common catalytic mechanism, but they differ in their sub-cellular localizations and responses to various regulators. The major regulators of tmACs are heterotrimeric G proteins, which transduce extracellular signals via G protein-coupled receptors. sAC enzymes, in contrast, are regulated by the intracellular signaling molecules bicarbonate and calcium. Here, we discuss and compare the biochemical, structural and regulatory characteristics of the two mammalian AC families. This comparison reveals the mechanisms underlying their different properties but also illustrates many unifying themes for these evolutionary related signaling enzymes.
| S-EPMC3662476 | biostudies-literature