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Current Biology : CB May 2015Polyploidy is defined as an increase in genome DNA content. Throughout the plant and animal kingdoms specific cell types become polyploid as part of their...
Polyploidy is defined as an increase in genome DNA content. Throughout the plant and animal kingdoms specific cell types become polyploid as part of their differentiation programs. When this occurs in subsets of tissues within an organism it is termed somatic polyploidy, because it is distinct from the increase in ploidy that is inherited through the germline and present in every cell type of the organism. Germline polyploidy is common in plants and occurs in some animals, such as amphibians, but will not be discussed further here. Somatic polyploid cells can be mononucleate or multinucleate, and the replicated sister chromatids can remain attached and aligned, producing polytene chromosomes, or they can be dispersed (Figure 1). In this Primer, we focus on why somatic polyploidy occurs and how cells become polyploid — the first of these issues being more speculative, given the status of the field.
Topics: Cell Cycle; Cell Size; DNA Replication; Gene Expression; Polyploidy
PubMed: 25942544
DOI: 10.1016/j.cub.2015.03.037 -
Nature Cell Biology Mar 2022Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial...
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription.
Topics: Chromosomes; Eukaryota; RNA; Ribonucleoproteins; Transcription, Genetic
PubMed: 35177821
DOI: 10.1038/s41556-022-00847-6 -
Chromosome Research : An International... Oct 2017In this era of high-resolution mapping of chromosome territories, topological interactions, and chromatin states, it is increasingly appreciated that the positioning of... (Review)
Review
In this era of high-resolution mapping of chromosome territories, topological interactions, and chromatin states, it is increasingly appreciated that the positioning of chromosomes and their interactions within the nucleus is critical for cellular function. Due to their large size and distinctive structure, polytene chromosomes have contributed a wealth of knowledge regarding chromosome regulation. In this review, we discuss the diversity of polytene chromosomes in nature and in disease, examine the recurring structural features of polytene chromosomes in terms of what they reveal about chromosome biology, and discuss recent advances regarding how polytene chromosomes are assembled and disassembled. After over 130 years of study, these giant chromosomes are still powerful tools to understand chromosome biology.
Topics: Animals; DNA Replication; Disease Susceptibility; Gene Expression Regulation; Gene-Environment Interaction; Genetic Loci; Genetics; Polyploidy; Polytene Chromosomes; Research
PubMed: 28779272
DOI: 10.1007/s10577-017-9562-z -
Epigenetics & Chromatin Jan 2018It is well recognized that the interphase chromatin of higher eukaryotes folds into non-random configurations forming territories within the nucleus. Chromosome...
BACKGROUND
It is well recognized that the interphase chromatin of higher eukaryotes folds into non-random configurations forming territories within the nucleus. Chromosome territories have biologically significant properties, and understanding how these properties change with time during lifetime of the cell is important. Chromosome-nuclear envelope (Chr-NE) interactions play a role in epigenetic regulation of DNA replication, repair, and transcription. However, their role in maintaining chromosome territories remains unclear.
RESULTS
We use coarse-grained molecular dynamics simulations to study the effects of Chr-NE interactions on the dynamics of chromosomes within a model of the Drosophila melanogaster regular (non-polytene) interphase nucleus, on timescales comparable to the duration of interphase. The model simulates the dynamics of chromosomes bounded by the NE. Initially, the chromosomes in the model are prearranged in fractal-like configurations with physical parameters such as nucleus size and chromosome persistence length taken directly from experiment. Time evolution of several key observables that characterize the chromosomes is quantified during each simulation: chromosome territories, chromosome entanglement, compactness, and presence of the Rabl (polarized) chromosome arrangement. We find that Chr-NE interactions help maintain chromosome territories by slowing down and limiting, but not eliminating, chromosome entanglement on biologically relevant timescales. At the same time, Chr-NE interactions have little effect on the Rabl chromosome arrangement as well as on how chromosome compactness changes with time. These results are rationalized by simple dimensionality arguments, robust to model details. All results are robust to the simulated activity of topoisomerase, which may be present in the interphase cell nucleus.
CONCLUSIONS
Our study demonstrates that Chr-NE attachments may help maintain chromosome territories, while slowing down and limiting chromosome entanglement on biologically relevant timescales. However, Chr-NE attachments have little effect on chromosome compactness or the Rabl chromosome arrangement.
Topics: Animals; Chromosomes, Insect; Drosophila melanogaster; Interphase; Models, Molecular; Nuclear Envelope; Polytene Chromosomes
PubMed: 29357905
DOI: 10.1186/s13072-018-0173-5 -
Heredity Jul 2019
Review
Topics: Animals; Caenorhabditis elegans; Drosophila; Halobacterium; Models, Genetic; Phycomyces; Polytene Chromosomes; RNA Interference; T-Phages; Tetrahymena
PubMed: 31189909
DOI: 10.1038/s41437-019-0191-5 -
Genetics Oct 2016The sex chromosomes have special significance in the history of genetics. The chromosomal basis of inheritance was firmly established when Calvin Bridges demonstrated... (Review)
Review
The sex chromosomes have special significance in the history of genetics. The chromosomal basis of inheritance was firmly established when Calvin Bridges demonstrated that exceptions to Mendel's laws of segregation were accompanied at the cytological level by exceptional sex chromosome segregation. The morphological differences between X and Y exploited in Bridges' experiments arose as a consequence of the evolution of the sex chromosomes. Originally a homologous chromosome pair, the degeneration of the Y chromosome has been accompanied by a requirement for increased expression of the single X chromosome in males. Drosophila has been a model for the study of this dosage compensation and has brought key strengths, including classical genetics, the exceptional cytology of polytene chromosomes, and more recently, comprehensive genomics. The impact of these studies goes beyond sex chromosome regulation, providing valuable insights into mechanisms for the establishment and maintenance of chromatin domains, and for the coordinate regulation of transcription.
Topics: Animals; Dosage Compensation, Genetic; Drosophila Proteins; Drosophila melanogaster; Evolution, Molecular; Male; Polytene Chromosomes; Transcription, Genetic; X Chromosome; Y Chromosome
PubMed: 27729494
DOI: 10.1534/genetics.115.185108 -
Proceedings of the National Academy of... Jun 2022Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100-...
Cryoelectron tomography of the cell nucleus using scanning transmission electron microscopy and deconvolution processing technology has highlighted a large-scale, 100- to 300-nm interphase chromosome structure, which is present throughout the nucleus. This study further documents and analyzes these chromosome structures. The paper is divided into four parts: 1) evidence (preliminary) for a unified interphase chromosome structure; 2) a proposed unified interphase chromosome architecture; 3) organization as chromosome territories (e.g., fitting the 46 human chromosomes into a 10-μm-diameter nucleus); and 4) structure unification into a polytene chromosome architecture and lampbrush chromosomes. Finally, the paper concludes with a living light microscopy cell study showing that the G1 nucleus contains very similar structures throughout. The main finding is that this chromosome structure appears to coil the 11-nm nucleosome fiber into a defined hollow structure, analogous to a Slinky helical spring [https://en.wikipedia.org/wiki/Slinky; motif used in Bowerman , 10, e65587 (2021)]. This Slinky architecture can be used to build chromosome territories, extended to the polytene chromosome structure, as well as to the structure of lampbrush chromosomes.
Topics: Cell Nucleus; Chromatin; Chromosomes, Human; Humans; Interphase; Nucleosomes
PubMed: 35749363
DOI: 10.1073/pnas.2119101119 -
Cells Nov 2020Dipterans exhibit a remarkable diversity of chromosome end structures in contrast to the conserved system defined by telomerase and short repeats. Within dipteran...
BACKGROUND
Dipterans exhibit a remarkable diversity of chromosome end structures in contrast to the conserved system defined by telomerase and short repeats. Within dipteran families, structure of chromosome termini is usually conserved within genera. With the aim to assess whether or not the evolutionary distance between genera implies chromosome end diversification, this report exploits two representatives of Sciaridae, , and .
METHODS
Probes and plasmid microlibraries obtained by chromosome end microdissection, in situ hybridization, cloning, and sequencing are among the methodological approaches employed in this work.
RESULTS
The data argue for the existence of either specific terminal DNA sequences for each chromosome tip in , or sequences common to all chromosome ends but their extension does not allow detection by in situ hybridization. Both sciarid species share terminal sequences that are significantly underrepresented in chromosome ends of .
CONCLUSIONS
The data suggest an unusual terminal structure in chromosomes compared to other dipterans investigated. A putative, evolutionary process of repetitive DNA expansion that acted differentially to shape chromosome ends of the two flies is also discussed.
Topics: Animals; Base Sequence; Chromosomes, Insect; DNA; Diptera; Gene Library; Microdissection; Plasmids; Polytene Chromosomes
PubMed: 33167604
DOI: 10.3390/cells9112425 -
Insects Apr 2022The represent a diverse group of closely related to Although they have radiated extensively in Australia, they have been the focus of few studies. Here, we...
The represent a diverse group of closely related to Although they have radiated extensively in Australia, they have been the focus of few studies. Here, we characterized the karyotypes of 12 species from several species groups and showed that they have undergone similar types of karyotypic change to those seen in . This includes heterochromatin amplification involved in length changes of the sex and 'dot' chromosomes as well as the autosomes, particularly in the group of species. Numerous weak points along the arms of the polytene chromosomes suggest the presence of internal repetitive sequence DNA, but these regions did not C-band in mitotic chromosomes, and their analysis will depend on DNA sequencing. The nucleolar organizing regions (NORs) are at the same chromosome positions in as in and the various mechanisms responsible for changing arm configurations also appear to be the same. These chromosomal studies provide a complementary resource to other investigations of this group, with several species currently being sequenced.
PubMed: 35447805
DOI: 10.3390/insects13040364 -
Chromosoma Jun 2019The fourth chromosome smallest in the genome of Drosophila melanogaster differs from other chromosomes in many ways. It has high repeat density in conditions of a large...
The fourth chromosome smallest in the genome of Drosophila melanogaster differs from other chromosomes in many ways. It has high repeat density in conditions of a large number of active genes. Gray bands represent a significant part of this polytene chromosome. Specific proteins including HP1a, POF, and dSETDB1 establish the epigenetic state of this unique chromatin domain. In order to compare maps of localization of genes, bands, and chromatin types of the fourth chromosome, we performed FISH analysis of 38 probes chosen according to the model of four chromatin types. It allowed clarifying the dot chromosome cytological map consisting of 16 loose gray bands, 11 dense black bands, and 26 interbands. We described the relation between chromatin states and bands. Open aquamarine chromatin mostly corresponds to interbands and it contains 5'UTRs of housekeeping genes. Their coding parts are embedded in gray bands substantially composed of lazurite chromatin of intermediate compaction. Polygenic black bands contain most of dense ruby chromatin, and also some malachite and lazurite. Having an accurate map of the fourth chromosome bands and its correspondence to physical map, we found that DNase I hypersensitivity sites, ORC2 protein, and P-elements are mainly located in open aquamarine chromatin, while element 1360, characteristic of the fourth chromosome, occupies band chromatin types. POF and HP1a proteins providing special organization of this chromosome are mostly located in aquamarine and lazurite chromatin. In general, band organization of the fourth chromosome shares the features of the whole Drosophila genome.
Topics: Animals; Chromosome Banding; Chromosomes, Insect; Drosophila Proteins; Drosophila melanogaster; Female; Genome, Insect; Male; Polytene Chromosomes
PubMed: 31041520
DOI: 10.1007/s00412-019-00703-x