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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 -
Methods (San Diego, Calif.) Aug 2009The giant polytene chromosomes from Drosophila third instar larval salivary glands provide an important model system for studying the architectural changes in chromatin... (Review)
Review
The giant polytene chromosomes from Drosophila third instar larval salivary glands provide an important model system for studying the architectural changes in chromatin morphology associated with the process of transcription initiation and elongation. Especially, analysis of the heat shock response has proved useful in correlating chromatin structure remodeling with transcriptional activity. An important tool for such studies is the labeling of polytene chromosome squash preparations with antibodies to the enzymes, transcription factors, or histone modifications of interest. However, in any immunohistochemical experiment there will be advantages and disadvantages to different methods of fixation and sample preparation, the relative merits of which must be balanced. Here we provide detailed protocols for polytene chromosome squash preparation and discuss their relative pros and cons in terms of suitability for reliable antibody labeling and preservation of high resolution chromatin structure.
Topics: Animals; Chromatin; Chromosomes; Drosophila; Epigenesis, Genetic; Immunoenzyme Techniques; Transcription, Genetic
PubMed: 19272452
DOI: 10.1016/j.ymeth.2009.02.019 -
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 -
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 -
American Journal of Human Genetics Jan 1981Descriptions are presented of four cases of attachment of chromosome material at the ends of normal chromosomes in Drosophila. Since no material appears to be missing...
Descriptions are presented of four cases of attachment of chromosome material at the ends of normal chromosomes in Drosophila. Since no material appears to be missing from the polytene chromosomes and there are no ill effects to the organism in morphology, viability, or fertility when the chromosome is made homozygous, it is argued that the attachment occurred without the loss of any essential genetic material and that, in all probability, the break at the end of the chromosome occurred within the telomere of the chromosome. These cases may serve as a parallel to cases of apparent terminal breakage and reunion in certain rearrangements in man.
Topics: Animals; Chromosomes; Drosophila; Drosophila melanogaster; Karyotyping; Translocation, Genetic
PubMed: 6781337
DOI: No ID Found -
PLoS Genetics Oct 2022Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of...
Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of Topologically Associating Domains (TADs). Here, we demonstrate an association between gypsy insulator proteins and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components su(Hw) and Cp190 results in a significant reduction in γH2Av levels in chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av, but not H2Av, is a component of insulator bodies, which are protein condensates that form during osmotic stress. Phosphatase activity is required for insulator body dissolution after stress recovery. Together, our results implicate the H2A variant with a novel mechanism of insulator function and boundary formation.
Topics: Animals; Chromatin; DNA; Drosophila; Drosophila Proteins; Drosophila melanogaster; Histones; Insulator Elements; Microtubule-Associated Proteins; Nuclear Proteins; Phosphoric Monoester Hydrolases; Polytene Chromosomes
PubMed: 36197938
DOI: 10.1371/journal.pgen.1010396 -
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 -
Frontiers in Bioscience (Landmark... Jan 2012Post-translational modification of histones is a major mechanism of epigenetic regulation of eukaryotic transcription. Drosophila has proven to be an important model... (Review)
Review
Post-translational modification of histones is a major mechanism of epigenetic regulation of eukaryotic transcription. Drosophila has proven to be an important model system for the study of histone modifying enzymes and the cross talk that occurs between the various modifications. Polytene chromosome analysis and genome-wide chromatin immunoprecipitation (ChIP) studies have provided much insight into the location of marks and many of the enzymes that perform the catalytic reactions. Gene specific effects have been determined through study of flies carrying mutations in histone modifying enzymes. This review will highlight classic studies and present recent progress on both the localization data and mutant analyses. This information has been used to assign function to the marks and to the enzymes that place or remove them, critical for the process of transcriptional regulation.
Topics: Animals; Drosophila; Epigenesis, Genetic; Genome, Insect; Heterochromatin; Histones; Male; Models, Genetic; Protein Processing, Post-Translational; Sex Chromosomes; Transcription, Genetic
PubMed: 22201781
DOI: 10.2741/3964