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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 -
Journal of Cell Science Sep 2015A universal feature of mitosis is that all chromosomes become aligned at the spindle equator--the halfway point between the two spindle poles--prior to anaphase onset.... (Review)
Review
A universal feature of mitosis is that all chromosomes become aligned at the spindle equator--the halfway point between the two spindle poles--prior to anaphase onset. This migratory event is called congression, and is powered by centromere-bound protein machines called kinetochores. This Commentary aims to document recent advances concerning the two kinetochore-based force-generating mechanisms that drive mitotic chromosome congression in vertebrate cells: depolymerisation-coupled pulling (DCP) and lateral sliding. We aim to explore how kinetochores can 'read-out' their spatial position within the spindle, and adjust these force-generating mechanisms to ensure chromosomes reach, and then remain, at the equator. Finally, we will describe the 'life history' of a chromosome, and provide a working model for how individual mechanisms are integrated to ensure efficient and successful congression.
Topics: Animals; Centromere; Chromosomal Puffs; Chromosome Pairing; Chromosome Segregation; HeLa Cells; Humans; Kinetochores; Models, Biological; Spindle Apparatus; Vertebrates
PubMed: 26330530
DOI: 10.1242/jcs.169367 -
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 -
Cold Spring Harbor Symposia on... 2017Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the...
Polytene chromosomes have for 80 years provided the highest resolution view of interphase genome structure in an animal cell nucleus. These chromosomes represent the normal genomic state of nearly all larval and many adult cells, and a better understanding of their striking banded structure has been sought for decades. A more recently appreciated characteristic of polytene cells is somatic genome instability caused by unfinished replication (UR). Repair of stalled forks generates enough deletions in polytene salivary gland cells to alter 10%-90% of the DNA strands within more than 100 UR regions comprising 20% of the euchromatic genome. We accurately map UR regions and show that most approximate large polytene bands, indicating that replication forks frequently stall near band boundaries in late S phase. Chromosome conformation capture has recently identified dense topologically associated domains (TADs) in many genomes and most UR bands are similar or slightly smaller than a cognate TAD. We argue that bands serve the evolutionarily ancient function of coordinating genome replication with local gene activity. We also discuss the relatively recent evolution of polyteny and somatic instability in Diptera and propose that these processes helped propel the amazing success of two-winged flies in becoming the most ecologically diverse insect group, with 200 times the number of species as mammals.
PubMed: 29167281
DOI: 10.1101/sqb.2017.82.033670 -
Cold Spring Harbor Protocols Dec 2022Chromosome visualization is a key step for developing cytogenetic maps and idiograms, analyzing inversion polymorphisms, and identifying mosquito species. Three types of...
Chromosome visualization is a key step for developing cytogenetic maps and idiograms, analyzing inversion polymorphisms, and identifying mosquito species. Three types of chromosomes-polytene, mitotic, and meiotic-are used in cytogenetic studies of mosquitoes. Here, we describe a detailed method for obtaining high-quality polytene chromosome preparations from the salivary glands of larvae and the ovaries of females for mosquitoes. We also describe how to obtain mitotic chromosomes from imaginal discs of fourth-instar larvae and meiotic chromosomes from the testes of male pupae for all mosquitoes. These chromosomes can be used for fluorescence in situ hybridization (FISH), a fundamental technique in cytogenetic research that is used for physical genome mapping, detecting chromosomal rearrangements, and studying chromosome organization.
Topics: Male; Animals; Female; In Situ Hybridization, Fluorescence; Polytene Chromosomes; Chromosomes; Anopheles; Chromosome Mapping; Cytogenetic Analysis; Larva
PubMed: 35960616
DOI: 10.1101/pdb.prot107872 -
Annual Review of Biochemistry 2015This article discusses three reviews on the theme of nuclear organization.
This article discusses three reviews on the theme of nuclear organization.
Topics: Animals; Cell Nucleus; Chironomidae; Chromosomal Puffs; Eukaryotic Cells; Nuclear Lamina; Ribosomes; Transcription, Genetic
PubMed: 25706897
DOI: 10.1146/annurev-biochem-020415-093225 -
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