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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 -
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 -
Doklady. Biochemistry and Biophysics 2016Genetic organization of bands and interbands in polytene chromosomes has long remained a puzzle for geneticists. It has been recently demonstrated that interbands...
Genetic organization of bands and interbands in polytene chromosomes has long remained a puzzle for geneticists. It has been recently demonstrated that interbands typically correspond to the 5'-ends of house-keeping genes, whereas adjacent loose bands tend to be composed of coding sequences of the genes. In the present work, we made one important step further and mapped two large introns of ubiquitously active genes on the polytene chromosome map. We show that alternative promoter regions of these genes map to interbands, whereas introns and coding sequences found between those promoters correspond to loose grey bands. Thus, a gene having its long intron "sandwiched" between to alternative promoters and a common coding sequence may occupy two interbands and one band in the context of polytene chromosomes. Loose, partially decompacted bands appear to host large introns.
Topics: Animals; Drosophila; Genes, Insect; Introns; Physical Chromosome Mapping; Polytene Chromosomes
PubMed: 27025489
DOI: 10.1134/S1607672916010178 -
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 -
Yi Chuan = Hereditas Jun 2015Drosophila salivary gland polytene chromosome, one of the three classical chromosomes with remarkable characteristics, has been used as an outstanding model for a... (Review)
Review
Drosophila salivary gland polytene chromosome, one of the three classical chromosomes with remarkable characteristics, has been used as an outstanding model for a variety of genetic studies since 1934. The greatest contribution of this model to genetics has been providing extraordinary angle of view in studying interphase chromosome structure and gene expression regulation. Additionally, it has been extensively used to understand some special genetic phenomena, such as dosage compensation and position-effect variegation. In this paper, we briefly review the advances in the study of Drosophila salivary gland chromosome, and try to systematically and effectively introduce this model system into genetics teaching practice in order to steer and inspire students' interest in genetics.
Topics: Animals; Chromosomes, Insect; Drosophila melanogaster; Genetics; Polytene Chromosomes; Salivary Glands; Teaching
PubMed: 26351058
DOI: 10.16288/j.yczz.14-364 -
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 -
Current Genomics Apr 2018This mini-review is devoted to the problem genetic meaning of main polytene chromosome structures - bands and interbands. Generally, densely packed chromatin forms black... (Review)
Review
This mini-review is devoted to the problem genetic meaning of main polytene chromosome structures - bands and interbands. Generally, densely packed chromatin forms black bands, moderately condensed regions form grey loose bands, whereas decondensed regions of the genome appear as interbands. Recent progress in the annotation of the Drosophila genome and epigenome has made it possible to compare the banding pattern and the structural organization of genes, as well as their activity. This was greatly aided by our ability to establish the borders of bands and interbands on the physical map, which allowed to perform comprehensive side-by-side comparisons of cytology, genetic and epigenetic maps and to uncover the association between the morphological structures and the functional domains of the genome. These studies largely conclude that interbands 5'-ends of housekeeping genes that are active across all cell types. Interbands are enriched with proteins involved in transcription and nucleosome remodeling, as well as with active histone modifications. Notably, most of the replication origins map to interband regions. As for grey loose bands adjacent to interbands, they typically host the bodies of house-keeping genes. Thus, the bipartite structure composed of an interband and an adjacent grey band functions as a standalone genetic unit. Finally, black bands harbor tissue-specific genes with narrow temporal and tissue expression profiles. Thus, the uniform and permanent activity of interbands combined with the inactivity of genes in bands forms the basis of the universal banding pattern observed in various Drosophila tissues.
PubMed: 29606905
DOI: 10.2174/1389202918666171016123830 -
Genome Jan 2009The present study constitutes the first attempt to construct a polytene chromosome map of an Anastrepha species, Anastrepha ludens (Loew), a major agricultural pest. The...
The present study constitutes the first attempt to construct a polytene chromosome map of an Anastrepha species, Anastrepha ludens (Loew), a major agricultural pest. The mitotic karyotype has a diploid complement of 12 acrocentric chromosomes, including five pairs of autosomes and an XX/XY sex chromosome pair. The analysis of salivary gland polytene chromosomes has shown a total number of five polytene elements that correspond to the five autosomes. The characteristic features and the most prominent landmarks of each chromosome are described. By comparing chromosome banding patterns, the possible chromosomal homology between A. ludens and Ceratitis capitata (Wiedemann) is presented. This work shows that polytene maps of A. ludens are suitable for cytogenetic studies in this species and may be used as reference for other Anastrepha species, most of which are also serious agricultural pests.
Topics: Animals; Chromosome Banding; Chromosome Mapping; Chromosomes; Cytogenetics; Karyotyping; Larva; Mitosis; Models, Genetic; Salivary Glands; Sex Chromosomes; Tephritidae
PubMed: 19132068
DOI: 10.1139/G08-099 -
Genetica 1991This is a review summarizing work carried out at the Laboratory of Molecular Cytogenetics in recent years. Problems of genetic organization of bands, interbands and... (Review)
Review
This is a review summarizing work carried out at the Laboratory of Molecular Cytogenetics in recent years. Problems of genetic organization of bands, interbands and puffs as well as intercalary heterochromatin and position effect variegation are discussed from the point of view of the dynamic model of polytene chromosome organization.
Topics: Animals; Chromosome Banding; Chromosome Mapping; Chromosomes; Drosophila melanogaster; Heterochromatin; Restriction Mapping; Transcription, Genetic
PubMed: 1778476
DOI: 10.1007/BF00056107 -
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