Polytene Chromosomes – A Portrait of Functional Organization of the Drosophila Genome

Zykova, Tatyana Yu; Levitsky, Victor G.; Belyaeva, E. S.; Жимулев, И. Ф.

doi:10.2174/1389202918666171016123830

Cited by 38 publications

(46 citation statements)

References 35 publications

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“…Aquamarine chromatin (former cyan) contains maximum amount of open chromatin proteins, that are the basis of the model, and occupies about 13 % of the genome. This chro matin state corresponds to 5′ UTRs of ubiquitously active genes (Zhimulev et al, 2014;Zykova et al, 2018). All the interbands with determined genomic coordinates contain this chromatin type (Zhimulev et al, 2014).…”

Section: The Model Of Four Chromatin Statesmentioning

confidence: 96%

Polytene chromosomes reflect functional organization of the Drosophila genome

et al. 2019

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Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. Each region of polytene chromosomes has a unique banding pattern. Using the model of four chromatin types that reveals domains of varying compaction degrees, we were able to correlate the physical and cytological maps of some polytene chromosome regions and to show the main properties of genetic and molecular organization of bands and interbands, that we describe in this review. On the molecular map of the genome, the interbands correspond to decompacted aquamarine chromatin and 5’ ends of ubiquitously active genes. Gray bands contain lazurite and malachite chromatin, intermediate in the level of compaction, and, mainly, coding parts of genes. Dense black transcriptionally inactive bands are enriched in ruby chromatin. Localization of several dozens of interbands on the genome molecular map allowed us to study in detail their architecture according to the data of whole genome projects. The distribution of proteins and regulatory elements of the genome in the promoter regions of genes localized in the interbands shows that these parts of interbands are probably responsible for the formation of open chromatin that is visualized in polytene chromosomes as interbands. Thus, the permanent genetic activity of interbands and gray bands and the inactivity of genes in black bands are the basis of the universal banding pattern in the chromosomes of all Drosophila tissues. The smallest fourth chromosome of Drosophila with an atypical protein composition of chromatin is a special case. Using the model of four chromatin states and fluorescent in situ hybridization, its cytological map was refined and the genomic coordinates of all bands and interbands were determined. It was shown that, in spite of the peculiarities of this chromosome, its band organization in general corresponds to the rest of the genome. Extremely long genes of different Drosophila chromosomes do not fit the common scheme, since they can occupy a series of alternating bands and interbands (up to nine chromosomal structures) formed by parts of these genes.

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Section: The Model Of Four Chromatin Statesmentioning

confidence: 96%

Polytene chromosomes reflect functional organization of the Drosophila genome

et al. 2019

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“…Developmental genes are located in the dense black bands, which are usually polygenic. It was demonstrated that, in the thinnest bands, DNA is enough predominantly for a single housekeeping gene, so the B. Judd's hypothesis "one gene-one band" was partly confirmed [40].…”

Section: Introductionmentioning

confidence: 98%

“…The development of molecular genetic methods of labeling P-element interband insertions helped to determine which types of proteins related to bands and interbands in general [27,[35][36][37]. The 4HMM mathematical model was developed using these data; it revealed four chromatin states that are distinguished by the presence of RNA polymerase II, Origin Recognition Complex (ORC), protein composition, and nucleosome modifications [38][39][40]. Aquamarine is predominantly localized in the polytene chromosome interbands, contains promoters of housekeeping genes and it is characterized by the specific set of proteins.…”

Section: Introductionmentioning

confidence: 99%

Genes Containing Long Introns Occupy Series of Bands and Interbands in Drosophila melanogaster Polytene Chromosomes

Khoroshko

Pokholkova

Levitsky

et al. 2020

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The Drosophila melanogaster polytene chromosomes are the best model for studying the genome organization during interphase. Despite of the long-term studies available on genetic organization of polytene chromosome bands and interbands, little is known regarding long gene location on chromosomes. To analyze it, we used bioinformatic approaches and characterized genome-wide distribution of introns in gene bodies and in different chromatin states, and using fluorescent in situ hybridization we juxtaposed them with the chromosome structures. Short introns up to 2 kb in length are located in the bodies of housekeeping genes (grey bands or lazurite chromatin). In the group of 70 longest genes in the Drosophila genome, 95% of total gene length accrues to introns. The mapping of the 15 long genes showed that they could occupy extended sections of polytene chromosomes containing band and interband series, with promoters located in the interband fragments (aquamarine chromatin). Introns (malachite and ruby chromatin) in polytene chromosomes form independent bands, which can contain either both introns and exons or intron material only. Thus, a novel type of the gene arrangement in polytene chromosomes was discovered; peculiarities of such genetic organization are discussed.

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“…active vs inactive regions) across the genome [31]. In these cells, DNA staining shows a typical banding pattern, with active genes localized in interbands, and silent, more compact, chromatin in darker bands [31][32][33][34][35][36].…”

Section: Introductionmentioning

confidence: 99%

Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes

Dialynas

Delabaere

Chiolo

2019

Preprint

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Repairing DNA double-strand breaks (DSBs) is particularly challenging in pericentromeric heterochromatin, where the abundance of repeated sequences exacerbates the risk of ectopic recombination. In Drosophila Kc cells, accurate homologous recombination (HR) repair of heterochromatic DSBs relies on the relocalization of repair sites to the nuclear periphery before Rad51 recruitment and strand invasion. This movement is driven by Arp2/3-dependent nuclear actin filaments and myosins' ability to walk along them. Conserved mechanisms enable the relocalization of heterochromatic DSBs in mouse cells, and their defects lead to massive ectopic recombination in heterochromatin and chromosome rearrangements. In Drosophila polytene chromosomes, extensive DNA movement is blocked by a stiff structure of chromosome bundles. Repair pathways in this context are poorly characterized, and whether heterochromatic DSBs relocalize in these cells is unknown. Here, we show that damage in heterochromatin results in relaxation of the heterochromatic chromocenter, consistent with a dynamic response in this structure. Arp2/3, the Arp2/3 activator Scar, and the myosin activator Unc45, are required for heterochromatin stability in polytene cells, suggesting that relocalization enables heterochromatin repair in this tissue. Together, these studies reveal critical roles for actin polymerization and myosin motors in heterochromatin repair and genome stability across different organisms and tissue types. Short Title: Nucleoskeleton functions in heterochromatic DNA repair. Impact StatementHeterochromatin relies on dedicated pathways for 'safe' recombinational repair. In mouse and fly cultured cells, DNA repair requires the movement of repair sites away from the heterochromatin 'domain' via nuclear actin filaments and myosins. Here, we explore the importance of these pathways in Drosophila salivary gland cells, which feature a stiff bundle of endoreduplicated polytene chromosomes. Repair pathways in polytene chromosomes are largely obscure and how nuclear dynamics operate in this context is unknown. We show that heterochromatin relaxes in response to damage, and relocalization pathways are necessary for repair and stability of heterochromatic sequences. This deepens our understanding of repair mechanisms in polytenes, revealing unexpected dynamics. It also provides a first understanding of nuclear dynamics responding to replication damage or rDNA breaks, providing a new understanding of the importance of the nucleoskeleton in genome stability. We expect these discoveries to shed light on tumorigenic processes, including therapy-induced cancer relapses.

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Polytene Chromosomes – A Portrait of Functional Organization of the Drosophila Genome

Cited by 38 publications

References 35 publications

Polytene chromosomes reflect functional organization of the Drosophila genome

Polytene chromosomes reflect functional organization of the Drosophila genome

Genes Containing Long Introns Occupy Series of Bands and Interbands in Drosophila melanogaster Polytene Chromosomes

Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes

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