Drosophila polytene chromosome bands formed by gene introns

Жимулев, И. Ф.; Boldyreva, Lidiya V.; Demakova, Olga V.; Poholkova, G V; Khoroshko, V. A.; Zykova, Tatyana Yu; Lavrov, Sergey; Belyaeva, E. S.

doi:10.1134/s1607672916010178

Cited by 5 publications

(7 citation statements)

References 12 publications

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“…This rule holds true for the organization of the fourth chromosome of Drosophila (Sidorenko et al, 2018). In addition, there are some atypical cases of band and interband genetic organization, with one long gene occupying up to nine cytological structures (Zhimulev et al, 2016;Khoroshko et al, 2019).…”

Section: Resultsmentioning

confidence: 92%

“…To sum up, it has been shown that the banding pattern is a universal principle of both polytene chromosome and diploid cell chromosome organization, and housekeeping genes are embedded in two interphase chromosome structures: their promoters are localized in the interbands, and the structural parts lie in adjacent loose bands (Zhimulev et al, 2014). In addition, it has recently been discovered that long D. melanogaster genes can occupy several morphological structures of polytene chromosomes (Zhimulev et al, 2016;Khoroshko et al, 2019). For example, using fluorescent in situ hybridization (FISH), it was shown that long introns of the ubiquitous active genes dlg1 (~18 kb) and CG43867 (~106 kb), interrupted by short rare exons, form loose gray bands 10В8-9 and 1D1-2, respectively, and their 5′ and 3′ regulatory regions lie in the decompacted interbands of the X chromosome .…”

Section: Atypical Cases Of Gene Localization In the Structures Of Polmentioning

confidence: 99%

“…For example, using fluorescent in situ hybridization (FISH), it was shown that long introns of the ubiquitous active genes dlg1 (~18 kb) and CG43867 (~106 kb), interrupted by short rare exons, form loose gray bands 10В8-9 and 1D1-2, respectively, and their 5′ and 3′ regulatory regions lie in the decompacted interbands of the X chromosome . Thus, it has been found that in some cases polytene chromosome bands can be formed from the material of only one part of a gene, namely, long noncoding introns of actively transcribed genes, which allowed the authors to conclude that there is a differential pattern of chromatin condensation of gene parts during its activation (Zhimulev et al, 2016). A spe cial case in studying gene localization in the morphological structures of polytene chromosomes is the dunce (dnc) gene, the size of which (167.3 kb) is 25fold longer than the average length of a D. melanogaster gene (Khoroshko et al, 2019).…”

Section: Atypical Cases Of Gene Localization In the Structures Of Polmentioning

confidence: 99%

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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: Resultsmentioning

confidence: 92%

Section: Atypical Cases Of Gene Localization In the Structures Of Polmentioning

confidence: 99%

Section: Atypical Cases Of Gene Localization In the Structures Of Polmentioning

confidence: 99%

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Polytene chromosomes reflect functional organization of the Drosophila genome

et al. 2019

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“…According to Bridges' map [25], two interbands and one grey band, being composed of intron material that is ~36 kb in length, are situated between the two probes ( Figure 14). 3.2.10. dlg1 dlg1 (discs large 1) is located on chromosome X in the 10B6-10B11 region (according to UCSC, Table 1); Zhimulev et al [46] have preliminarily localized it in the 10B8-1011 region. The gene length is 40.1 kb (81.9% of it accrues to introns); 21 transcripts are read from dlg1 (only three are shown in Figure 15D, Table 1).…”

Section: Nrgmentioning

confidence: 99%

“…When compared with the DNA length in the bands, introns up to 400 kb are quite large and, therefore, must somehow be detected at the chromosome level; at least, it can be expected that structures that are based on such long introns can be seen under the light microscope, but such data are unavailable in literature. According to our recently obtained preliminary data, certain large genes can occupy extended sections of chromosomes [45,46]. In the present study, we examined the localization sites of the genes that are mentioned above; in addition to that, we picked 12 new regions and analyzed their gene, intron, and chromatin composition, as well as studied their cytological location.…”

Section: Introductionmentioning

confidence: 95%

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

Khoroshko

Pokholkova

Levitsky

et al. 2020

Genes

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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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Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila melanogaster

Sidorenko

Zykova

et al. 2019

Chromosoma

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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. Electronic supplementary material The online version of this article (10.1007/s00412-019-00703-x) contains supplementary material, which is available to authorized users.

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Drosophila polytene chromosome bands formed by gene introns

Cited by 5 publications

References 12 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

Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila melanogaster

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