Identification and molecular genetic characterization of the polytene chromosome interbands in Drosophila melanogaster

Vatolina, T. Yu.; Демаков, С. А.; Semeshin, V. F.; Makunin, Igor V.; Babenko, Vladimir N.; Belyaeva, E. S.; Жимулев, И. Ф.

doi:10.1134/s1022795411040144

Cited by 13 publications

(24 citation statements)

References 38 publications

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“…These are exactly the same properties that we previously found specific for 13 interbands mapped throughout the analysis of P-transgene insertions [50]. In that work we showed, that 11 of the 13 transgene-tagged interbands corresponded to either intergenic regions or 5′-ends of genes.…”

Section: Resultssupporting

confidence: 88%

Identical Functional Organization of Nonpolytene and Polytene Chromosomes in Drosophila melanogaster

et al. 2011

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Salivary gland polytene chromosomes demonstrate banding pattern, genetic meaning of which is an enigma for decades. Till now it is not known how to mark the band/interband borders on physical map of DNA and structures of polytene chromosomes are not characterized in molecular and genetic terms. It is not known either similar banding pattern exists in chromosomes of regular diploid mitotically dividing nonpolytene cells. Using the newly developed approach permitting to identify the interband material and localization data of interband-specific proteins from modENCODE and other genome-wide projects, we identify physical limits of bands and interbands in small cytological region 9F13-10B3 of the X chromosome in D. melanogaster, as well as characterize their general molecular features. Our results suggests that the polytene and interphase cell line chromosomes have practically the same patterns of bands and interbands reflecting, probably, the basic principle of interphase chromosome organization. Two types of bands have been described in chromosomes, early and late-replicating, which differ in many aspects of their protein and genetic content. As appeared, origin recognition complexes are located almost totally in the interbands of chromosomes.

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Section: Resultssupporting

confidence: 88%

Identical Functional Organization of Nonpolytene and Polytene Chromosomes in Drosophila melanogaster

et al. 2011

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“…(Fig. 3A and in 17, 91). These regions also displayed reduced nucleosome density, sites of hypersensitivity to DNase I, and gaps in H1 histone distribution; all of which also feature in open interband chromatin.…”

Section: Interbands As Universal Basic Structural Units Of Interphasementioning

confidence: 88%

“… Frequencies of chromatin protein localization in the interband regions of polytene and non‐polytene chromosomes. The proteins were determined from 13 interbands 17, 91 marked with transposon insertions ( A ) and in nine interbands located in the 9F13–10B3 region 90 ( B ), based on modEncode 33, 34. The abscissa shows the proteins studied and the percentage of interband regions bound by those proteins.…”

Section: Interbands As Universal Basic Structural Units Of Interphasementioning

confidence: 99%

“…Thus, exact localization of transposon insertions on both cytological and physical maps allows precise identification of the sequences adjacent to the integration site as an interband. Using this approach, 13 interband regions have been mapped to the Drosophila genome 16, 17. Clearly, this approach only allows mapping of interband sequences around transposon insertion sites.…”

Section: Introductionmentioning

confidence: 99%

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Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA‐binding protein occupancy

et al. 2012

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The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome-wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with "active" chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non-polytene chromosomes.

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“…Progressively more detailed optical and electron microscopic analysis of polytene chromosomes in Drosophila melanogaster have identified a stereotyped banding pattern with compacted, DNA-rich "bands" alternating with extended, DNApoor "interband" regions (6)(7)(8)(9)(10). While much is now known about the molecular properties of these two types of chromatin (11)(12)(13)(14)(15)(16)(17)(18)(19)(20), the precise molecular nature of the banding structure remains elusive.…”

Section: Introductionmentioning

confidence: 99%

A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps

Stadler

2017

Preprint

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Insulator proteins bind to specific genomic loci and have been shown to play a role in partitioning genomes into independent domains of gene expression and chromatin structure. Despite decades of study, the mechanism by which insulators establish these domains remains elusive. Here, we use genome-wide chromatin conformation capture (Hi-C) to generate a highresolution map of spatial interactions of chromatin from Drosophila melanogaster embryos. We show that from the earliest stages of development the genome is divided into distinct topologically associated domains (TADs), that we can map the boundaries between TADs to subkilobase resolution, and that these boundaries correspond to 500-2000 bp insulator elements. Comparing this map with a detailed assessment of the banding pattern of a region of a polytene chromosome, we show that these insulator elements correspond to low density polytene interbands that divide compacted bands, which correspond to TADs. It has been previously shown that polytene interbands have low packing ratios allowing the conversion of small genomic distances (in base pairs) into a large physical distances. We therefore suggest a simple mechanism for insulator function whereby insulators increase the physical space between adjacent domains via the unpacking and extension of intervening chromatin. This model provides an intuitive explanation for known features of insulators, including the ability to block enhancerpromoter interactions, limit the spread of heterochromatin, and organize the structural features of interphase chromosomes. IntroductionBeginning in the late 19th century, cytological investigations of the polytene chromosomes of insect salivary glands implicated the physical structure of interphase chromosomes in their metabolic functions (1-5). Progressively more detailed optical and electron microscopic analysis of polytene chromosomes in Drosophila melanogaster have identified a stereotyped banding pattern with compacted, DNA-rich "bands" alternating with extended, DNApoor "interband" regions(6-10). While much is now known about the molecular properties of these two types of chromatin (11)(12)(13)(14)(15)(16)(17)(18)(19)(20), the precise molecular nature of the banding structure remains elusive.Several methods have been developed in the past decade for the isolation and highthroughput characterization of chromosomal regions that are colocalized within nuclei (21-24), yielding genome-wide maps of chromatin structure in a number of organisms and tissues. These experiments revealed that the interphase chromatin fiber is organized into topologicallyassociated domains (TADs), contiguous regions of the genome that exhibit enriched threedimensional contacts between loci within the TAD, and depleted contacts between loci in different TADs. Eagen et al. recently showed that TADs identified from genome-wide chromatin conformation capture (Hi-C) at approximately 15 kb resolution from polytene nuclei of Drosophila melanogaster largely correspond to the bands of polytene chromosomes, ...

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Identification and molecular genetic characterization of the polytene chromosome interbands in Drosophila melanogaster

Cited by 13 publications

References 38 publications

Identical Functional Organization of Nonpolytene and Polytene Chromosomes in Drosophila melanogaster

Identical Functional Organization of Nonpolytene and Polytene Chromosomes in Drosophila melanogaster

Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA‐binding protein occupancy

A chromatin extension model for insulator function based on comparison of high-resolution chromatin conformation capture and polytene banding maps

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