High-resolution in situ hybridization analysis on the chromosomal interval 61C7-61C8 of Drosophila melanogaster reveals interbands as open chromatin domains

Zielke, Thomas; Глотов, А.Г.; Saumweber, Harald

doi:10.1007/s00412-015-0554-5

Cited by 6 publications

(11 citation statements)

References 46 publications

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“…A major limitation of understanding bands has been the difficulty of mapping them precisely onto the genome sequence (see Zielke et al 2016). Most in situ hybridization mapping as summarized in FlyBase (Marygold et al 2016) has been performed at a resolution far lower than that of individual bands and with sometimes-contradictory results due to the difficulty of high-resolution polytene mapping.…”

Section: Mapping Ur Regions and Polytene Bands Using High-resolution mentioning

confidence: 99%

“…Putative interband regions are enriched in specific chromatin proteins, active histone marks, transcribed genes, replication origins, and P element insertion sites. Comparison of features such as chromatin marks and gene activity suggests that the domain structure of the Drosophila genome is highly similar between polytene and diploid cells (Vatolina et al 2011;Zielke et al 2016). Insulator proteins were localized at the junction of bands and interbands and were proposed to organize chromatin domains (Pai et al 2004;Gerasimova et al 2007).…”

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confidence: 99%

“…Only a handful of small differences in band patterns have been identified between different tissues (Hochstrasser 1987;Heino 1989;Richards 1980), suggesting that banding corresponds to a general aspect of genome organization minimally related to tissue differentiation. How bands and interbands correspond to functional genomic features has been studied in a few favorable chromosome regions (Vatolina et al 2011;Zhimulev et al 2014;Zielke et al 2016). Putative interband regions are enriched in specific chromatin proteins, active histone marks, transcribed genes, replication origins, and P element insertion sites.…”

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confidence: 99%

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Polytene Chromosome Structure and Somatic Genome Instability

Spradling

2017

Cold Spring Harb Symp Quant Biol

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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 Drosophila 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 Drosophila 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 Drosophila 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.

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Section: Mapping Ur Regions and Polytene Bands Using High-resolution mentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Polytene Chromosome Structure and Somatic Genome Instability

Spradling

2017

Cold Spring Harb Symp Quant Biol

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“…D - Types of chromosomal structures (grey and black bands, interbands) (according to [ 14 ] with modifications).…”

Section: Chromatin Domains In Interphase Chromosomesmentioning

confidence: 99%

“…Several proteins and histone modifications implicated in gene silencing turned out to be significantly underrepresented in the aquamarine chromatin. Comparison of protein localization data for three cell lines (S2, BG3 and Cl.8) was indicative of high degree of similarity in protein and histone modification profiles between these cells [ 14 ] (Fig. 2 ).…”

Section: Chromatin Domains In Interphase Chromosomesmentioning

confidence: 99%

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

Zykova

Levitsky

Belyaeva

et al. 2018

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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.

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Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes

et al. 2016

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MYST family histone acetyltransferases play important roles in gene regulation. Here, we have characterized the Drosophila MYST histone acetyltransferase (HAT) encoded by cg1894, whose closest homolog is Drosophila MOF, and which we have termed MYST5. We found it localized to a large number of interbands as well as to the telomeres of polytene chromosomes, and it showed strong colocalization with the interband protein Z4/Putzig and RNA polymerase II. Accordingly, genome-wide location analysis by ChIP-seq showed co-occurrence of MYST5 with the Z4-interacting partner Chriz/Chromator. Interestingly, MYST5 bound to the promoter of actively transcribed genes, and about half of MYST5 sites colocalized with the transcription factor DNA replication-related element-binding factor (DREF), indicating a role for MYST5 in gene expression. Moreover, we observed substantial overlap of MYST5 binding with that of the insulator proteins CP190, dCTCF, and BEAF-32, which mediate the organization of the genome into functionally distinct topological domains. Altogether, our data suggest a broad role for MYST5 both in gene-specific transcriptional regulation and in the organization of the genome into chromatin domains, with the two roles possibly being functionally interconnected.

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High-resolution in situ hybridization analysis on the chromosomal interval 61C7-61C8 of Drosophila melanogaster reveals interbands as open chromatin domains

Cited by 6 publications

References 46 publications

Polytene Chromosome Structure and Somatic Genome Instability

Polytene Chromosome Structure and Somatic Genome Instability

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

Widespread colocalization of the Drosophila histone acetyltransferase homolog MYST5 with DREF and insulator proteins at active genes

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