Functional analysis of Drosophila polytene chromosomes decompacted unit: the interband

Berkaeva, M B; Демаков, С. А.; Schwartz, Yuri B.; Жимулев, И. Ф.

doi:10.1007/s10577-009-9065-7

Cited by 9 publications

(6 citation statements)

References 32 publications

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“…So we can not exclude the possibility that disruption of some other regulatory elements could cause bantam inactivation. However it is important to mention that our mutation does not destroy the core elements of the neighboring DPE-containing promotor (Berkaeva et al, 2009). Further experiments with point replacement in consensus sequences are needed to assert with the confidence that the ADF1-binding disruption is responsible for the effects we observe in "ADF" transgenic flies.…”

Section: Resultsmentioning

confidence: 89%

“…We propose that the initial step of the interband formation involves DNA binding by some regulatory proteins which further recruit chromatin remodeling complexes capable of establishing and maintening the "open" chromatin structure. Putative binding sites for several proteins were identified within the "4.7" sequence, but only ADF1 and BEAF-32 were precisely mapped to the 61C7/C8 interband in salivary glands (Berkaeva et al, 2009). Therefore we asked whether these proteins may have a role in interband formation.…”

Section: Resultsmentioning

confidence: 99%

“…Both of the proteins are involved in the establishment and maintenance of local chromatin state (Jiang et al, 2009;Orsi et al, 2014). Previously, we showed that ADF1 and BEAF-32 localized to the 61C7/C8 interband in salivary gland polytene chromosomes (Berkaeva et al, 2009). BEAF-32 is known as an interband-specific protein (Zhimulev et al, 2014) and its binding to DNA is crucial for the polytene chromosome structure (Gilbert et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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ADF1 and BEAF-32 chromatin proteins affect nucleosome positioning and DNA decompaction in 61C7/C8 interband region of Drosophila melanogaster polytene chromosomes

2019

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The formation of interphase chromosomes is a multi-level process in which DNA is compacted several thousandfold by association with histones and non-histone proteins. The first step of compaction includes the formation of nucleosomes – the basic repeating units of chromatin. Further packaging occurs due to DNA binding to histone H1 and non-histone proteins involved in enhancer-promoter and insulator interactions. Under these conditions, the genome retains its functionality due to the dynamic and uneven DNA compaction along the chromatin fiber. Since the DNA compaction level affects the transcription activity of a certain genomic region, it is important to understand the interplay between the factors acting at different levels of the packaging process. Drosophila polytene chromosomes are an excellent model system for studying the molecular mechanisms that determine DNA compaction degree. The unevenness of DNA packaging along the chromatin fiber is easily observed along these chromosomes due to their large size and specific banding pattern. The purpose of this study was to figure out the role of two non-histone regulatory proteins, ADF1 and BEAF-32, in the DNA packaging process from nucleosome positioning to the establishment of the final chromosome structure. We studied the impact of mutations that affect ADF1 and BEAF-32 binding sites on the formation of 61C7/C8 interband – one of the decompacted regions of Drosophila polytene chromosomes. We show that such mutations led to the collapse of an interband, which was accompanied with increased nucleosome stability. We also find that ADF1 and BEAF-32 binding sites are essential for the rescue of lethality caused by the null allele of bantam microRNA gene located in the region 61C7/C8.

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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ADF1 and BEAF-32 chromatin proteins affect nucleosome positioning and DNA decompaction in 61C7/C8 interband region of Drosophila melanogaster polytene chromosomes

2019

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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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“…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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Functional analysis of Drosophila polytene chromosomes decompacted unit: the interband

Cited by 9 publications

References 32 publications

ADF1 and BEAF-32 chromatin proteins affect nucleosome positioning and DNA decompaction in 61C7/C8 interband region of Drosophila melanogaster polytene chromosomes

ADF1 and BEAF-32 chromatin proteins affect nucleosome positioning and DNA decompaction in 61C7/C8 interband region of Drosophila melanogaster polytene chromosomes

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

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

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