Multi-Scale Organization of the Drosophila melanogaster Genome

Peterson, Samantha C; Samuelson, Kaylah B; Hanlon, Stacey L

doi:10.3390/genes12060817

Cited by 17 publications

(10 citation statements)

References 156 publications

(193 reference statements)

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“…Insulator proteins are classically associated with demarcating the boundaries of chromatin domains in order to block the spreading of repressive chromatin and inhibit enhancer-promoter contacts (Moretti et al 2020). Further studies revealed their roles in mediating long-range interactions between distant genomic sequences, and in the formation of the 3D chromatin structure (Moretti et al 2020; Peterson et al 2021). Moreover, the involvement of insulator proteins in PcG function becomes more and more apparent.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide temperature-sensitivity of PcG regulation and reduction thereof in temperateDrosophila melanogaster

Voigt

Froschauer

2023

Preprint

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Epigenetic regulation varies with the environment. In the fruit fly Drosophila melanogaster, environmental temperature can affect chromatin-based gene regulation. Genes regulated by the Polycomb group (PcG) can vary in their transcriptional output in response to changes in temperature, which typically increases with decreasing temperature. Here, we studied temperature-sensitive expression of PcG target genes on a genome-wide scale, as well as temperature-sensitive enrichment of two histone modifications associated with the regulation of PcG target genes, H3K27me3 and H3K4me3. We investigated temperature-sensitivity in adult flies, and possible differences thereof between populations adapted to temperate and tropical climates. Compared to genes not targeted by the PcG, an elevated number of target genes showed higher expression at the lower temperature, as it is typically observed for PcG regulation. Many of the PcG target genes also exhibited temperature-sensitive H3K4me3 enrichment in the same direction, and the H3K4me3 temperature response correlated positively with that of expression. A small set of target sites also showed temperature-sensitive enrichment of H3K27me3, again with a higher proportion corresponding to increased transcriptional activation at the lower temperature. Overall, higher transcriptional activity at lower temperature was less pronounced in males compared to females, and in temperate compared to tropical flies. Possible trans- and cis-acting factors responsible for reduced expression plasticity in temperate flies were identified, including factors belonging to the Trithorax group (TrxG) and insulator binding proteins, respectively.

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Section: Discussionmentioning

confidence: 99%

Genome-wide temperature-sensitivity of PcG regulation and reduction thereof in temperateDrosophila melanogaster

Voigt

Froschauer

2023

Preprint

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“…Insulator elements organize the genome into chromatin loops 5 that are involved in the formation of topologically associating domains, TADs [29][30][31] . In mammals, CTCF-dependent loop formation requires ATP-driven motor activity of SMC complex cohesin 32 .…”

Section: Discussionmentioning

confidence: 99%

“…Insulator elements organize the genome into chromatin loops (Gerasimova et al, 1995) that are involved in the formation of topologically associating domains, TADs (Peterson, Samuelson, & Hanlon, 2021; Rowley et al, 2017; Szabo, Bantignies, & Cavalli, 2019). In mammals, CTCF-dependent loop formation requires ATP-driven motor activity of SMC complex cohesin (Davidson et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Drosophila SUMM4 complex couples insulator function and DNA replication timing control

Andreyeva

Emelyanov

Nevil³

et al. 2021

Preprint

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The asynchronous timing of replication of different chromosome domains is essential for eukaryotic genome stability, but the mechanisms establishing replication timing programs remain incompletely understood. Drosophila SNF2-related factor SUUR imparts under-replication (UR) of late-replicating intercalary heterochromatin (IH) domains in polytene chromosomes1. SUUR negatively regulates DNA replication fork progression across IH; however, its mechanism of action remains obscure2,3. Here we developed a novel method termed MS-Enabled Rapid protein Complex Identification (MERCI) to isolate a stable stoichiometric native complex SUMM4 that comprises SUUR and a chromatin boundary protein Mod(Mdg4)-67.24,5. In vitro, Mod(Mdg4) stimulates the ATPase activity of SUUR, although neither SUUR nor SUMM4 can remodel nucleosomes. Mod(Mdg4)-67.2 and SUUR distribution patterns in vivo partially overlap, and Mod(Mdg4) is required for a normal spatiotemporal distribution of SUUR in chromosomes. SUUR and Mod(Mdg4)-67.2 mediate insulator activities of the gypsy mobile element that disrupt enhancer-promoter interactions and establish euchromatin-heterochromatin barriers in the genome. Furthermore, mutations of SuUR or mod(mdg4) reverse the locus-specific UR. These findings reveal that DNA replication can be delayed by a chromatin barrier and thus, uncover a critical role for architectural proteins in replication timing control. They also provide a biochemical link between ATP-dependent motor factors and the activity of insulators in regulation of gene expression and chromatin partitioning.

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“…Scale bars: 20 μm. b Volume quantification of Raeppli clones in the VNC at ALH0 (n = 7), ALH24 (n = 25), ALH48 (n = 21),ALH72 (n = 32) and ALH96 (n = 30 intimately joined from end to end 46,47 . Moreover, multiple copies of homologous chromosome also appear to be paired along their length in extreme case of endoreplication (polytene chromosomes).…”

Section: Cg Undergo Both Endoreplicative and Mitotic Eventsmentioning

confidence: 99%

An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche in Drosophila

et al. 2022

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Neural stem cells (NSCs) live in an intricate cellular microenvironment supporting their activity, the niche. Whilst shape and function are inseparable, the morphogenetic aspects of niche development are poorly understood. Here, we use the formation of a glial niche to investigate acquisition of architectural complexity. Cortex glia (CG) in Drosophila regulate neurogenesis and build a reticular structure around NSCs. We first show that individual CG cells grow tremendously to ensheath several NSC lineages, employing elaborate proliferative mechanisms which convert these cells into syncytia rich in cytoplasmic bridges. CG syncytia further undergo homotypic cell–cell fusion, using defined cell surface receptors and actin regulators. Cellular exchange is however dynamic in space and time. This atypical cell fusion remodels cellular borders, restructuring the CG syncytia. Ultimately, combined growth and fusion builds the multi-level architecture of the niche, and creates a modular, spatial partition of the NSC population. Our findings provide insights into how a niche forms and organises while developing intimate contacts with a stem cell population.

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Multi-Scale Organization of the Drosophila melanogaster Genome

Cited by 17 publications

References 156 publications

Genome-wide temperature-sensitivity of PcG regulation and reduction thereof in temperateDrosophila melanogaster

Genome-wide temperature-sensitivity of PcG regulation and reduction thereof in temperateDrosophila melanogaster

Drosophila SUMM4 complex couples insulator function and DNA replication timing control

An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche in Drosophila

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