Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins

Chetverina, Darya; Vorobyeva, Nadezhda E.; Mazina, M. Yu.; Fab, Lika V; Lomaev, D. V.; Golovnina, Alexandra; Mogila, Vladic; Georgiev, Pavel; Ziganshin, Rustam H.; Erokhin, Maksim

doi:10.1007/s00018-022-04383-2

Cited by 11 publications

(44 citation statements)

References 135 publications

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“…Moreover, recent immunoa nity puri cation of the Combgap interactome coupled with high throughput mass spectrometry (IP/LC-MS) revealed statistically signi cant enrichment of Su(Hw) and its partners Mod(mdg4) and CP190, further supporting the existence of protein-protein interaction between Su(Hw) and Combgap 19 .…”

Section: Su(hw) Enables the Indirect Binding Of Combgap To Chromatinmentioning

confidence: 87%

“…The following previously described ChIP-Seq data for the S2 Drosophila cell line were used: H3K27me3 23 (GSE41440), Combgap 19 (GSE200213), Su(Hw) 17 (GSE30740), Rpb3, NELF-A 21 (GSE156847). For the ovaries of egg chamber stages 1-8 we used the following the ChIP-Seq and MNase-Seq data previously described: ChIP-Seq for Su(Hw), Brm, ISWI, Mi2, CHD1 17 (GSE168894) and MNase-Seq data for follicular cells from egg chambers stages 1-8 26 (NCBI-SRA BioProject SRP057811).…”

Section: Chip-seq Chip-seq Analysismentioning

confidence: 99%

“…For the co-immunoprecipitations and ChIP-Seq experiments we used previously described antibodies against Combgap 19 , Su(Hw) 17 and Su(Hw) LOF ovaries. The image was generated using pyGenomeTracks 59 .…”

Section: Antibodiesmentioning

confidence: 99%

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Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Vorobyeva

Краснов

Erokhin

et al. 2023

Preprint

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Insulator-binding proteins (IBPs) play a critical role in genome architecture by forming and maintaining contact domains. While the involvement of several IBPs in organising chromatin architecture in Drosophila has been described, the specific contribution of the Suppressor of Hairy wings (Su(Hw)) IBP to genome topology remains unclear. In this study, we provide evidence for the existence of long-range interactions (LRIs) between Su(Hw) and Combgap ChIP-Seq peaks, reflected in the indirect binding of these proteins to chromatin in ChIP experiments. Loss of Su(Hw) binding results in the disappearance of Su(Hw)-Combgap LRIs and a decrease in spatial self-interactions among a subset of Su(Hw) sites. Our findings suggest that Su(Hw)-Combgap LRIs are associated with active chromatin rather than Polycomb-directed repression. Furthermore, we observe that the majority of transcription start sites that are down-regulated upon loss of Su(Hw) binding to chromatin are located within 2 kb of Combgap peaks and exhibit Su(Hw)-dependent changes in Combgap and transcriptional regulators’ binding.

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Section: Su(hw) Enables the Indirect Binding Of Combgap To Chromatinmentioning

confidence: 87%

Section: Chip-seq Chip-seq Analysismentioning

confidence: 99%

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Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Vorobyeva

Краснов

Erokhin

et al. 2023

Preprint

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“…Since ~50% of TET peaks colocalized with PRC1 and ph knockdown reduced TET binding, TET could be recruited to chromatin together with PRC1 by the combinatorial action of PcG recruiters such as GAF or Cg, which are strong PRC1 interactors ( 79 ). However, other determinants could be involved.…”

Section: Discussionmentioning

confidence: 99%

Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity

Gilbert,

Renaud,

Teste

et al. 2024

Sci. Adv.

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Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila , whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS.

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“…Moreover, the involvement of insulator proteins in PcG function becomes more and more apparent. They are involved in long-range spreading of H3K27me3 (Heurteau et al 2020), interact with many of the PcG recruiter proteins (Chetverina et al 2022a), and are often located next to PREs (Hagstrom et al 1997; Mihaly et al 1997; Gruzdeva et al 2005; Kyrchanova et al 2018) whose function they are able to enhance and even induce (Erokhin et al 2021; Chetverina et al 2022b). Binding sites for insulator proteins appear to evolve more swiftly than those of other transcription factors (Nègre et al 2010).…”

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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Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins

Cited by 11 publications

References 135 publications

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity

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

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