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Drosophila embryo extract assisted in vitro chromatin assembly in presence of foldamer

ABSTRACT: Drosophila preblastoderm embryo extract assisted chromatin assembly with or without 16mer DNA mimic. Pull down of chromatin fiber to reveal chromatin binders in the system.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

SUBMITTER: Axel Imhof

LAB HEAD: Axel Imhof

PROVIDER: PXD039966 | Pride | 2023-09-07

REPOSITORIES: Pride

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			Action	DRS
	Groups_LFQ.txt	Txt
	Ref3346_VK_01_20200821.raw	Raw
	Ref3346_VK_02_20200821.raw	Raw
	Ref3346_VK_03_20200821.raw	Raw
	Ref3346_VK_04_20200821.raw	Raw

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1 - 5 of 66

Publications

DNA mimic foldamers affect chromatin composition and disturb cell cycle progression.

Kleene Vera V Corvaglia Valentina V Chacin Erika E Forne Ignasi I Konrad David B DB Khosravani Pardis P Douat Céline C Kurat Christoph F CF Huc Ivan I Imhof Axel A

Nucleic acids research 20231001 18

The use of synthetic chemicals to selectively interfere with chromatin and the chromatin-bound proteome represents a great opportunity for pharmacological intervention. Recently, synthetic foldamers that mimic the charge surface of double-stranded DNA have been shown to interfere with selected protein-DNA interactions. However, to better understand their pharmacological potential and to improve their specificity and selectivity, the effect of these molecules on complex chromatin needs to be inve ...[more]

PMID: 37650653

Similar Datasets

DNA mimicking 32mer foldamers interfere with in vitro chromatin assembly in drosophila embryo extract

Project description:Systematic study of the influence of different concentrations of DNA-mimicking foldamers (32mer) on the chromatin-bound bound proteome using an in vitro chromatin assembly extract

2023-09-07 | PXD040158 | Pride

Subcellular fractionation of Drosophila S2 cells upon foldamer treatment

Project description:The use of synthetic chemicals to selectively interfere with chromatin and the chromatin-bound proteome represents a great opportunity for pharmacological intervention. Recently, synthetic foldamers that mimic the charge surface of double-stranded DNA have been shown to interfere with selected protein-DNA interactions. However, to better understand their pharmacological potential and to improve their specificity and selectivity their effect on complex chromatin needs to be investigated. We therefore systematically studied the influence of these DNA-mimicking foldamers on the chromatin-bound bound proteome using an in vitro chromatin assembly extract. Our studies revealed an efficient interference with the chromatin-associated origin recognition complex that plays an important role in initiating eukaryotic chromatin replication. This interference is mediated by a strong direct interaction between the foldamers and the origin recognition complex and has an effect in tissue culture cells where the addition of foldamer led to an S-phase arrest. Foldamers that mimic double-stranded nucleic acids thus emerge as a powerful tool with designable features to alter chromatin assembly and selectively interfere with biological mechanisms.

2023-09-04 | PXD042288 | Pride

Pulldown with DNA mimicking foldamers in preblastoderm Drosophila embryo extract

Project description:16mer and 32mer biotinylated DNA mimics (“foldamers”) bound to streptavidin beads, AP-MS after 1h incubation in Drosophila preblastoderm embryo extract.

2023-09-07 | PXD040157 | Pride

Divergent evolutionary strategies for selective sex chromosome regulation in Drosophila

Project description:The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX sites are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a non-productive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a low-diffusion chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of similar components.

2021-06-23 | PXD023747 | Pride

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA-binding winged helix domainThe histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA-binding winged helix domain

Project description:The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrated that a winged helix domain at the N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A to unmethylated CpG islands (CGIs) genome wide. Mutation of the essential amino acids completely abrogates the enrichment of KAT6A at CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases

2023-01-14 | PXD034833 | Pride

IRF2BP2 counteracts the ATF7/JDP2 heterodimer to prevent inflammatory overactivation in AML cells

Project description:Acute myeloid leukemia (AML) is a hematological malignancy characterized by the abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator that has been implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that in AML cells IRF2BP2 interacts with the transcriptional heterodimer ATF7/JDP2, which is involved to activate inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene activating function. Loss of IRF2BP2 leads to the overactivation of inflammatory pathways, resulting in immediate cell death. Our findings suggest that a delicate balance of activating and repressive transcriptional mechanisms establishes a pro-oncogenic inflammatory set-up in AML cells, and that manipulation of the ATF7/JDP2-IRF2BP2 regulatory axis may offer a potential vulnerability for AML treatment. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.

2024-05-16 | PXD041817 | Pride

Identification of Snf2L-associated chromatin remodeling complex subunits in Plasmodium falciparum

Project description:ATP-dependent chromatin remodeling enzymes re-position and evict nucleosomes at specific genomic loci and therefore are essential regulators of all DNA dependent processes. They act in the context of large multiprotein complexes. The malaria-causing parasite Plasmodium falciparum (Pf) possesses a reduced set of chromatin remodeling enzymes, which are highly divergent, and no associated complex subunits are known. Within a detailed characterization of the ISWI-type remodeler PfSnf2L (PF3D7_1104200), potential interactors were identified. The protein was tagged endogenously in the parasite and co-immunoprecipitated. Subsequent LC-MS/MS analysis provided a list of specific protein interactors with a strong link to chromatin organization including nucleosome assembly factors, transcription factors as well as Plasmodium-specific uncharacterized proteins. The results suggest a functional role of PfSnf2L in nucleosome assembly and transcription regulation and point towards novel Plasmodium-specific chromatin remodeling complexes.

2024-10-17 | PXD041155 | Pride

ANP32B is a macroh2A histone chaperone

Project description:Interaction proteomics in cell extracts on tagged macroH2A, either expressed in cells or using recombinant dimers with H2B.

2023-10-24 | PXD045696 | Pride

Interaction network of the Cysteine Repeat Modular protein complex of Toxoplasma gondii

Project description:Apicomplexa are obligate intracellular parasites. While most species are restricted to specific hosts and cell types, Toxoplasma gondii can invade every nucleated cell derived from warm-blooded animals. This broad host range suggests that this parasite can recognize multiple host cell ligands or structures, leading to the activation of a central protein complex, which should be conserved in all apicomplexans. During invasion, the unique secretory organelles (micronemes and rhoptries) are sequentially released and several micronemal proteins have been suggested to be required for host cell recognition and invasion. However, to date only few micronemal proteins have been demonstrated to be essential for invasion. Cysteine Repeat Modular Proteins (CRMPs) are a family of apicomplexan specific proteins. In Toxoplasma gondii, two CRMPs are present in the genome. The Kringle domain containing protein (CRMPA) and the GCC2 GCC3 domain containing protein (CRMPB). Here we demonstrate that both proteins form a complex that contains additional micronemal proteins. Disruption of this complex results in a block of rhoptry secretion and parasites being unable to invade the host cell. In conclusion, this complex is a central invasion complex conserved in all apicomplexans.

2023-01-30 | PXD035654 | Pride

JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila

Project description:In Drosophila the chromosomal kinase JIL-1 is responsible for most interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from acquiring heterochromatic marks, like dimethylated histone H3K9 (H3K9me2) and HP1. Here, we show that JIL-1’s targeting to chromatin depends on a PWWP domain-containing protein JASPer (JIL-1 Anchoring and Stabilizing Protein). The JASPer-JIL-1 (JJ)-complex is the major form of the kinase in vivo and is targeted to active genes and telomeric transposons via binding of the PWWP domain of JASPer to H3K36me3 nucleosomes, where the complex modulates the transcriptional output. JIL-1 and JJ-complex depletion in cycling cells lead to small changes in H3K9me2 distribution at active genes and telomeric transposons. Finally, we identify several interactors of the endogenous JJ-complex and propose that JIL-1 not only prevents heterochromatin formation but also coordinates chromatin-based regulation in the transcribed part of the genome.

2019-10-09 | PXD012790 | Pride

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