Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1313088 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2-cyclopropene containing oleic acid analogue, as a bioorthogonal probe. We here show that this lipid can be readily taken up by dendritic cells without toxic side-effects, and that it can subsequently be visualised in live cells using an inverse electron-demand Diels-Alder (IEDDA) reaction with quenched tetrazine fluorophores. Furthermore, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper-catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging. Aside from lipid imaging, the uptake and protein modification of sterculic acid can be studied in live cells via chemical proteomics.
2023-04-28 | PXD033831 | Pride
Project description:We report proteomic data from living constructs assembled entirely from human cells covalently tethered via interfacial bridges with a glycosaminoglycan. Here, bioorthogonal azide groups are installed in cell surface glycoproteins via metabolic glycoengineering, allowing for catalyst-free click-chemistry coupling with a complementary hyaluronan biopolymer. This cell-to-cell tethering strategy enables the use of human cells as active crosslinkers and main building blocks of macroscale, tissue-dense living materials. In light of this, we explore the secretome profile of these constructs following a maturation period of 3 days. Bioinformatic analysis and matrisome annotation revealed the presence of a wide range of proteins related to extracellular matrix organization, assembly and remodeling, as well as proteins involved in cell signaling and migration. These findings highlight the potential of this cell-to-cell tethering strategy for creating nascent living tissue mimetics that can be explored in tissue engineering and regenerative medicine endeavors.
2024-07-25 | PXD042343 | Pride
Project description:Chemical modification of histones dynamically regulates gene transcription and is closely related to disease pathogenesis including cancer. Targeting epigenome is thus a promising strategy for cancer chemotherapy. Here we report a novel histone acetylation catalyst BAHA-LANA-PEG-CPP44 that can intervene into cancer epigenome. The catalyst selectively entered leukemia cells, bound to chromatin, and acetylated endogenous histones, especially at H2BK120, in a HAT-independent manner. The catalytic histone acetylation attenuated chromatin binding of negative elongation factor E (NELFE), an RNA polymerase II pausing factor, and reprogramed transcription profile in leukemia cells. The in-cell chemical catalysis retarded proliferation of leukemia cells and reduced their tumorigenic potential in mice. Our catalyst is orthogonal to cancer epigenetic drugs targeting histone-modifying enzymes and may lead to a novel anti-cancer strategy.
2024-12-04 | GSE259437 | GEO
Project description:The RSC chromatin remodeling complex recruits the cohesin loader Scc2-Scc4 by a direct protein interaction. Nucleosome-free DNA is the substrate for the cohesin loading reaction.
2019-03-19 | GSE117881 | GEO
Project description:5-Hydroxymethyluracil (5hmU) is a thymine modification existing in the genomes of a number of living organisms. The post-replicative formation of 5hmU occurs via hydroxylation of thymine, which can be mediated by the ten-eleven translocation (TET) dioxygenases in mammalian and J-binding proteins (JBPs) in protozoan genomes, respectively. In addition, 5hmU also can be generated through oxidation of thymine by reactive oxygen species or from deamination of 5hmC by activation-induced cytidine deaminase (AID) or APOBEC family enzymes. While the biological roles of 5hmU have not been fully explored, identifying its genomic location will assist in elucidating its functions. Herein, we report a method of enzyme-mediated bioorthogonal labeling to selectively enrich genomic regions containing 5hmU. 5hmU DNA kinase (5hmUDK) was utilized to selectively install an azide group or alkynyl group into the hydroxyl group of 5hmU followed by incorporation of the biotin linker through click chemistry and capture of 5hmU-containing DNA fragments via streptavidin pull-down. The enriched fragments were applied to deep sequencing to map the location of 5hmU. With this established enzyme-mediated bioorthogonal labeling strategy, we achieved the genome-wide mapping of 5hmU in Trypanosoma brucei (T. brucei) genomes. The method described here will allow for a better understanding of the functional roles and dynamics of 5hmU in genomes
2021-07-11 | GSE179809 | GEO
Project description:Bacteroides thetaiotaomicron, one of the most eminent representative gut commensal Bacteroides species, is able to use the L-fucose in host-derived and dietary polysaccharides to modify its capsular polysaccharides and glycoproteins through a mammalian-like salvage metabolic pathway. This process is essential for the colonization of the bacteria and for symbiosis with the host. However, despite the importance of fucosylated proteins (FGPs) in Bacteroide thetaiotaomicron, their types, distribution, and functions remain unclear. In this project, the effects of different saccharide (glucose, corn starch, mucin, and fucoidan) nutrition conditions on FGP expressions and fucosylation are investigated using a chemical biological method based on metabolic labeling and bioorthogonal reaction. According to the results of label-free quantification, 559 FGPs (205 downregulated and 354 upregulated) are affected by the dietary conditions. Of these differentially expressed proteins, 65 proteins show extremely sensitive fucosylation levels. Specifically, the fucosylation of the chondroitin sulfate ABC enzyme, Sus proteins, and cationic efflux system proteins varies significantly upon the addition of mucin, corn starch, or fucoidan. Moreover, these polysaccharides can trigger an appreciable increase in the fucosylation level of the two-component system and ammonium transport proteins. These results highlight the efficiency of the combined metabolic glycan labeling and bio-orthogonal reaction in enriching the intestinal Bacteroide glycoproteins. Moreover, it emphasize the sensitivity of Bacteroides fucosylation to polysaccharide nutrition conditions, which allows for the regulation of bacterial growth.
2022-02-08 | PXD023756 | Pride
Project description:We report here a Cu-catalyzed azide-alkyne-thiol reaction forming thiotriazoles as the major by-product under widely used bioorthogonal protein labelling “click” conditions. The development of Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) had tremendous impact on many biological discoveries. However, the considered chemoselectivity of CuAAC is hampered by high reactivity of cysteine free thiols yielding thiotriazole protein conjugates. The reaction by-products generate false positive protein hits in “functional” proteomic studies. The reported detail investigation of conjugates between chemical probes containing terminal alkynes, azide-tags and cell lysates reveals formation of thiotriazoles, which can be readily detected by in-gel fluorescence scanning or after peptide and protein enrichment by MS-based proteomics. The produced fluorescent bands or enriched proteins may not result from the important enzymatically driven reaction and can be falsely assigned as hits. This study provides a complete list of the most common background proteins. The knowledge of this previously overlooked reactivity now leads to improved experimental design. Here, we present modified CuAAC conditions, which avoids the undesired product formation and diminishes the background.
2024-01-12 | PXD043402 | Pride
Project description:Histone variant H2A.Z-containing nucleosomes are incorporated at most eukaryotic promoters. This incorporation is mediated by the conserved SWR1 complex, which replaces histone H2A in canonical nucleosomes with H2A.Z in an ATP-dependent manner. Here, we show that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosomes containing one, two, or no H2A.Z molecules. SWR1-catalyzed H2A.Z replacement in vitro occurs in a stepwise and unidirectional fashion, one H2A.Z-H2B dimer at a time, producing heterotypic nucleosomes as intermediates and homotypic H2A.Z nucleosomes as end products. The ATPase activity of SWR1 is specifically stimulated by H2A-containing nucleosomes without ensuing histone H2A eviction. Remarkably, further addition of free H2A.Z-H2B dimer leads to hyperstimulation of ATPase activity, eviction of nucleosomal H2A-H2B and deposition of H2A.Z-H2B. These results suggest that the combination of H2A-containing nucleosome and free H2A.Z-H2B dimer acting as both effector and substrate for SWR1 governs the specificity and outcome of the replacement reaction.
2010-10-12 | GSE24618 | GEO
Project description:Chemical modification of histones dynamically regulates gene transcription and is closely related to disease pathogenesis including cancer. Targeting epigenome is thus a promising strategy for cancer chemotherapy. Here we report a novel histone acetylation catalyst BAHA-LANA-PEG-CPP44 that can intervene into cancer epigenome. The catalyst selectively entered leukemia cells, bound to chromatin, and acetylated endogenous histones, especially at H2BK120, in a HAT-independent manner. The catalytic histone acetylation attenuated chromatin binding of negative elongation factor E (NELFE), an RNA polymerase II pausing factor, and reprogramed transcription profile in leukemia cells. The in-cell chemical catalysis retarded proliferation of leukemia cells and reduced their tumorigenic potential in mice. Our catalyst is orthogonal to cancer epigenetic drugs targeting histone-modifying enzymes and may lead to a novel anti-cancer strategy.
2024-12-04 | GSE259436 | GEO
Project description:Following the identification of the 80S ribosome as a putative target of the tetracycline analogs Col3 and doxycycline, we next sought to identify the precise binding sites for these tetracyclines within the ribonucleoprotein complex. We incorporated dual bioorthogonal handles into tetracycline-based probes, containing both a photoactive diazirine to enable direct probe crosslinking to the human ribosome and an azide handle to allow selective enrichment of crosslinked biomolecules via copper-free click chemistry. The Col-3 and doxycycline probes were each incubated with A375 cells, followed by irradiation at 365 nm to induce photolysis of the diazirine moiety and subsequent crosslinking to adjacent ribosomal components. Pulldown and RNA-Seq of the crosslinked RNAs from our experiments were used to identify enrichment of reverse transcription (RT) stops at ribosomal RNA sites caused by local crosslinking of our probes. This RNA-Seq based RT stop enrichment analysis was compared to results using an non-specific aniline control probe and untreated controls.
2018-08-30 | E-MTAB-7147 | biostudies-arrayexpress