Project description:We report DNA content of yeast strains that are growing asynchronously or treated with hydroxyurea (HU). We selected two strains from our Epi-Decoder library, that are wild-type but have BAR1 or RPO21 TAP-tagged. This reveals that HU-treated samples have peaks in DNA content representing stalled replication forks.
2018-07-16 | GSE114290 | GEO
Project description:Epi-Decoder in GCG1/SUT098 perform in Marquardt lab
| PRJNA1055500 | ENA
Project description:Epi-Decoder in GCG1/SUT098 perform in Fred van Leuween lab
Project description:Transcription of transfer-RNA genes (tDNAs) by RNA Polymerase III (RNAPIII) is tightly regulated upon nutrient and stress signaling. However, identical tDNAs across the genome are differentially regulated, suggesting regulation at the chromatin-level plays a crucial role. This study aimed to identify such mechanisms by decoding the chromatin proteome of a native tDNA locus in yeast using Epi-Decoder. The tDNA proteome showed dynamic binding of both known and unknown factors upon nutrient stress, including Ykr011c (Fpt1), a protein of unknown function. Decoding the tDNA proteome in the absence of Fpt1 revealed a role in the eviction of RNAPIII during repressed transcription. Fpt1 exclusively occupied RNAPIII-regulated genes, but cells without Fpt1 also showed impaired shutdown of RNAPII-transcribed ribosome biogenesis genes in changing nutrient conditions. These findings provide support for a novel chromatin-associated regulator required for proper RNAPIII assembly that also tunes an integrated physiological response to changing metabolic conditions.
Project description:we examined the glycoproteomics of N-glycosylation in untreated LNCaP (NC), ST-EPI, LT-EPI, ST-ENZ, and LT-ENZ groups using Tandem Mass Tag (TMT) labels by nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS).LNCaP-NC, SP-EPI, SP-ENZ, LP-EPI, and LP-ENZ cells each with two biological replicates were used for glycoproteomics analysis.
Project description:Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage ΦKZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.
Project description:Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage ΦKZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.