Project description:To analyse the genome-wide impact of inactivation of the ATAC or SAGA coactivator complexes on RNA polymerase II (Pol II) transcription, we purified newly synthesized RNA from mutant mouse embryonic stem (ES) cell lines in which subunits of ATAC (Yeats2, Zzz3) or SAGA (Supt7l) are inactivated or depleted. We also performed this analysis in mutant cell lines in which a subunit (Tada3) of the shared histone acetyltransferase activity of these two complexes is depleted. Newly synthesized RNA was purified following the 4sU labelling method (more details in extract protocol). For two wildtype samples, the total RNA input was also analysed.
Project description:24 polypeptides (21 amino acids long) were synthesized and mixed as a substrate library. Then, these substrates were acetylated by acetyl-CoA
Project description:We developed a method to deconvolute decays of m6A mRNAs and their unmethylated isoforms from newly synthesized total RNAs across the transcriptome to study the effects of m6A modification on decays of not only the m6A-modified RNA pool but also the unmehnylated isoform pool.
Project description:Using a newly-developed workflow for quantitative newly synthesized proteome analysis (QuaNPA), featuring automated sample processing and multiplexed DIA (plexDIA) analysis, changes in the newly synthesized proteome of IFN-gamma treated Hela cells were monitored over time.
Project description:Extrachromosomal circular DNA (eccDNA) is generated from chromosomal templates to play multiple biological roles in different types of cells. However, it is unknown whether viral infection could cause cells to generate viral non-genomic circular DNA (vcDNA). Here, we demonstrated for the first time that Varicella zoster virus (VZV)-infected cells and tissues generate an abundance of vcDNA. We developed a Cre/loxP-mediated in vitro vcDNA/eccDNA synthesizing method. We transfected the synthesized vcDNA into HEK293T cells, RNA-seq analysis indicated that VZV vcDNA 76509|75569 effectively mitigated the innate immune response that was stimulated by linear VZV 75569-76509 DNA.