Project description:Based on our previous O-Search strategy, we have developed a new search method, O-Search-Pattern, to process searching for O-glycopeptide. In comparison of analyzing our human serum dataset generated from optimized energy, our new method can generate more GPSMs glycopeptide sequences than currently state-of-the-art search tools.
Project description:The goal of this study is to identify the effect of inhibition of Aurora-A kinase activity on gene expression and RNA splicing. The perturbation of Aurora-A is well known to affect cell cycle distribution. Therefore, we coupled the inhibition of Aurora-A with cell synchronization procedure in order to avoid the indirect effect of cell cycle perturbation on splicing changes. The mRNA -seq libraries were prepared and subjected to paired-end sequencing on Illumina HiSeq 2500 lanes. Differential gene expression and splicing analysis were carried using the edgeR tool and VAST-tools respectively. The RNA seq analysis identified that pharmacological inhibition of Aurora-A affects alternative splicing of 505 genes while having a marginal effect on gene expression. Overall our work identified Aurora-A as a novel splicing kinase and for the first time, describes a broad role of Aurora-A in regulating alternative splicing.
Project description:Tools to edit DNA methylation in a targeted manner are vital for clarifying the causal relationships between DNA methylation and its function, as well as for plant breeding and gene therapy; non-specific tools that induce genome-wide DNA methylation changes are valuable for the creation of novel epialleles and performing large-scale screens. Here, by constructing dCas9 fusions to a panel of effectors and cofactors, we uncovered a range of tools for editing DNA methylation, including five tools for DNA methylation and six tools for DNA demethylation. Our tools show diversity of performance in terms of specificity and efficiency, offering either the capacity to target editing DNA methylation or the ability to edit DNA methylation at the genome-wide level. Remarkably, DNA methylation edited by these tools was inherited in the absence of transgene. These versatile tools pave the way for diverse applications in DNA methylation editing and hold promise for advancing plant epigenetic breeding.
Project description:State-of-the-art algorithms for m6A detection and quantification via nanopore direct RNA sequencing have been continuously developed, little is known about their capacities and limitations, which makes a comprehensive assessment in urgent need. Therefore, we performed comprehensive benchmarking of 10 computational tools relying on current-based and base-calling “errors” strategies for m6A detection by nanopore sequencing.