Project description:At genome-wide level, loss of OsChz1 causes mis-regulation of thousands of genes and broad alterations of nucleosome occupancy as well as reduction of H2A.Z-enrichment within chromatin along the gene body and at TSS. While OsChz1 associates with chromatin regions enriched of repressive histone marks (H3K27me3 and H4K4me2), its loss does not affect the genome landscape of DNA methylation.
Project description:Plasmodium falciparum malaria remains a global health challenge and causes a significant number of deaths in tropical and subtropical countries annually. Merozoite surface proteins, located of the surface of the invasive stage of the parasite, are targets of immunity and have been explored as vaccine candidates. Here we removed the highly abundant surface protein MSP2 by CRISPR Cas9 to study the role of this protein. RNA samples were taken of schizonts stage parasites to examine any changes at the transcriptome level as a consequence of MSP2 KO. P. falciparum cultures were centirfuged before resuspension in Trizol and RNA purification performed using chloroform in combination with RNeasy Kit (Qiagen). DNAseing was performed to ensure absence of genomic DNA. RNA sequencing of the schizont stage transcriptome of Pf3D7 MSP2 KO and Pf3D7 WT was performed using the Illumina total RNA with Ribo Zero plus for library preparation and sequenced on the NovaSeq 6000 platform with 2×150 bp paired end reads.
Project description:Background/Objectives: Radiotherapy (RT) is a fundamental treatment for brain tumors but often leads to long-term neurotoxicity, partly caused by microglial dysfunction. In this study, we used long-read RNA sequencing (LR-RNA-seq) to map the isoform-specific transcriptome of human microglial HMC3 cells after RT exposure Methods: HMC3 Microglial cell line was treated with standard radiotherapy and, after RNA extraction and library preparation, long reads RNAseq has been carried out. Further bioinformatic analyses allowed to investigate on the isoform switching pattern after radiation therapy exposure. Results: Gene-level analysis found 591 differentially expressed genes, with increased activity in PI3K/AKT signaling pathways and decreased translation-related processes. Isoform-level analysis uncovered 827 significant isoform switching events across 420 genes, often involving shifts from protein-coding transcripts to non-coding variants. Functional annotation showed that most isoform switches resulted in the loss of open reading frames and protein domains, especially in ribosomal proteins and translation machinery components
