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:It is well understood how proteins regulate cell fate, both in normal development and disease. However, a substantial fraction of the genome is transcribed in a cell type- specific manner, producing long non-coding RNAs (lncRNA) rather than protein- coding transcripts. Here we systematically characterize transcriptional dynamics (both mRNA and lncRNA) during hematopoiesis and in hematological malignancies. We present de novo assembled transcriptome models and expression values for hematopoietic lncRNAs. We found lncRNAs to be regulated during differentiation and misregulated in disease. We assessed lncRNA function via an in vivo RNAi screen in a model of acute myeloid leukemia. With this approach, we identified several lncRNAs essential for leukemia maintenance, and found that a number act by promoting leukemia stem cell signatures. Leukemia blasts show a myeloid differentiation phenotype when these lncRNAs were depleted, and our data indicates that this effect is mediated via effects on the c-MYC oncogene.
