Project description:Y-box binding factor 1 (YB1) has been associated with prognosis in many tumor types. Reduction of YB-1 inhibits tumor cell growth in vitro and in vivo Total RNA was isolated from A549, MCF7 and HCT116 tumor cell lines following 48hr treatment with 5nM Yb1 siRNA
Project description:We performed poly(A)+ stranded RNA-seq of a panel of human primary or transformed cell lines (BJ, IMR90, MRC5, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep). In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same cell lines using bs-ATLAS-seq (E-MTAB-10895). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.
Project description:We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of human full-length LINE-1 elements (L1). The approach is focused on the youngest family (L1HS), but it also catches a significant fraction of L1PA2 to L1PA8 elements. This was performed in a panel of 12 human primary or transformed cell lines (BJ, IMR90, MRC5, H1, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep).
Project description:We perform polyA independent deep sequencing of chromatin associated primary transcripts across three different cell lines to obtain a global view on in vivo microRNA processing. We use these data to define a MicroProcessing Index (MPI), to quantify the cleavage efficiency of the Microprocessor complex. Hallmarks of efficient Drosha-mediated processing are confirmed by means of deep sequencing of chromatin-associated transcripts upon Drosha knockdown. Our results suggest that both sequence features and thermodynamic properties, e.g. secondary structure of the regions flanking the pre-miRNA hairpins are determinants for efficient processing. Our data furthermore enables us to observe endogenous microprocessor cleavage sites at nucleotide resolution. This analysis reveals the presence of non-canonical processing events occurring one helical turn distal of most efficiently cleaved miRNA precursors. We performed polyA independent deep sequencing of the chromatin-isolated RNA fraction for 5 samples: 2 replicates in HeLa cells, 1 Drosha knock down in HeLa cells, 1 sample for A549 cells and 1 sample for HEK293 cells. We also performed deep sequencing of the small RNA fraction in the same cell lines.