Project description:We report the identification of small RNAs in undifferentiated (d0) and differentiating (d4) mouse embryonic stem (ES) cells using high-throughput sequencing. The goal of this study was to identify small RNAs involved in X-chromosome inactivation (XCI). We have identified a subset of small RNAs that are generated from transposon sequences and map to the X-chromosome, suggesting their involvement in transposon control on the inactivating X-chromosome.
Project description:RNA-interference (RNAi) refers to a growing class of gene silencing phenomena defined by a requirement for small RNAs of 20-32 nt and the action of the Argonaute (Ago) family of ribonucleases. We have previously identified developmentally regulated small RNAs, using Northern blot analysis, that are expressed during X-chromosome inactivation in differentiating female mouse ES cels. We sought to identify these small RNAs using deep sequencing. We identified small RNAs that align to retrotransposon sequences and are enriched on the X-chromosome. LINE elements have been proposed to act as way stations during X-inactivation for the spreading of silencing along the entire chromosome, and our findings suggest that LINE elements found on the X-chromosome may be enriched for small RNAs relative to the genome. These results suggest that RNAi pathways are involved in regulating LINE elements during X-inactivation and ES cell differentiation. We size-fractionated total RNA from differentiating female mouse ES cells (day 4) into 18-24 nt and 25-45 nt populations and sequenced each fraction separately using the 454 platform. We used a karyotypically stable 40XX female ES cell line (EL16.7) with one X each of 129 and M. castaneus origins: 129 x (M.castaneus x 129).
Project description:Small RNAs are emerging as important molecules for cross-species communication. Thanks to available and affordable sequencing technologies it is now possible to sequence small RNAs (sRNA-Seq) present in samples of interacting organisms. A first step when analyzing sRNA-Seq of two interacting species is to determine which sequences are being produced by which organism. Due to their small size (18-30), small RNAs could easily map to both host and parasite genomes. Here we produced data for Mus musculus intestinal epithelial cells treated with Extracellular Vesicles (EV) produced by the parasitic nematode Heligmosomoides bakeri.