Project description:To investigate the role of translation in the decay of cytoplasmic lncRNAs, we performed RNA-Seq in WT and upf1-delta yeast cells, treated or not with CHX.
Project description:To investigate the role of translation in the decay of cytoplasmic lncRNAs, we performed RNA-Seq in WT and upf1-delta yeast cells, treated or not with CHX.
Project description:To analyze the effect of global translation initiation inhibition associated to glucose deprivation on cytoplasmic lncRNAs levels, we performed RNA-Seq using WT, xrn1-delta and upf1-delta cells grown in glucose-containing complete synthetic medium (CSM) and then shifted for 16 min in glycerol- and ethanol-containing medium. In parallel, control cells were maintained for the same time in glucose-containing CSM. For the WT strains, we also included a treatment of 15 min with CHX (100 μg/ml final concentration) or an equal volume of DMSO (Mock).
Project description:CHX is an inhibitor of translation elongation often used in ribosome profiling experiments. There is evidence that CHX treatment of cells may cause artefacts in the distribution of ribosomes on mRNAs. We investigate this possibility in S. pombe by performing ribosome profiling in the presence and absence of this drug.
Project description:To characterize the effect of cell cyle elongation on nascent transcription during zygotic genome activation (ZGA) of Xenopus laevis embryos, we microinjected 5-ethynyl uridine (EU) into 1-cell stage embryos and treated the embryos with 0.2 mg/ml of cycloheximide (CHX) to arrest them in interphase from 5 hpf to 7.5 hpf. Control and CHX-arrested embryos were collected for isolating total RNAs, followed by biotinylation using disulfide biotin azide via click reaction and purification of nascent transcripts using streptavidin beads. Libraries were constructed and sequenced on illumina NextSeq 500.
Project description:Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomere associated long ncRNAs (TERRA, telomeric repeat containing RNA) in mammalian and yeast cells but their function(s) remain(s) poorly characterized. Here, we report the existence in S. cerevisiae of several sense and antisense Cryptic Unstable Transcripts (CUTs) and Xrn1-sensitive Unstable Transcripts (XUT) initiating within the subtelomeric repeated region Y’. We show that the Y’ ncRNAs, subTERRA, are distinct from TERRA and are mainly destabilized by the general cytoplasmic and nuclear 5’- and 3’- RNA decays in a sense-dependent manner. subTERRA transcription is mainly sustained by RNAPII and subTERRA accumulate preferentially during the G1/S transition and in C-terminal rap1 mutants independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomere length, loss of telomeric clustering in mitotic cells, indicating that subTERRA might compete with factors involved in telomere elongation, tethering and/or clustering. We propose that subtelomeric RNAs expression links telomere maintenance with RNA degradation pathways. Exmination of two yeast mutants for RNA decay.
Project description:To investigate the role of cytoplasmic helicases in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells.