Project description:Widely transcribed and compact genomes face the major challenge of coping with frequent overlapping or concurrent transcription events. Efficient and timely transcription termination is crucial to control pervasive transcription. In yeast, RNA polymerase II (RNAPII) termination mainly occurs via two pathways, one generating mRNAs and one dedicated to non-coding RNAs, and is triggered by signals that are recognized on the nascent RNA by a specific complex. We describe here a novel pathway of RNAPII transcription termination that is triggered by the binding to the DNA of the transcriptional activator Reb1p. We show that termination follows road-block induced pausing of RNAPII and requires ubiquitylation of RNAPII. The released RNAs are rapidly degraded, which defines a new class of cryptic unstable transcripts. We show that Reb1p-dependent termination can prevent transcriptional interference. This work reveals a novel role for Reb1p and a new paradigm for preserving the functional integrity of nucleosome free regions.
Project description:The present study aimed to identify the persistent molecular changes occurring in Atlantic Salmon salmon (Salmo salar) eggs after 24h exposure to high concentrations (5000 mg/L) of road salt at fertilization. Atlantic Salmon (Salmo salar) eggs after fertilization were exposed to high concentrations (5000 mg/L) of road salt for 24 h and used for gene expression analysis.
Project description:The present study aimed to identify the persistent molecular changes occurring in Atlantic Salmon salmon (Salmo salar) eggs after 24h exposure to high concentrations (5000 mg/L) of road salt at fertilization.
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
Project description:Single-cell RNA-seq suffers from unwanted technical variation between cells, caused by its complex experiments and shallow sequencing depths. We present GTestimate a new normalization method based on the Good-Turing estimator, which improves upon conventional methods by accounting for unobserved genes. We validate GTestimate using new ultra-deep sequencing data, generated via a novel cell targeted PCR-amplification approach, and show substantial improvements in cell-cell distance estimation and downstream results.
