Project description:In the present study we diagnosed cleaved transcripts in either healthy or virus infected plants, by sRNAome and metagenome of degraded mRNAs. We integrated the experimentally obtained data with publicly available annotations and we gained a deep insight into the parallel evolution of gene families and the transcriptional regulation mediated by miRNAs in Tomato. Gene expression is finely regulated to specific paralogues in gene families such as the squamosa-promoter binding protein-like, the Auxin Response Factor, the Class III homeodomain-leucine zipper, the Argonaute gene families, just to name a few. In some cases, different miRNA are expressed to target different copies of the same family. Size fractionated small RNA from total RNA extracts of Solanum lycopesicum cv. "Money Maker" were ligated to adapters, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina high throughput pyrosequencing. The kit used is TrueSeq Small RNA kit, Illumina. Please see www.illumina.com for details of the sequencing technology. PARE libraries were generated starting from Poly(A) fraction used for sRNA isolation. The protocol used have been previously described in German et al., 2009, Nature protocols. Please see www.illumina.com for details of the sequencing technology.
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:We analyzed gene expression changes in BEM46 knock out and over expression strains of Neurospora crassa in different developmental stages in concrete germinating conidiospores and mycelia.
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.
