Project description:Recently a dRNA-Seq study with Haloferax volcanii has been published that led to the discovery of nearly 2800 novel transcription start sites for non-coding RNAs. However, the dRNA-Seq results are confined to the 5'-end of transcripts and does not contain any length information. Therefore, a major aim of the present RNA-Seq study was the elucidation of the lengths of the novel non-coding RNAs. A second aim was to analyze the operon structure of protein-coding genes. The recent dRNA-Seq study was confined to cultures grown under optimal conditions. It was revealed that less than half of the protein-coding genes were expressed. Therefore, the present RNA-Seq study used cultures grown under four different conditions to identify further transcripts of protein-coding genes that are not needed under optimal conditions. RNA samples from the four conditions were mixed prior to the RNA-Seq analyses (mixed RNA-Seq). The results allowed to characterize the sum of transcriptomes of H. volcanii under four conditions. Northern blot analyses were used to characterize selected examples in detail. Many important results were obtained, including the length determination of all transcripts, a genome-wide operon analysis, verification of a high fraction of antisense RNAs, and the discovery that 30% of all protein-coding transcripts have overlapping 3'-UTRs.
Project description:Transcriptome analysis based on total RNA-seq was performed on different Haloferax volcanii strains including mutants strains iincluding deletion strains for two small proteins. Differential expression analysis showed that a subset of genes were found to be regulated in the absence of the small proteins.
Project description:Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii
Project description:Purpose: The Haloferax volcanii ∆tfeB strain provided a unique opportunity to study a putative role of TFEβ in the regulation of gene expression. Results: The deletion of the tfeB gene in H. volcanii results in the aberrant expression of approximately one third of all genes, consistent with its function as a basal transcription initiation factor. Interestingly, tfeB deletion particularly affects foreign genes including a prophage region. Conclusions: Our results confirm the dual function of TFE as basal factor and regulator of transcription
