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• W2971103222 startingPage "748780" @default.
• W2971103222 abstract "Currently, little is known about transcription termination in archaea. Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression, since faulty termination, for instance, can result in aberrant transcription of downstream genes. A systematic analysis of transcription termination sites (TTS) using RNAseq data has hitherto only been performed for two archaea, Methanosarcina mazei and Sulfolobus solfataricus. In this study, only regions directly downstream of annotated genes were analysed, and thus, only a part of the genome was investigated. Furthermore, the analysis was performed on reads originating from a total RNA fraction, representing a mixture of 39 ends resulting from transcription termination as well as from processing. Here, we developed a novel algorithm (Internal Enrichment-Peak Calling) that allows an unbiased, genome-wide identification of TTS independent of annotation. In addition, we treated the RNA fraction used for cDNA preparation with terminator exonuclease, to enrich original transcription termination ends. We employed this approach in the model archaeon Haloferax volcanii and identified 1,543 transcription termination sites. Approximately half of the termination sites were located in intergenic regions, and the remainder were found in coding regions. We determined distinct termination motifs for intergenic and coding regions. In intergenic regions, the termination signal consisted of stretches of Ts upstream of the termination, followed in most cases by a C at the termination site. Termination signals in coding regions differed, and they were prevalently associated with the motif AGATC, which was located directly downstream of the termination site. In vivo reporter gene tests of selected TTS confirmed termination at these sites. In several cases, more than one termination site was present downstream of a gene, resulting in transcripts with different lengths of the 39 untranslated region (39 UTR). The median 39 UTR length was 97 nucleotides, which is longer than the median 39 UTR length recently reported for the two archaea M. mazei and S. solfataricus and the bacterium Bacillus subtilis." @default.
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• W2971103222 date "2019-08-28" @default.
• W2971103222 modified "2023-09-23" @default.
• W2971103222 title "Unbiased Map of Transcription Termination Sites in Haloferax volcanii reveals manifold termination patterns" @default.
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