Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
Copyright policy )Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5′ RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA- and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
[SDV]Life Sciences [q-bio], Post-Transcriptional, Nucleic Acid Denaturation, Quantitative Biology - Quantitative Methods, MESH: Sequence Tagged Sites*, Methods, Enterococcus faecalis, RNA Processing, Post-Transcriptional, Promoter Regions, Genetic, Quantitative Methods (q-bio.QM), Bacterial/genetics*, Sequence Tagged Sites, ta214, Bacterial, Chromosome Mapping, Genetik och genomik, MESH: Chromosome Mapping/methods*, MESH: Gene Expression Regulation, Enterococcus faecalis; Primary RNA; Processed RNA; Promoter; RNA degradation, [SDV] Life Sciences [q-bio], Processed RNA, processed RNA, RNA, Bacterial, RNA/methods*, MESH: Transcription Initiation Site, Transcription Initiation Site, 570, MESH: 5' Untranslated Regions/genetics*, ta221, MESH: Promoter Regions, Bioinformatics and Computational Biology, 610, MESH: Nucleic Acid Denaturation, Microbiology, Primary RNA, MESH: Sequence Analysis, RNA degradation, MESH: RNA, primary RNA, MESH: Genome, Quantitative Biology - Genomics, ta218, Genetic/genetics, ta113, Genomics (q-bio.GN), promoter, ta114, MESH: Enterococcus faecalis/genetics*, Sequence Analysis, RNA, MESH: Transcriptome, Promoter, Genetics and Genomics, Biomolecules (q-bio.BM), Gene Expression Regulation, Bacterial, MESH: RNA Processing, Mikrobiologi, Bioinformatik och beräkningsbiologi, Quantitative Biology - Biomolecules, FOS: Biological sciences, 5' Untranslated Regions, Transcriptome, Genome, Bacterial
[SDV]Life Sciences [q-bio], Post-Transcriptional, Nucleic Acid Denaturation, Quantitative Biology - Quantitative Methods, MESH: Sequence Tagged Sites*, Methods, Enterococcus faecalis, RNA Processing, Post-Transcriptional, Promoter Regions, Genetic, Quantitative Methods (q-bio.QM), Bacterial/genetics*, Sequence Tagged Sites, ta214, Bacterial, Chromosome Mapping, Genetik och genomik, MESH: Chromosome Mapping/methods*, MESH: Gene Expression Regulation, Enterococcus faecalis; Primary RNA; Processed RNA; Promoter; RNA degradation, [SDV] Life Sciences [q-bio], Processed RNA, processed RNA, RNA, Bacterial, RNA/methods*, MESH: Transcription Initiation Site, Transcription Initiation Site, 570, MESH: 5' Untranslated Regions/genetics*, ta221, MESH: Promoter Regions, Bioinformatics and Computational Biology, 610, MESH: Nucleic Acid Denaturation, Microbiology, Primary RNA, MESH: Sequence Analysis, RNA degradation, MESH: RNA, primary RNA, MESH: Genome, Quantitative Biology - Genomics, ta218, Genetic/genetics, ta113, Genomics (q-bio.GN), promoter, ta114, MESH: Enterococcus faecalis/genetics*, Sequence Analysis, RNA, MESH: Transcriptome, Promoter, Genetics and Genomics, Biomolecules (q-bio.BM), Gene Expression Regulation, Bacterial, MESH: RNA Processing, Mikrobiologi, Bioinformatik och beräkningsbiologi, Quantitative Biology - Biomolecules, FOS: Biological sciences, 5' Untranslated Regions, Transcriptome, Genome, Bacterial
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