ArticleMolecular systems biology2009
Prevalence of transcription promoters within archaeal operons and coding sequences.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- The chromatin landscape of the histone-possessingGenome research · 2025Article
- A conserved transcription factor controls gluconeogenesis via distinct targets in hypersaline-adapted archaea with diverse metabolic capabilities.PLoS genetics · 2024Article
- The chromatin landscape of the euryarchaeon Haloferax volcanii.Genome biology · 2023Article
- The landscape of the histone-organized chromatin of Bdellovibrionota bacteria.bioRxiv : the preprint server for biology · 2023Article
- An archaeal histone-like protein regulates gene expression in response to salt stress.Nucleic acids research · 2021Article
- The Complex Transcriptional Landscape of Magnetosome Gene Clusters in Magnetospirillum gryphiswaldense.mSystems · 2021Article
- Article
- StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.Frontiers in bioinformatics · 2021Review
- The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances.Microorganisms · 2020Article
- Redefining fundamental concepts of transcription initiation in bacteria.Nature reviews. Genetics · 2020Review
- Article
- Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum.mSystems · 2020Article
- Regulated Iron Siderophore Production of the Halophilic ArchaeonBiomolecules · 2020Article
- Identification of RNA 3´ ends and termination sites inRNA biology · 2020Article
- The Primary Antisense Transcriptome ofGenes · 2019Article
- Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq.PloS one · 2019Article
- Copy number variation is associated with gene expression change in archaea.Microbial genomics · 2018Article
- Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Genome research · 2018Article
- RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.BMC genomics · 2018Article
16 more citing papers are in PubMed but not listed here.
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15 authors.
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Abstract
Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes-events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.
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