ArticleNucleic acids research2016
Comparative transcriptomics across the prokaryotic tree of life.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 51 citations in OpenAlex.
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- Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids.Extremophiles : life under extreme conditions · 2024Review
- 5'-untranslated region sequences enhance plasmid-based protein production inFrontiers in microbiology · 2024Article
- The biology of thermoacidophilic archaea from the order Sulfolobales.FEMS microbiology reviews · 2021Article
- A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations.BMC bioinformatics · 2021Article
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- Identification of RNA 3´ ends and termination sites inRNA biology · 2020Article
- FttA is a CPSF73 homologue that terminates transcription in Archaea.Nature microbiology · 2020Article
- Advances in bacterial transcriptome understanding: From overlapping transcription to the excludon concept.Molecular microbiology · 2020Review
- iRAPs curb antisense transcription in E. coli.Nucleic acids research · 2019Article
- AmBio · 2019Article
- A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.Nature communications · 2019Article
- Article
- The Impact of Pyroglutamate:Archaea (Vancouver, B.C.) · 2019Article
- YtrAFrontiers in microbiology · 2019Article
- Widespread Antisense Transcription in Prokaryotes.Microbiology spectrum · 2018Review
- Extensive reshaping of bacterial operons by programmed mRNA decay.PLoS genetics · 2018Article
- RNAseq analysis of α-proteobacterium Gluconobacter oxydans 621H.BMC genomics · 2018Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to 'transcriptional noise'. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5'UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.