ArticleNucleic acids research2009
Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 15 citations in OpenAlex.
- aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy.eLife · 2021Article
- The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.Nucleic acids research · 2020Article
- Characterization of the Methanomicrobial Archaeal RNase Zs for Processing the CCA-Containing tRNA Precursors.Frontiers in microbiology · 2020Article
- A Genetic System forFrontiers in microbiology · 2019Article
- Expression of Pyridoxal 5'-Phosphate-Independent Racemases Can Reduce 2-Aminoacrylate Stress in Salmonella enterica.Journal of bacteriology · 2018Article
- A global analysis of transcription reveals two modes of Spt4/5 recruitment to archaeal RNA polymerase.Nature microbiology · 2017Article
- Bypassing the Need for the Transcriptional Activator EarA through a Spontaneous Deletion in the BRE Portion of theFrontiers in microbiology · 2017Article
- Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus.Scientific reports · 2015Article
- Eukaryotic and archaeal TBP and TFB/TF(II)B follow different promoter DNA bending pathways.Nucleic acids research · 2014Article
- The Sulfolobus initiator element is an important contributor to promoter strength.Journal of bacteriology · 2013Article
- Messenger RNA processing in Methanocaldococcus (Methanococcus) jannaschii.RNA (New York, N.Y.) · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although Methanocaldococcus (Methanococcus) jannaschii was the first archaeon to have its genome sequenced, little is known about the promoters of its protein-coding genes. To expand our knowledge, we have experimentally identified 131 promoters for 107 protein-coding genes in this genome by mapping their transcription start sites. Compared to previously identified promoters, more than half of which are from genes for stable RNAs, the protein-coding gene promoters are qualitatively similar in overall sequence pattern, but statistically different at several positions due to greater variation among their sequences. Relative binding affinity for general transcription factors was measured for 12 of these promoters by competition electrophoretic mobility shift assays. These promoters bind the factors less tightly than do most tRNA gene promoters. When a position weight matrix (PWM) was constructed from the protein gene promoters, factor binding affinities correlated with corresponding promoter PWM scores. We show that the PWM based on our data more accurately predicts promoters in the genome and transcription start sites than could be done with the previously available data. We also introduce a PWM logo, which visually displays the implications of observing a given base at a position in a sequence.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.