ArticleNucleic acids research2014
The structural code of cyanobacterial genomes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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.
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Who cites it
5 citing papers in PubMed, 10 citations in OpenAlex.
- DNA structural properties of DNA binding sites for 21 transcription factors in the mycobacterial genome.Frontiers in cellular and infection microbiology · 2023Article
- Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis.Nucleic acids research · 2022Article
- From sequence to information.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Selection for ancient periodic motifs that do not impart DNA bending.PLoS genetics · 2020Article
- A Metagenomic Approach to Cyanobacterial Genomics.Frontiers in microbiology · 2017Review
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 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A periodic bias in nucleotide frequency with a period of about 11 bp is characteristic for bacterial genomes. This signal is commonly interpreted to relate to the helical pitch of negatively supercoiled DNA. Functions in supercoiling-dependent RNA transcription or as a 'structural code' for DNA packaging have been suggested. Cyanobacterial genomes showed especially strong periodic signals and, on the other hand, DNA supercoiling and supercoiling-dependent transcription are highly dynamic and underlie circadian rhythms of these phototrophic bacteria. Focusing on this phylum and dinucleotides, we find that a minimal motif of AT-tracts (AT2) yields the strongest signal. Strong genome-wide periodicity is ancestral to a clade of unicellular and polyploid species but lost upon morphological transitions into two baeocyte-forming and a symbiotic species. The signal is intermediate in heterocystous species and weak in monoploid picocyanobacteria. A pronounced 'structural code' may support efficient nucleoid condensation and segregation in polyploid cells. The major source of the AT2 signal are protein-coding regions, where it is encoded preferentially in the first and third codon positions. The signal shows only few relations to supercoiling-dependent and diurnal RNA transcription in Synechocystis sp. PCC 6803. Strong and specific signals in two distinct transposons suggest roles in transposase transcription and transpososome formation.
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Registered trials
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