ArticleNucleic acids research2012
The processing of repetitive extragenic palindromes: the structure of a repetitive extragenic palindrome bound to its associated nuclease.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
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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
19 citing papers in PubMed, 44 citations in OpenAlex.
- De novo origin of numerous microproteins in enterobacteria.Nucleic acids research · 2025Article
- Structure, function and evolution of the bacterial DinG-like proteins.Computational and structural biotechnology journal · 2025Review
- Metabolomics and metagenomics reveal the impact of γδ T inhibition on gut microbiota and metabolism in periodontitis-promoting OSCC.mSystems · 2024Article
- The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end.Molecular cell · 2021Article
- TnpAREP and REP sequences dissemination in bacterial genomes: REP recognition determinants.Nucleic acids research · 2021Article
- How sequence populations persist inside bacterial genomes.Genetics · 2021Article
- Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches.Acta crystallographica. Section D, Structural biology · 2020Article
- Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases.BMC genomics · 2018Article
- Discovering Complete Quasispecies in Bacterial Genomes.Genetics · 2017Article
- Identification and Characterization of Domesticated Bacterial Transposases.Genome biology and evolution · 2017Article
- DNA repeat sequences: diversity and versatility of functions.Current genetics · 2017Review
- Conformational diversity of single-stranded DNA from bacterial repetitive extragenic palindromes: Implications for the DNA recognition elements of transposases.Biopolymers · 2015Article
- Mechanisms of DNA Transposition.Microbiology spectrum · 2015Review
- Bacterial insertion sequences: their genomic impact and diversity.FEMS microbiology reviews · 2014Review
- Breaking and joining single-stranded DNA: the HUH endonuclease superfamily.Nature reviews. Microbiology · 2013Review
- GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes.BMC genomics · 2013Article
- Single-stranded DNA-binding proteins: multiple domains for multiple functions.Structure (London, England : 1993) · 2013Review
- Evolution of REP diversity: a comparative study.BMC genomics · 2013Article
- Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in Archaea.Biochemical Society transactions · 2013Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Extragenic sequences in genomes, such as microRNA and CRISPR, are vital players in the cell. Repetitive extragenic palindromic sequences (REPs) are a class of extragenic sequences, which form nucleotide stem-loop structures. REPs are found in many bacterial species at a high copy number and are important in regulation of certain bacterial functions, such as Integration Host Factor recruitment and mRNA turnover. Although a new clade of putative transposases (RAYTs or TnpA(REP)) is often associated with an increase in these repeats, it is not clear how these proteins might have directed amplification of REPs. We report here the structure to 2.6 Å of TnpA(REP) from Escherichia coli MG1655 bound to a REP. Sequence analysis showed that TnpA(REP) is highly related to the IS200/IS605 family, but in contrast to IS200/IS605 transposases, TnpA(REP) is a monomer, is auto-inhibited and is active only in manganese. These features suggest that, relative to IS200/IS605 transposases, it has evolved a different mechanism for the movement of discrete segments of DNA and has been severely down-regulated, perhaps to prevent REPs from sweeping through genomes.
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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.