ArticleNucleic acids research2015
Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 28 citations in OpenAlex.
- The MHC-I related protein 1 MR1 can bind host purine catabolites.The Journal of biological chemistry · 2026Article
- Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs.Molecules (Basel, Switzerland) · 2024Review
- Distant sequence regions of JBP1 contribute to J-DNA binding.Life science alliance · 2023Article
- G-Quadruplexes as Key Transcriptional Regulators in Neglected Trypanosomatid Parasites.Chembiochem : a European journal of chemical biology · 2023Review
- Behind Base J: The Roles of JBP1 and JBP2 on Trypanosomatids.Pathogens (Basel, Switzerland) · 2023Review
- Article
- Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination inmSphere · 2021Article
- Latest techniques to study DNA methylation.Essays in biochemistry · 2019Review
- The domain architecture of the protozoan protein J-DNA-binding protein 1 suggests synergy between base J DNA binding and thymidine hydroxylase activity.The Journal of biological chemistry · 2019Article
- Parasitic Protozoa: Unusual Roles for G-Quadruplexes in Early-Diverging Eukaryotes.Molecules (Basel, Switzerland) · 2019Review
- Sequencing 5-Hydroxymethyluracil at Single-Base Resolution.Angewandte Chemie (International ed. in English) · 2018Article
- Intrinsic DNA curvature in trypanosomes.BMC research notes · 2017Article
- International Standards for Genomes, Transcriptomes, and Metagenomes.Journal of biomolecular techniques : JBT · 2017Review
- Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania.Genome biology · 2017Article
- A method for the efficient and selective identification of 5-hydroxymethyluracil in genomic DNA.Biology methods & protocols · 2017Article
- Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing.Bioscience reports · 2016Article
- Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut.Science (New York, N.Y.) · 2016Review
- Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in trypanosomatid telomeric DNA.Molecular and biochemical parasitology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 4 institutions in 2 countries.
Funding
Abstract
Base J (β-D-glucosyl-hydroxymethyluracil) replaces 1% of T in the Leishmania genome and is only found in telomeric repeats (99%) and in regions where transcription starts and stops. This highly restricted distribution must be co-determined by the thymidine hydroxylases (JBP1 and JBP2) that catalyze the initial step in J synthesis. To determine the DNA sequences recognized by JBP1/2, we used SMRT sequencing of DNA segments inserted into plasmids grown in Leishmania tarentolae. We show that SMRT sequencing recognizes base J in DNA. Leishmania DNA segments that normally contain J also picked up J when present in the plasmid, whereas control sequences did not. Even a segment of only 10 telomeric (GGGTTA) repeats was modified in the plasmid. We show that J modification usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides. Modifications occur near G-rich sequences capable of forming G-quadruplexes and JBP2 is needed, as it does not occur in JBP2-null cells. We propose a model whereby de novo J insertion is mediated by JBP2. JBP1 then binds to J and hydroxylates another T 13 bp downstream (but not upstream) on the complementary strand, allowing JBP1 to maintain existing J following DNA replication.
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.