ArticleThe Journal of experimental medicine2003
Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.
Article in The Journal of experimental medicine, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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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
34 citing papers in PubMed.
- Article
- The nonamer code for RAG-mediated recombination in vivo.Nucleic acids research · 2025Article
- VH-replacement shapes the antibody repertoire by removing the genes of non-functional heavy-chains.The EMBO journal · 2025Article
- HTS and scRNA-seq revealed that the location and RSS quality of the mammalian TRBV and TRBJ genes impact biased rearrangement.BMC genomics · 2024Article
- The reverse TRBV30 gene of mammals: a defect or superiority in evolution?BMC genomics · 2024Article
- Article
- Review
- Poor-Quality Vβ Recombination Signal Sequences and the DNA Damage Response ATM Kinase Collaborate to Establish TCRβ Gene Repertoire and Allelic Exclusion.Journal of immunology (Baltimore, Md. : 1950) · 2022Article
- Poor quality Vβ recombination signal sequences stochastically enforce TCRβ allelic exclusion.The Journal of experimental medicine · 2020Article
- Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination.Nucleic acids research · 2020Article
- Article
- Transcriptional programming and T cell receptor repertoires distinguish human lung and lymph node memory T cells.Communications biology · 2019Article
- Germline DNA Retention in Murine and Human Rearranged T Cell Receptor Gene Coding Joints: Alternative Recombination Signal Sequences and V(D)J Recombinase Errors.Frontiers in immunology · 2019Article
- The Bayesian optimist's guide to adaptive immune receptor repertoire analysis.Immunological reviews · 2018Review
- Biochemical Characterization of Nonamer Binding Domain of RAG1 Reveals its Thymine Preference with Respect to Length and Position.Scientific reports · 2016Article
- Heavy-chain receptor editing unbound.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Deep sequencing of the murine IgH repertoire reveals complex regulation of nonrandom V gene rearrangement frequencies.Journal of immunology (Baltimore, Md. : 1950) · 2013Article
- Unifying model for molecular determinants of the preselection Vβ repertoire.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A Novel Quantitative Fluorescent Reporter Assay for RAG Targets and RAG Activity.Frontiers in immunology · 2013Article
- Chromatin conformation governs T-cell receptor Jβ gene segment usage.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The recombination signals (RS) that guide V(D)J recombination are phylogenetically conserved but retain a surprising degree of sequence variability, especially in the nonamer and spacer. To characterize RS variability, we computed the position-wise information, a measure correlated with sequence conservation, for each nucleotide position in an RS alignment and demonstrate that most position-wise information is present in the RS heptamers and nonamers. We have previously demonstrated significant correlations between RS positions and here show that statistical models of the correlation structure that underlies RS variability efficiently identify physiologic and cryptic RS and accurately predict the recombination efficiencies of natural and synthetic RS. In scans of mouse and human genomes, these models identify a highly conserved family of repetitive DNA as an unexpected source of frequent, cryptic RS that rearrange both in extrachromosomal substrates and in their genomic context.
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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.