Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling

Lindsay G. Cowell, Marco Davila, Kaiyong Yang, Thomas B. Kepler, Garnett Kelsoe

Research output: Contribution to journalArticle

48 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)207-220
Number of pages14
JournalJournal of Experimental Medicine
Issue number2
Publication statusPublished - Jan 20 2003



  • Cryptic recombination signal
  • Illegitimate V(D)J recombination
  • Recombination efficiency
  • Recombination signal models
  • Recombination signal sequence

ASJC Scopus subject areas

  • Immunology

Cite this