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

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Cowell, LG; Davila, M; Yang, K; Kepler, TB; Kelsoe, G

Published Date

  • January 20, 2003

Published In

Volume / Issue

  • 197 / 2

Start / End Page

  • 207 - 220

PubMed ID

  • 12538660

Pubmed Central ID

  • PMC2193808

International Standard Serial Number (ISSN)

  • 0022-1007

Digital Object Identifier (DOI)

  • 10.1084/jem.20020250


  • eng

Conference Location

  • United States