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

Publication ,  Journal Article
Cowell, LG; Davila, M; Yang, K; Kepler, TB; Kelsoe, G
Published in: J Exp Med
January 20, 2003

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.

Duke Scholars

Published In

J Exp Med

DOI

ISSN

0022-1007

Publication Date

January 20, 2003

Volume

197

Issue

2

Start / End Page

207 / 220

Location

United States

Related Subject Headings

  • Sequence Homology, Nucleic Acid
  • Recombination, Genetic
  • Molecular Sequence Data
  • Models, Statistical
  • Models, Genetic
  • Mice
  • Immunology
  • Humans
  • Genome, Human
  • Genome
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Cowell, L. G., Davila, M., Yang, K., Kepler, T. B., & Kelsoe, G. (2003). Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling. J Exp Med, 197(2), 207–220. https://doi.org/10.1084/jem.20020250
Cowell, Lindsay G., Marco Davila, Kaiyong Yang, Thomas B. Kepler, and Garnett Kelsoe. “Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.J Exp Med 197, no. 2 (January 20, 2003): 207–20. https://doi.org/10.1084/jem.20020250.
Cowell, Lindsay G., et al. “Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.J Exp Med, vol. 197, no. 2, Jan. 2003, pp. 207–20. Pubmed, doi:10.1084/jem.20020250.

Published In

J Exp Med

DOI

ISSN

0022-1007

Publication Date

January 20, 2003

Volume

197

Issue

2

Start / End Page

207 / 220

Location

United States

Related Subject Headings

  • Sequence Homology, Nucleic Acid
  • Recombination, Genetic
  • Molecular Sequence Data
  • Models, Statistical
  • Models, Genetic
  • Mice
  • Immunology
  • Humans
  • Genome, Human
  • Genome