Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system.

ABSTRACT: The innate immune response provides a first line of defense against pathogens by targeting generic differential features that are present in foreign organisms but not in the host. These innate responses generate selection forces acting both in pathogens and hosts that further determine their co-evolution. Here we analyze the nucleic acid sequence fingerprints of these selection forces acting in parallel on both host innate immune genes and ssRNA viral genomes. We do this by identifying dinucleotide biases in the coding regions of innate immune response genes in plasmacytoid dendritic cells, and then use this signal to identify other significant host innate immune genes. The persistence of these biases in the orthologous groups of genes in humans and chickens is also examined. We then compa

SUBMITTER: Greenbaum BD 

PROVIDER: S-EPMC2694999 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature