Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures.

ABSTRACT:

Background

Genomes possess different levels of non-randomness, in particular, an inhomogeneity in their nucleotide composition. Inhomogeneity is manifest from the short-range where neighboring nucleotides influence the choice of base at a site, to the long-range, commonly known as isochores, where a particular base composition can span millions of nucleotides. A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression.

Results

We present novel data and approaches that show that a mid-range inhomogeneity (~30 to 1000 nt) not only exists in mammalian genomes but is also significantly associated with strong RNA SS. A whole-genome bioinformatics investigation of local SS in a set of 11,315 non-redundan

SUBMITTER: Bechtel JM 

PROVIDER: S-EPMC2442090 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature