Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence.

ABSTRACT: To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate. By analyzing yeast coding and promoter sequences, we find that neutral mutation rates in yeast are uniform genome-wide, in contrast to mammals, where neutral mutation rates vary along chromosomes. We develop an approach that uses this uniform rate to estimate the amount of promoter sequence under purifying selection. This amount is approximately 30%, corresponding to roughly 90 bp for a typical promoter. Furthermore, using a hidden Markov model, we are able to separate each

SUBMITTER: Chin CS 

PROVIDER: S-EPMC546519 | biostudies-literature | 2005 Feb

REPOSITORIES: biostudies-literature