Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq.

ABSTRACT: Sequencing DNA fragments associated with proteins following in vivo cross-linking with formaldehyde (known as ChIP-seq) has been used extensively to describe the distribution of proteins across genomes. It is not widely appreciated that this method merely estimates a protein's distribution and cannot reveal changes in occupancy between samples. To do this, we tagged with the same epitope orthologous proteins in Saccharomyces cerevisiae and Candida glabrata, whose sequences have diverged to a degree that most DNA fragments longer than 50 bp are unique to just one species. By mixing defined numbers of C. glabrata cells (the calibration genome) with S. cerevisiae samples (the experimental genomes) prior to chromatin fragmentation and immunoprecipitation, it is possible to derive a quantitativ

SUBMITTER: Hu B 

PROVIDER: S-EPMC4787748 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature