ChIPseq mapping of chromatin proteins Cren7 and Sso7D in the Sulfolobus solfataricus genome

Purpose: To identify the genome binding sites of Cren7 and Sso7D, and to determine whether binding patterns differ between wild type and an epigenetically evolved strain in which they are heritably hypomethylated. Because methylated residues were solvent facing, it was predicted that binding patterns would not change between the strains. Methods: Chromosomal fragments 300-500bp long were immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D and sequenced using Illumina Hiseq. Results: Cren7 and Sso7D had distinct binding patterns. ChIPseq peak patterns had slight variation between wild type and the evolved strain, but not at genes whose expression was thought to be epigentically dependent. Conclusions: As predicted, neither binding location or binding affinity correlated with epigenetic expression patterns in the evolved strain. Overall design: Chromosomal fragments 300-500bp long were immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D and sequenced using Illumina HiSeq3000