Chromatin immunoprecipitation (ChIP) is the gold-standard technique for 
localizing nuclear proteins in the genome. We used ChIP, in combination with 
deep sequencing (Seq), to study the genome-wide distribution of the Silent 
information regulator (Sir) complex in Saccharomyces cerevisiae. We analyzed 
ChIP-Seq peaks of the Sir2, Sir3, and Sir4 silencing proteins and discovered 238 
unexpected euchromatic loci that exhibited enrichment of all three. 
Surprisingly, published ChIP-Seq datasets for the Ste12 transcription factor and 
the centromeric Cse4 protein indicated that these proteins were also enriched in 
the same euchromatic regions with the high Sir protein levels. The 238 loci, 
termed "hyper-ChIPable", were in highly expressed regions with strong polymerase 
II and polymerase III enrichment signals, and the correlation between 
transcription level and ChIP enrichment was not limited to these 238 loci but 
extended genome-wide. The apparent enrichment of various proteins at 
hyper-ChIPable loci was not a consequence of artifacts associated with deep 
sequencing methods, as confirmed by ChIP-quantitative PCR. The localization of 
unrelated proteins, including the entire silencing complex, to the most highly 
transcribed genes was highly suggestive of a technical issue with the 
immunoprecipitations. ChIP-Seq on chromatin immunoprecipitated with a 
nuclear-localized GFP reproduced the above enrichment in an expression-dependent 
manner: induction of the GAL genes resulted in an increased ChIP signal of the 
GFP protein at these loci, with presumably no biological relevance. Whereas ChIP 
is a broadly valuable technique, some published conclusions based upon ChIP 
procedures may merit reevaluation in light of these findings.