Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

Significance Chromatin immunoprecipitation (ChIP) is a gold standard technique for genomic protein localization. We have discovered an artifact in ChIP that leads to reproducible but biologically meaningless enrichment of proteins at highly expressed genes, caused by high levels of polymerase II and polymerase III transcription. These findings call into question reports of unexpected localization of transcription factors, repressors, and cytosolic proteins to highly expressed genes. We suggest caution when interpreting ChIP enrichment at highly expressed genes and suggest a heterologous protein control in ChIP experiments to discern biologically meaningful from artifactual enrichment.