The CLOCK/BMAL1 protein interaction landscape at the chromatin reveals homeodomain transcription factors as modulators of tissue-specific circadian transcription

To experimentally explore how the core CLOCK/BMAL1 heterodimer achieves this specificity, we investigated its protein interaction landscape at the chromatin by employing a method that combines chromatin immunoprecipitation with mass spectrometry-based quantitative proteomics (ChIP–MS).

This approach yielded the first two-dimensional (temporal and tissue-specific) interaction map of CLOCK/BMAL1 at the chromatin and revealed a complex organ-dependent landscape of clock-associated protein interactions. Among these we identified three homeodomain containing transcription factors -PROX1, HFN1B and HOXA5- in liver, kidney and lung, respectively. Functional analyses demonstrated that these factors colocalize with CLOCK/BMAL1 at the chromatin physically interacting via their homeodomain and the BMAL1 C-terminal transactivation domain and act as transcriptional repressors.