Chromatin immunoprecipitation (ChIP) assay is a powerful tool to study protein-DNA interaction and chromatin changes associated with gene expression. In the related article, we used ChIP assay to evaluate CCA1 binding to the CCA1, LHY, TOC1 and GI upstream region, as well as histone modifications at these loci in A. thaliana, A. arenosa and the two independently re-synthesized allotetraploids (Allo733 and Allo738). The ChIP protocol is modified from those of Gendrel et al. (2002) (1) and Lawrence et al. (2004) (2).