Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

The cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TF-specific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism. [Display omitted] •2.7 million binding targets for hundreds of TFs define the Arabidopsis cistrome•Methylation sensitivities of 76% of TFs surveyed shape the Arabidopsis epicistrome•Strong enrichment of relevant gene functions is predicted for TF target genes•Auxin response factor motif architecture promotes cooperative binding A new method for pinpointing transcription factor binding sites in the Arabidopsis genome and their responsiveness to DNA methylation demonstrates the impact of tissue-specific DNA chemical modifications on gene regulation, potentially for any organism.