Sea-ATI unravels novel vocabularies of plant active cistrome

The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants. [GRAPHICS] .

Automated summary

The cistrome is composed of cis-acting regulatory elements recognized by transcription factors (TFs), but only a fraction of them are active in specific tissues. This study introduces a low-input method called sea-ATI to profile the active cistrome in plants and identify previously unidentified cis-regulatory vocabularies. The functionality of the new cis-elements was confirmed through ATAC-seq and RNA-seq analyses, and sea-ATI was shown to be able to identify both positive and negative regulatory cis-elements.