Cytokinin modulates chromatin accessibility in a context-dependent manner through the type-B response regulators

The plant hormone cytokinin regulates diverse aspects of plant growth and development, likely through context-dependent transcriptional regulation that relies on a dynamic interplay between regulatory proteins and chromatin. We employed the Assay for Transposase Accessible Chromatin (ATAC-Seq) to profile changes in the chromatin landscape of Arabidopsis roots and shoots in response to cytokinin. Our results reveal differentially accessible chromatin regions indicative of dynamic regulation in response to cytokinin. These changes in chromatin occur preferentially upstream of genes whose expression changes in response to cytokinin and largely overlap with binding sites for the type-B ARRs, transcription factors that mediate the primary response to cytokinin. Further, the type-B ARRs were found to be necessary for the changes in chromatin state in response to cytokinin. Lastly, we find context-dependent responses by comparing root and shoot profiles. These datasets provide new insights into the transcriptional regulatory mechanisms involved in the cytokinin response and how cytokinin mediates its pleiotropic effects. Harvested plants were treated with BA for 45 minutes. For ATAC analyses, four biological replicates of root samples (-/+ cytokinin), two biological replicates of shoot samples (-/+ cytokinin), two biological replicates of arr1,10,12 root samples (-/+ cytokinin). For RNA analyses, three biological reps of root and shoots samples (-/+ cytokinin) was performed.