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

Abstract

The phytohormone cytokinin regulates diverse aspects of plant growth and development, probably through context-dependent transcriptional regulation that relies on a dynamic interplay between regulatory proteins and chromatin. We employed the assay for transposase accessible chromatin with sequencing 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 cytokinin-regulated genes. The changes also largely overlap with binding sites for the type-B ARABIDOPSIS RESPONSE REGULATORS (ARRs), transcription factors that mediate the primary response to cytokinin. Furthermore, the type-B ARRs were found to be necessary for the changes in chromatin state in response to cytokinin. Last, we identified context-dependent responses by comparing root and shoot profiles. This study provides new insight into the dynamics between cytokinin and chromatin with regard to directing transcriptional programmes and how cytokinin mediates its pleiotropic effects.

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Data availability

The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.The raw and processed RNA-seq and ATAC-seq data described in this study have been deposited to the NCBI Short Read Archive (SRA) database under PRJNA415015 and Gene Expression Omnibus under Series GSE116287,respectively.

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Acknowledgements

This work was supported by a grant from the National Science Foundation Plant Genome Research Program (IOS-1238051) to J.J.K. and G.E.S., and a National Science Foundation Plant Genome Research Program Initiative Postdoctoral Fellowship in Biology (1611875) to K.C.P. The authors thank the UNC High-Throughput Sequencing Facility and the Flow Cytometry Core Facility. The MoFlo XDP used in this study is funded by the North Carolina Biotech Center Institutional Support Grant 2005-IDG-1016. Thanks are also given to D. McKay, R. Deal, B. Schmitz and members of their labs for their assistance with the ATAC assay and the computational analyses.

Author information

K.C.P., G.E.S. and J.J.K. conceptualized and designed the research. K.C.P. conducted the experiments with assistance from J.W. K.C.P., G.E.S. and J.J.K. performed data analyses. K.C.P. and J.J.K. wrote the manuscript with input from G.E.S.

Competing interests

The authors declare no competing interests.

Correspondence to Joseph J. Kieber.

Supplementary information

Supplementary Information

Supplementary Figures 1–8 and Supplementary Tables 7 and 8.

Reporting Summary

Supplementary Table 1

Statistics of ATAC-seq libraries.

Supplementary Table 2

Root differential accessible regions in response to cytokinin treatment.

Supplementary Table 3

Statistics of RNA-seq libraries.

Supplementary Table 4

Root differentially expressed genes in response to cytokinin treatment.

Supplementary Table 5

Shoot differentially expressed genes in response to cytokinin treatment.

Supplementary Table 6

Shoot differential accessible regions in response to cytokinin treatment.

Supplementary Table 9

Primers used for ATAC-qPCR analysis.

Supplementary Table 10

Intersection of ARR10 binding sites.

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Fig. 1: Determining cytokinin-induced chromatin accessibility changes.
Fig. 2: Context-dependent accessibility changes in response to cytokinin treatment in shoots versus roots.
Fig. 3: Type-B ARRs are necessary for chromatin accessibility changes.