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.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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.

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.

References

  1. 1.

    Asensi-Fabado, M. A., Amtmann, A. & Perrella, G. Plant responses to abiotic stress: the chromatin context of transcriptional regulation. Biochim. Biophys. Acta 1860, 106–122 (2017).

    CAS  Article  Google Scholar 

  2. 2.

    Kieber, J. J. & Schaller, G. E. Cytokinins. Arabidopsis Book 12, e0168 (2014).

    Article  Google Scholar 

  3. 3.

    Wulfetange, K. et al. The cytokinin receptors of Arabidopsis are located mainly to the endoplasmic reticulum. Plant Physiol. 156, 1808–1818 (2011).

    CAS  Article  Google Scholar 

  4. 4.

    Caesar, K. et al. Evidence for the localization of the Arabidopsis cytokinin receptors AHK3 and AHK4 in the endoplasmic reticulum. J. Exp. Bot. 62, 5571–5580 (2011).

    CAS  Article  Google Scholar 

  5. 5.

    Punwani, J. A., Hutchison, C. E., Schaller, G. E. & Kieber, J. J. The subcellular distribution of the Arabidopsis histidine phosphotransfer proteins is independent of cytokinin signaling. Plant J. 62, 473–482 (2010).

    CAS  Article  Google Scholar 

  6. 6.

    Hutchison, C. E. et al. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. Plant Cell 18, 3073–3087 (2006).

    CAS  Article  Google Scholar 

  7. 7.

    Hwang, I., Sheen, J. & Muller, B. Cytokinin signaling networks. Annu. Rev. Plant. Biol. 63, 353–380 (2012).

    CAS  Article  Google Scholar 

  8. 8.

    Zubo, Y. O. et al. Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis. Proc. Natl Acad. Sci. USA 114, E5995–E6004 (2017).

    CAS  Article  Google Scholar 

  9. 9.

    Cuvier, O. & Fierz, B. Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells. Nat. Rev. Genet. 18, 457–472 (2017).

    CAS  Article  Google Scholar 

  10. 10.

    Spitz, F. & Furlong, E. E. Transcription factors: from enhancer binding to developmental control. Nat. Rev. Genet. 13, 613–626 (2012).

    CAS  Article  Google Scholar 

  11. 11.

    Voss, T. C. & Hager, G. L. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat. Rev. Genet. 15, 69–81 (2014).

    CAS  Article  Google Scholar 

  12. 12.

    Bhargava, A. et al. Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiol. 162, 272–294 (2013).

    CAS  Article  Google Scholar 

  13. 13.

    Brenner, W. G. & Schmulling, T. Summarizing and exploring data of a decade of cytokinin-related transcriptomics. Front. Plant Sci. 6, 29 (2015).

    Article  Google Scholar 

  14. 14.

    Brenner, W. G., Ramireddy, E., Heyl, A. & Schmulling, T. Gene regulation by cytokinin in Arabidopsis. Front. Plant Sci. 3, 8 (2012).

    CAS  Article  Google Scholar 

  15. 15.

    Brenner, W. G. & Schmulling, T. Transcript profiling of cytokinin action in Arabidopsis roots and shoots discovers largely similar but also organ-specific responses. BMC Plant Biol. 12, 112 (2012).

    CAS  Article  Google Scholar 

  16. 16.

    Wang, J. et al. Cytokinin signaling activates WUSCHEL expression during axillary meristem initiation. Plant Cell 29, 1373–1387 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Furuta, K. et al. The CKH2/PKL chromatin remodeling factor negatively regulates cytokinin responses in Arabidopsis calli. Plant Cell Physiol. 52, 618–628 (2011).

    CAS  Article  Google Scholar 

  18. 18.

    Efroni, I. et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell 24, 438–445 (2013).

    CAS  Article  Google Scholar 

  19. 19.

    Fry, C. J. & Farnham, P. J. Context-dependent transcriptional regulation. J. Biol. Chem. 274, 29583–29586 (1999).

    CAS  Article  Google Scholar 

  20. 20.

    McKay, D. J. & Lieb, J. D. A common set of DNA regulatory elements shapes Drosophila appendages. Dev. Cell 27, 306–318 (2013).

    CAS  Article  Google Scholar 

  21. 21.

    Daugherty, A. C. et al. Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Res. 27, 2096–2107 (2017).

    CAS  Article  Google Scholar 

  22. 22.

    Uyehara, C. M. et al. Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev. 31, 862–875 (2017).

    CAS  Article  Google Scholar 

  23. 23.

    Sullivan, A. M. et al. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep. 8, 2015–2030 (2014).

    CAS  Article  Google Scholar 

  24. 24.

    Pajoro, A. et al. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol. 15, R41 (2014).

    Article  Google Scholar 

  25. 25.

    Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).

    CAS  Article  Google Scholar 

  26. 26.

    Xie, M. et al. A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development. Nat. Commun. 9, 1604 (2018).

    Article  Google Scholar 

  27. 27.

    Maher, K. A. et al. Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cell 30, 15–36 (2018).

    CAS  Article  Google Scholar 

  28. 28.

    Sijacic, P., Bajic, M., McKinney, E. C., Meagher, R. B. & Deal, R. B. Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks. Plant J. 94, 215–231 (2018).

    CAS  Article  Google Scholar 

  29. 29.

    Lu, Z., Hofmeister, B. T., Vollmers, C., DuBois, R. M. & Schmitz, R. J. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res. 45, e41 (2017).

    Article  Google Scholar 

  30. 30.

    Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

    CAS  Article  Google Scholar 

  31. 31.

    Shen, L. et al. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS ONE 8, e65598 (2013).

    CAS  Article  Google Scholar 

  32. 32.

    Sullivan, A. M., Bubb, K. L., Sandstrom, R., Stamatoyannopoulos, J. A. & Queitsch, C. DNase I hypersensitivity mapping, genomic footprinting, and transcription factor networks in plants. Curr. Plant Biol. 3-4, 40–47 (2015).

    Article  Google Scholar 

  33. 33.

    Yu, G., Wang, L. G. & He, Q. Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).

    CAS  Article  Google Scholar 

  34. 34.

    Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

    CAS  Article  Google Scholar 

  35. 35.

    D’Agostino, I. B., Deruere, J. & Kieber, J. J. Characterization of the response of the Arabidopsis response regulator gene family to cytokinin. Plant Physiol. 124, 1706–1717 (2000).

    Article  Google Scholar 

  36. 36.

    Dello Ioio, R. et al. A genetic framework for the control of cell division and differentiation in the root meristem. Science 322, 1380–1384 (2008).

    CAS  Article  Google Scholar 

  37. 37.

    Schaller, G. E., Bishopp, A. & Kieber, J. J. The yin-yang of hormones: cytokinin and auxin interactions in plant development. Plant Cell 27, 44–63 (2015).

    CAS  Article  Google Scholar 

  38. 38.

    Street, I. H. et al. Cytokinin acts through the auxin influx carrier AUX1 to regulate cell elongation in the root. Development 143, 3982–3993 (2016).

    CAS  Article  Google Scholar 

  39. 39.

    Steiner, E. et al. The Arabidopsis O-linked N-acetylglucosamine transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers. Plant Cell 24, 96–108 (2012).

    CAS  Article  Google Scholar 

  40. 40.

    Simonini, S. & Kater, M. M. Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance. J. Exp. Bot. 65, 1455–1465 (2014).

    CAS  Article  Google Scholar 

  41. 41.

    Shanks, C. M. et al. Role of BASIC PENTACYSTEINE transcription factors in a subset of cytokinin signaling responses. Plant J. 95, 458–473 (2018).

    CAS  Article  Google Scholar 

  42. 42.

    Reyes-Olalde, J. I. et al. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet. 13, e1006726 (2017).

    Article  Google Scholar 

  43. 43.

    Ohashi-Ito, K. et al. A bHLH complex activates vascular cell division via cytokinin action in root apical meristem. Curr. Biol. 24, 2053–2058 (2014).

    CAS  Article  Google Scholar 

  44. 44.

    Cluis, C. P., Mouchel, C. F. & Hardtke, C. S. The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways. Plant J. 38, 332–347 (2004).

    CAS  Article  Google Scholar 

  45. 45.

    Dobisova, T. et al. Light controls cytokinin signaling via transcriptional regulation of constitutively active sensor histidine kinase CKI1. Plant Physiol. 174, 387–404 (2017).

    CAS  Article  Google Scholar 

  46. 46.

    Vandenbussche, F. et al. HY5 is a point of convergence between cryptochrome and cytokinin signalling pathways in Arabidopsis thaliana. Plant J. 49, 428–441 (2007).

    CAS  Article  Google Scholar 

  47. 47.

    Zdarska, M. et al. Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development. J. Exp. Bot. 66, 4913–4931 (2015).

    CAS  Article  Google Scholar 

  48. 48.

    Argyros, R. D. et al. Type B response regulators of Arabidopsis play key roles in cytokinin signaling and plant development. Plant Cell 20, 2102–2116 (2008).

    CAS  Article  Google Scholar 

  49. 49.

    Ishida, K., Yamashino, T., Yokoyama, A. & Mizuno, T. Three type-B response regulators, ARR1, ARR10 and ARR12, play essential but redundant roles in cytokinin signal transduction throughout the life cycle of Arabidopsis thaliana. Plant Cell Physiol. 49, 47–57 (2008).

    CAS  Article  Google Scholar 

  50. 50.

    Weber, B., Zicola, J., Oka, R. & Stam, M. Plant enhancers: a call for discovery. Trends Plant Sci. 21, 974–987 (2016).

    CAS  Article  Google Scholar 

  51. 51.

    Liu, Y. et al. Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness. Sci. Rep. 7, 4093 (2017).

    CAS  Article  Google Scholar 

  52. 52.

    Shu, H., Wildhaber, T., Siretskiy, A., Gruissem, W. & Hennig, L. Distinct modes of DNA accessibility in plant chromatin. Nat. Commun. 3, 1281 (2012).

    Article  Google Scholar 

  53. 53.

    Wisecaver, J. H. et al. A global coexpression network approach for connecting genes to specialized metabolic pathways in plants. Plant Cell 29, 944–959 (2017).

    CAS  Article  Google Scholar 

  54. 54.

    Field, B. et al. Formation of plant metabolic gene clusters within dynamic chromosomal regions. Proc. Natl Acad. Sci. USA 108, 16116–16121 (2011).

    CAS  Article  Google Scholar 

  55. 55.

    Reimegard, J. et al. Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. Nucleic Acids Res. 45, 3253–3265 (2017).

    Article  Google Scholar 

  56. 56.

    Yu, N. et al. Delineation of metabolic gene clusters in plant genomes by chromatin signatures. Nucleic Acids Res. 44, 2255–2265 (2016).

    CAS  Article  Google Scholar 

  57. 57.

    Nutzmann, H. W. & Osbourn, A. Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytol. 205, 503–510 (2015).

    Article  Google Scholar 

  58. 58.

    Meng, H. & Bartholomew, B. Emerging roles of transcriptional enhancers in chromatin looping and promoter-proximal pausing of RNA polymerase II. J. Biol. Chem. 293, 13786–13794 (2018).

    CAS  Article  Google Scholar 

  59. 59.

    Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227–2241 (2011).

    CAS  Article  Google Scholar 

  60. 60.

    Iwafuchi-Doi, M. et al. The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation. Mol. Cell 62, 79–91 (2016).

    CAS  Article  Google Scholar 

  61. 61.

    Zhang, T. Q. et al. A two-step model for de novo activation of WUSCHEL during plant shoot regeneration. Plant Cell 29, 1073–1087 (2017).

    CAS  Article  Google Scholar 

  62. 62.

    Murashige, T. & Skoog, F. A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol. Plant. 15, 473–497 (1962).

    CAS  Article  Google Scholar 

  63. 63.

    Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402–408 (2001).

    CAS  Article  Google Scholar 

  64. 64.

    Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article  Google Scholar 

  65. 65.

    Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article  Google Scholar 

  66. 66.

    Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A. & Manke, T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. 42, W187–W191 (2014).

    CAS  Article  Google Scholar 

  67. 67.

    John, S. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat. Genet. 43, 264–268 (2011).

    CAS  Article  Google Scholar 

  68. 68.

    Nicol, J. W., Helt, G. A., Blanchard, S. G. Jr, Raja, A. & Loraine, A. E. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730–2731 (2009).

    CAS  Article  Google Scholar 

  69. 69.

    Quinlan, A. R. BEDTools: the Swiss-Army tool for genome feature analysis. Curr. Protoc. Bioinform. 47, 11–34 (2014).

    Article  Google Scholar 

  70. 70.

    Warnes, G. R. et al. gplots: Various R Programming Tools for Plotting Data v3.0.1 (CRAN, 2016); https://CRAN.R-project.org/package=gplots

  71. 71.

    Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919–1920 (2012).

    CAS  Article  Google Scholar 

  72. 72.

    Katari, M. S. et al. VirtualPlant: a software platform to support systems biology research. Plant Physiol. 152, 500–515 (2010).

    CAS  Article  Google Scholar 

  73. 73.

    Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    CAS  Article  Google Scholar 

  74. 74.

    Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

    CAS  Article  Google Scholar 

  75. 75.

    Risso, D., Ngai, J., Speed, T. P. & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896–902 (2014).

    CAS  Article  Google Scholar 

  76. 76.

    Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57, 289–300 (1995).

    Google Scholar 

Download references

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

Affiliations

Authors

Contributions

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.

Corresponding author

Correspondence to Joseph J. Kieber.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Potter, K.C., Wang, J., Schaller, G.E. et al. Cytokinin modulates context-dependent chromatin accessibility through the type-B response regulators. Nature Plants 4, 1102–1111 (2018). https://doi.org/10.1038/s41477-018-0290-y

Download citation

Further reading

Search

Quick links

Sign up for the Nature Briefing newsletter for a daily update on COVID-19 science.
Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing