Abstract
The Arabidopsis ROS1/DEMETER family of 5-methylcytosine (5mC) DNA glycosylases are the first genetically characterized DNA demethylases in eukaryotes. However, the features of ROS1-targeted genomic loci are not well understood. In this study, we characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. We found that ROS1 preferentially targets transposable elements (TEs) and intergenic regions. Compared with most TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting that ROS1 may prevent DNA methylation spreading from TEs to nearby genes. ROS1-targeted TEs are specifically enriched for H3K18Ac and H3K27me3, and depleted of H3K27me and H3K9me2. Importantly, we identified thousands of previously unknown RNA-directed DNA methylation (RdDM) targets following depletion of ROS1, suggesting that ROS1 strongly antagonizes RdDM at these loci. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at some loci. Our results provide important insights into the genome-wide targets of ROS1 and the crosstalk between DNA methylation and ROS1-mediated active DNA demethylation.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Collier, J. Epigenetic regulation of the bacterial cell cycle. Curr. Opin. Microbiol. 12, 722–729 (2009).
He, X.-J., Chen, T. & Zhu, J.-K. Regulation and function of DNA methylation in plants and animals. Cell Res. 21, 442–465 (2011).
Zhu, J.-K. Active DNA demethylation mediated by DNA glycosylases. Annu. Rev. Genet. 43, 143–166 (2009).
Yang, D.-L. et al. Dicer-independent RNA-directed DNA methylation in Arabidopsis. Cell Res. 26, 66–82 (2016).
Zhai, J. et al. A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Cell 163, 445–455 (2015).
Ye, R. et al. A dicer-independent route for biogenesis of siRNAs that direct DNA methylation in Arabidopsis. Mol. Cell 61, 222–235 (2016).
Blevins, T. et al. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife 4, e09591 (2015).
Gong, Z. et al. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase. Cell 111, 803–814 (2002).
Agius, F., Kapoor, A. & Zhu, J.-K. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation. Proc. Natl Acad. Sci. USA 103, 11796–11801 (2006).
Morales-Ruiz, T. et al. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc. Natl Acad. Sci. USA 103, 6853–6858 (2006).
Li, Y. et al. An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected]. PLoS Genet. 11, e1004905 (2015).
Martínez-Macías, M. I. et al. A DNA 3’ phosphatase functions in active DNA demethylation in Arabidopsis. Mol. Cell 45, 357–370 (2012).
Li, Y., Duan, C.-G., Zhu, X., Qian, W. & Zhu, J.-K. A DNA ligase required for active DNA demethylation and genomic imprinting in Arabidopsis. Cell Res. 25, 757–760 (2015).
Qian, W. et al. A histone acetyltransferase regulates active DNA demethylation in Arabidopsis. Science 336, 1445–1448 (2012).
Lang, Z. et al. The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing. Mol. Cell 57, 971–983 (2015).
Wang, C. et al. Methyl-CpG-binding domain protein MBD7 is required for active DNA demethylation in Arabidopsis. Plant Physiol. 167, 905–914 (2015).
Zhu, J., Kapoor, A., Sridhar, V. V., Agius, F. & Zhu, J.-K. The DNA glycosylase/lyase ROS1 functions in pruning DNA methylation patterns in Arabidopsis. Curr. Biol. 17, 54–59 (2007).
Yamamuro, C. et al. Overproduction of stomatal lineage cells in Arabidopsis mutants defective in active DNA demethylation. Nat. Commun. 5, 4062 (2014).
Le, T.-N. et al. DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol. 15, 458 (2014).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
Zheng, X., Zhu, J., Kapoor, A. & Zhu, J.-K. Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J. 26, 1691–1701 (2007).
Penterman, J., Uzawa, R. & Fischer, R. L. Genetic interactions between DNA demethylation and methylation in Arabidopsis. Plant Physiol. 145, 1549–1557 (2007).
Huettel, B. et al. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 25, 2828–2836 (2006).
Lei, M. et al. Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc. Natl Acad. Sci. USA 112, 3553–3557 (2015).
Williams, B. P., Pignatta, D., Henikoff, S. & Gehring, M. Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. PLoS Genet. 11, e1005142 (2015).
Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA 104, 6752–6757 (2007).
Matzke, M. A. & Mosher, R. A. RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat. Rev. Genet. 15, 394–408 (2014).
Zhang, H. & Zhu, J.-K. Active DNA demethylation in plants and animals. Cold Spring Harb. Symp. Quant. Biol. 77, 161–173 (2012).
Law, J. A. et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498, 385–389 (2013).
Zemach, A. et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013).
He, X.-J. et al. A conserved transcriptional regulator is required for RNA-directed DNA methylation and plant development. Genes Dev. 23, 2717–2722 (2009).
Gao, Z. et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465, 106–109 (2010).
Stroud, H. et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21, 64–72 (2014).
Mathieu, O., Reinders, J., Caikovski, M., Smathajitt, C. & Paszkowski, J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130, 851–862 (2007).
Eskandarian, H. A. et al. A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection. Science 341, 1238858 (2013).
Luo, C. et al. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J. 73, 77–90 (2013).
Rose, C. M., van den Driesche, S., Meehan, R. R. & Drake, A. J. Epigenetic reprogramming: preparing the epigenome for the next generation. Biochem. Soc. Trans. 41, 809–814 (2013).
Ponferrada-Marín, M. I., Martínez-Macías, M. I., Morales-Ruiz, T., Roldán-Arjona, T. & Ariza, R. R. Methylation-independent DNA binding modulates specificity of Repressor of Silencing 1 (ROS1) and facilitates demethylation in long substrates. J. Biol. Chem. 285, 23032–23039 (2010).
Harris, E. Y., Ponts, N., Le Roch, K. G. & Lonardi, S. BRAT-BW: efficient and accurate mapping of bisulfite-treated reads. Bioinformatics 28, 1795–1796 (2012).
Ausin, I. et al. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc. Natl Acad. Sci. USA 109, 8374–8381 (2012).
Huang, C.-F. et al. A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis. PLoS Genet. 9, e1003779 (2013).
Ibarra, C. A. et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360–1364 (2012).
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).
Zhang, H. et al. An Rrp6-like protein positively regulates noncoding RNA levels and DNA methylation in Arabidopsis. Mol. Cell 54, 418–430 (2014).
Acknowledgements
This work was supported by National Institutes of Health Grant R01GM070795 and by the Chinese Academy of Sciences (to J.-K. Z.).
Author information
Authors and Affiliations
Contributions
J.-K.Z, Z.L. and K.T. designed the study, interpreted the data and wrote the manuscript. K.T. and Z.L. did the bioinformatics analysis. H.Z. performed sequencing experiments.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary Information
Supplementary Figures 1–6 (PDF 1973 kb)
Supplementary Table 1
Table of the percentiles of the length of ROS1-targeted TEs and all TEs. (XLSX 38 kb)
Supplementary Table 2
Table of previously published data used in this study. (XLSX 37 kb)
Rights and permissions
About this article
Cite this article
Tang, K., Lang, Z., Zhang, H. et al. The DNA demethylase ROS1 targets genomic regions with distinct chromatin modifications. Nature Plants 2, 16169 (2016). https://doi.org/10.1038/nplants.2016.169
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/nplants.2016.169
This article is cited by
-
Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation
Plant Cell Reports (2024)
-
Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae)
BMC Biology (2023)
-
Long-lasting memory of jasmonic acid-dependent immunity requires DNA demethylation and ARGONAUTE1
Nature Plants (2023)
-
ROS1-mediated decrease in DNA methylation and increase in expression of defense genes and stress response genes in Arabidopsis thaliana due to abiotic stresses
BMC Plant Biology (2022)
-
Multi-omics data integration reveals link between epigenetic modifications and gene expression in sugar beet (Beta vulgaris subsp. vulgaris) in response to cold
BMC Genomics (2022)