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DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

Nature Structural & Molecular Biology volume 19, pages 870–875 (2012)Cite this article

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Abstract

The plant-specific DNA-dependent RNA polymerase V (Pol V) evolved from Pol II to function in an RNA-directed DNA methylation pathway. Here, we have identified targets of Pol V in Arabidopsis thaliana on a genome-wide scale using ChIP-seq of NRPE1, the largest catalytic subunit of Pol V. We found that Pol V is enriched at promoters and evolutionarily recent transposons. This localization pattern is highly correlated with Pol V–dependent DNA methylation and small RNA accumulation. We also show that genome-wide chromatin association of Pol V is dependent on all members of a putative chromatin-remodeling complex termed DDR. Our study presents a genome-wide view of Pol V occupancy and sheds light on the mechanistic basis of Pol V localization. Furthermore, these findings suggest a role for Pol V and RNA-directed DNA methylation in genome surveillance and in responding to genome evolution.

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Figure 1: Identification of NRPE1-enriched sites by ChIP-seq and characterization of epigenetic marks at those sites.
Figure 2: The DDR complex is required for stable association of Pol V with chromatin.
Figure 3: NRPE1 is enriched at gene promoters.
Figure 4: NRPE1 is enriched at the intersection of promoters and transposons.
Figure 5: Loss of NRPE1 causes changes in protein-coding gene expression.
Figure 6: NRPE1 is enriched at transposons that are relatively new in the A. thaliana genome.

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Acknowledgements

We thank T. Lagrange at the Université de Perpignan, Perpignan, France, for the NRPE1-Flag transgenic seeds and M. Akhavan for assistance with high-throughput sequencing. X.Z. is supported by Ruth L. Kirschstein National Research Service grant F32GM096483-01. C.J.H. is supported by the Damon Runyon Cancer Research Foundation fellowship. S.F. is supported by the Leukemia & Lymphoma Society Special fellowship. This work was supported by NIH grant GM60398, and S.E.J. is supported as an investigator of the Howard Hughes Medical Institute.

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Author notes

  1. Xuehua Zhong and Christopher J Hale: These authors contributed equally to this work. Correspondence should be addressed to S.E.J. (jacobsen@ucla.edu).

  2. These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA

    Xuehua Zhong, Christopher J Hale, Julie A Law, Lianna M Johnson, Suhua Feng, Andy Tu & Steven E Jacobsen

  2. Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, USA

    Steven E Jacobsen

  3. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, California, USA

    Steven E Jacobsen

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  1. Xuehua Zhong
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Contributions

X.Z., C.J.H. and S.E.J. designed the experiments. X.Z., C.J.H., J.A.L., L.M.J., A.T. and S.F. performed the experiments. X.Z. and C.J.H. analyzed the data and wrote the manuscript.

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Correspondence to Steven E Jacobsen.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Tables 3–4 (PDF 1879 kb)

Supplementary Table 1

Genomic locations of identified NRPE1-enrichment sites and relative enrichment in NRPE1-FLAG ChIP-seq libraries compared to Col ChIP-seq libraries. (XLSX 405 kb)

Supplementary Table 2

“Ancient" transposons and corresponding blast hits between A. thaliana and A. lyrata. (XLSX 1072 kb)

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Zhong, X., Hale, C., Law, J. et al. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol 19, 870–875 (2012). https://doi.org/10.1038/nsmb.2354

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