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RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis

Nature Plantsvolume 4pages11121123 (2018) | Download Citation

Abstract

RNA polymerase II (Pol II) plays an essential role in gene expression. We used plant native elongating transcript sequencing and global run-on sequencing to profile nascent RNAs genome wide in Arabidopsis. We found that Pol II tends to accumulate downstream of the transcription start site (TSS). Moreover, Pol II with an unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream of the TSS, while Pol II with a Ser 5P CTD associates with spliceosomes, and Pol II with a Ser 2P CTD presents a sharp peak within 250 base pairs downstream of the polyadenylation site (PAS). Pol II pausing both at promoter-proximal regions and after PAS affects the transcription rate. Interestingly, active genes can be classified into three clusters based on the different modes of transcription. We demonstrate that these two methods are suitable to study Pol II dynamics in planta. Although transcription is conserved overall within eukaryotes, there is plant-specific regulation.

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Data availability

The sequencing data and processed files are available at the Gene Expression Omnibus under accession numbers GSE109974 and GSE117014.

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Acknowledgements

This work was supported by the General Programme of the National Natural Science Foundation of China (grant numbers 31471165 and 31271318) and the Key Laboratory of Plant Resource Conservation and Sustainable Utilization, Chinese Academy of Sciences, to Z.D.

Author information

Author notes

  1. These authors contributed equally: Jiafu Zhu and Min Liu.

Affiliations

  1. Plant Gene Engineering Centre, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China

    • Jiafu Zhu
    • , Min Liu
    • , Xiaobin Liu
    •  & Zhicheng Dong
  2. University of Chinese Academy of Sciences, Beijing, China

    • Jiafu Zhu
  3. School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, Guangzhou, China

    • Min Liu
    •  & Zhicheng Dong
  4. Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, China

    • Min Liu

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Contributions

Z.D. designed the research. J.Z. and X.L. performed experiments. M.L. analysed data. Z.D., M.L. and J.Z. wrote the manuscript.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Zhicheng Dong.

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DOI

https://doi.org/10.1038/s41477-018-0280-0