J Integr Plant Biol. ›› 2022, Vol. 64 ›› Issue (12): 2374-2384.DOI: 10.1111/jipb.13376

• Research Articles • Previous Articles     Next Articles

Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis

Yue Wang1,2†, Yi Liu2†, Shaofeng Qu1, Wenjie Liang2, Linhua Sun1, Dong Ci3, Zhitong Ren1, Liu‐Min Fan2 and Weiqiang Qian1,3*   

  1. 1 State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
    2 School of Life Sciences, Peking University, Beijing 100871, China
    3 Peking University Institute of Advanced Agricultural Sciences, Weifang 261000, China

    These two authors contributed equally to this work.
    *Correspondence: Weiqiang Qian (wqqian@pku.edu.cn)
  • Received:2022-06-30 Accepted:2022-09-30 Online:2022-09-30 Published:2022-12-01

Abstract:

Nitrogen (N) availability is a major limiting factor for plant growth and agricultural productivity. Although the gene regulation network in response to N starvation has been extensively studied, it remains unknown whether N starvation has an impact on the activity of transposable elements (TEs). Here, we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions. Through genetic screening of idm1-14 suppressors, we cloned GLU1, which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway. We found that glutamate synthase 1 (GLU1) and its functional homologs GLU2 and glutamate transport 1 (GLT1) are redundantly required for TE silencing, suggesting that N metabolism can regulate TE activity. Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation. Genetic analysis indicated that N starvation-induced TE activation is also independent of other well-established epigenetic mechanisms, including histone methylation and heterochromatin decondensation. Our results provide new insights into the regulation of TE activity under stressful environments in planta.

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