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Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA

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  • Xinyue Zhao

    (Center for Plant Biology, School of Life Sciences, Tsinghua University
    Tsinghua-Peking Center for Life Sciences)

  • Jingrui Li

    (Center for Plant Biology, School of Life Sciences, Tsinghua University
    Tsinghua-Peking Center for Life Sciences)

  • Bi Lian

    (Center for Plant Biology, School of Life Sciences, Tsinghua University
    Tsinghua-Peking Center for Life Sciences)

  • Hanqing Gu

    (Center for Plant Biology, School of Life Sciences, Tsinghua University
    Tsinghua-Peking Center for Life Sciences)

  • Yan Li

    (Center for Plant Biology, School of Life Sciences, Tsinghua University)

  • Yijun Qi

    (Center for Plant Biology, School of Life Sciences, Tsinghua University
    Tsinghua-Peking Center for Life Sciences)

Abstract

Long non-coding RNAs (lncRNAs) have emerged as important regulators of gene expression and plant development. Here, we identified 6,510 lncRNAs in Arabidopsis under normal or stress conditions. We found that the expression of natural antisense transcripts (NATs) that are transcribed in the opposite direction of protein-coding genes often positively correlates with and is required for the expression of their cognate sense genes. We further characterized MAS, a NAT-lncRNA produced from the MADS AFFECTING FLOWERING4 (MAF4) locus. MAS is induced by cold and indispensable for the activation of MAF4 transcription and suppression of precocious flowering. MAS activates MAF4 by interacting with WDR5a, one core component of the COMPASS-like complexes, and recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3). Our study greatly extends the repertoire of lncRNAs in Arabidopsis and reveals a role for NAT-lncRNAs in regulating gene expression in vernalization response and likely in other biological processes.

Suggested Citation

  • Xinyue Zhao & Jingrui Li & Bi Lian & Hanqing Gu & Yan Li & Yijun Qi, 2018. "Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07500-7
    DOI: 10.1038/s41467-018-07500-7
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    Cited by:

    1. Zhen-Hui Wang & Xin-Feng Wang & Tianyuan Lu & Ming-Rui Li & Peng Jiang & Jing Zhao & Si-Tong Liu & Xue-Qi Fu & Jonathan F. Wendel & Yves Peer & Bao Liu & Lin-Feng Li, 2022. "Reshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    2. Benjamin J. M. Tremblay & Cristina P. Santini & Yajiao Cheng & Xue Zhang & Stefanie Rosa & Julia I. Qüesta, 2024. "Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

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