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A comparative analysis of differential N6-methyladenosine (m6A) modification between non-transgenic and LBD15 overexpressing Poplar 84 K plants

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Abstract

N6-methyladenosine (m6A) plays an important role in the gene expression regulation. Previously, we found an ortholog of Arabidopsis LBD15 that showed xylem preferential expression and involved in leaf development in Poplar 84 K. In order to investigate whether m6A modification affects the function of LBD15, the m6A-immunoprecipitation sequence and the matched input RNA sequence for non-transgenic plants (CK) and the LBD15 overexpression (LBD15-oe) plants were compared and analyzed. As a result, 7,156 differential m6A peaks were identified, with 2,896 upregulated m6A peaks and 4,260 downregulated m6A peaks. Correlation analysis of differential expression genes and differential m6A peaks indicated that a total of 119 differently methylated genes showed a negative correlation with the differentially expressed genes. Among them, Nudix hydrolase, LRR receptor-like serine/threonine-protein kinase, tubulin, vacuole membrane protein KMS1, and MYB family transcription factor PHL11 may be involved in the posttranscriptional gene regulation in LBD15 overexpression plants. The expression of ten m6A-modified genes was validated by qRT-PCR. Our results will provide a basis for the further elucidation of the regulatory mechanism of m6A modification and the epigenetic regulation of LBD15.

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Data availability

The data presented in this study have been submitted to the SRA database under the accession number PRJNA725116.

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Funding

This research was funded by the Fundamental Research Funds for the Central Nonprofit Research Institution of CAF (CAFYBB2019SY006) and the National Key Research and Development Program of China (2017YFD0600205).

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Authors and Affiliations

  1. State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China

    Fenjuan Shao, Xiaochen Sun, Wenli Wu, Qiang Lu & Deyou Qiu

  2. CSIRO Agriculture and Food, Canberra, ACT, Australia

    Iain Wilson

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  1. Fenjuan Shao
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  2. Xiaochen Sun
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  3. Wenli Wu
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  4. Qiang Lu
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  6. Deyou Qiu
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Correspondence to Deyou Qiu.

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Shao, F., Sun, X., Wu, W. et al. A comparative analysis of differential N6-methyladenosine (m6A) modification between non-transgenic and LBD15 overexpressing Poplar 84 K plants. Tree Genetics & Genomes 17, 39 (2021). https://doi.org/10.1007/s11295-021-01521-y

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