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Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa

文献类型： 外文期刊

作者： Ye, Xiaoxue 1 ; Wang, Shuo 1 ; Zhao, Xijuan 1 ; Gao, Ni 1 ; Wang, Yao 2 ; Yang, Yanmei 1 ; Wu, Ernest 4 ; Jiang, Cheng 1 ; Cheng, Yuxiang 5 ; Wu, Wenwu 1 ; Liu, Shenkui 1 ;

作者机构： 1.Zhejiang A&F Univ, State Key Lab Subtrop Silviculture, Hangzhou 311300, Peoples R China

2.Northeast Forestry Univ, Coll Life Sci, Key Lab Saline Alkali Vegetat Ecol Restorat, Minist Educ, Harbin 150040, Peoples R China

3.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Haikou 571101, Hainan, Peoples R China

4.Univ British Columbia, Fac Forestry, Dept Forest & Conservat Sci, Vancouver, BC V6T 1Z4, Canada

5.Northeast Forestry Univ, State Key Lab Tree Genet & Breeding, Sch Forestry, Harbin 150040, Peoples R China

关键词： lncRNA; salt stress; co-expression network; RNA-seq; cis-regulation; trans-regulation; Populus trichocarpa; NAC72

期刊名称：PLANT JOURNAL （ 影响因子：7.091； 五年影响因子：8.028 ）

ISSN： 0960-7412

年卷期： 2022 年 110 卷 4 期

页码：

收录情况： SCI

摘要： Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5 ' untranslated region (5 '-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.

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