The long noncoding <scp>RNA </scp><i>T5120</i> regulates nitrate response and assimilation in Arabidopsis

Liu, Fei; Xu, Yiran; Chang, Kexin; Li, Shuna; Liu, Zhiguang; Qi, Shengdong; Jia, Jingbo; Zhang, Min; Crawford, Nigel M.; Wang, Yong

doi:10.1111/nph.16038

Cited by 63 publications

(46 citation statements)

References 99 publications

(143 reference statements)

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Section: Regulation Of Lateral Roots and Root Hair Development By A Nmentioning

confidence: 99%

“…In Arabidopsis, TCONS_00005120(T5120) was identified as a novel long non-coding RNA (lncRNA) induced by external nitrate, using high-throughput strand-specific RNA-seq ( Liu et al , 2019 ). The expression of T5120 was very low in all tested organs, and it was strongly induced by nitrate in a time- and concentration-dependent manner ( Liu et al , 2019 ). In an NR-null mutant ( nia1 nia2 ), the expression of T5120 could still be specifically induced by external nitrate, meaning that T5120 responds to nitrate itself but not its reduction products ( Liu et al , 2019 ).…”

Section: Regulation Of Lateral Roots and Root Hair Development By A Nmentioning

confidence: 99%

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Nitrate regulation of lateral root and root hair development in plants

Liu

Yang

et al. 2019

Journal of Experimental Botany

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Nitrogen (N) is one of the most important macronutrients for plant growth and development. However, the concentration and distribution of N varies in soil due to a variety of environmental factors. In response, higher plants have evolved a developmentally flexible root system to efficiently take up N under N-limited conditions. Over the past decade, significant progress has been made in understanding this form of plant ‘root-foraging’ behavior, which is controlled by both a local and a long-distance systemic nitrate signaling pathway. In this review, we focus on the key components of nitrate perception, signaling, and transduction and its role in lateral root development. We also highlight recent findings on the molecular mechanisms of the nitrate systemic signaling pathway, including small signaling peptides involved in long-distance shoot–root communication. Furthermore, we summarize the transcription factor networks responsible for nitrate-dependent lateral root and root hair development.

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Section: Regulation Of Lateral Roots and Root Hair Development By A Nmentioning

confidence: 99%

Section: Regulation Of Lateral Roots and Root Hair Development By A Nmentioning

confidence: 99%

Nitrate regulation of lateral root and root hair development in plants

Liu

Yang

et al. 2019

Journal of Experimental Botany

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“…Recently, a high‐throughput sequencing approach discovered nutrient‐responsive lncRNAs in Arabidopsis (Nishida et al , ; Fukuda et al , ). An lncRNA T5120 , activated by the transcription factor AtNLP7 under nitrate signalling, can function in regulating nitrate assimilation and root development (Liu et al , ). In this study, a novel ncRNA S21 of c. 30–100 nt length was observed in roots (Figure d).…”

Section: Discussionmentioning

confidence: 99%

Distinct non‐coding RNAs confer root‐dependent sense transgene‐induced post‐transcriptional gene silencing and nitrogen‐dependent post‐transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots

Zhang

Yuan

2020

The Plant Journal

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High-affinity ammonium uptake in roots mediate by AMT1-type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, in addition to the transcriptional and post-translational controls, an organ-dependent and N-dependent post-transcriptional regulation was suggested as an additional regulatory step for fine tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35s:AtAMT1;1-transformed atamt1;1-1 Arabidopsis plants resulted from RDR6-dependent sense transgene-induced post-transcriptional gene silencing (S-PTGS). The siRNAs for S-PTGS may derive from the aberrant RNA, of which the production was co-determined by sequence feature and excessive expression of AtAMT1;1. Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA-targeted hotspots reduced AtAMT1;1-specific siRNAs and overcame S-PTGS in roots. In roots of these lines, however, the steady-state transcript levels of AtAMT1;1 still significantly decreased under conditions of N-sufficiency compared with N-deficiency, confirming a N-dependent post-transcriptional regulatory manner. A crucial role of the 207-bp 3 0 -end sequence of AtAMT1;1 was further demonstrated by N-dependent accumulation of chimeric-AtAMT1;1 transcript in T-DNA insertion lines and of GFP-tagged chimeric-AtAMT1;1 transcript in transgenic lines. A novel non-coding RNA (ncRNA), which was highly abundant in N-sufficient roots, may target the above-identified 3 0 -end region for the degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on the AtAMT1;1 transcript at a potential cleavage site (+1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots.

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“…Emerging work has revealed that many lncRNAs regulate gene expression and have great influence on genome stability in plant [23,24]. Studies on Arabidopsis show that lncRNA can serve as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time[25,26]. Many plants reduce expression of some lncRNAs to affect developmental phenotypes or molecular changes [27].…”

Section: Discussionmentioning

confidence: 99%

A comparative transcriptional landscape of two castor cultivars obtained by single-molecule sequencing comparative analysis

Zhou

Guo-li

et al. 2020

Preprint

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Background and Objectives Castor ( Ricinus communis L.) is an important non-edible oilseed crop. Lm type female strains and normal amphiprotic strains are important castor cultivars, and are mainly different in inflorescence structures and leaf shapes. To better understand the mechanisums underling these differences at the molecular level, we performed comparative transcriptional analysis. Materials and Methods Full-length transcriptome sequencing and short-read RNA sequencing were employed. Results A total of 76,068 and 44,223 non-redundant transcripts were obtained from high-quality transcripts of Lm type female strains and normal amphiprotic strains, respectively. In Lm female strain and normal amphiprotic strains 51,613 and 20,152 alternative splicing events were found, respectively. There were 13,239 transcription factors identified from the full-length transcriptomes. Comparative analysis showed great different gene expression of common and unique transcription factors between the two cultivars. Meanwhile, functional analysis of isoform was conducted. Full-length sequences were used as a reference genome, and short-read RNA sequencing analysis was performed to conduct differential gene analysis. Furthermore, the function of DEGs were performed to annotation analysis. Conclusions The results revealed considerable difference and expression diversity between two cultivars, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two cultivars.

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The long noncoding RNA T5120 regulates nitrate response and assimilation in Arabidopsis

Cited by 63 publications

References 99 publications

Nitrate regulation of lateral root and root hair development in plants

Nitrate regulation of lateral root and root hair development in plants

Distinct non‐coding RNAs confer root‐dependent sense transgene‐induced post‐transcriptional gene silencing and nitrogen‐dependent post‐transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots

A comparative transcriptional landscape of two castor cultivars obtained by single-molecule sequencing comparative analysis

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