The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

Shi, Wan; Quan, Mingyang; Du, Qingzhang; Zhang, Deqiang

doi:10.3389/fpls.2017.01035

Cited by 13 publications

(9 citation statements)

References 55 publications

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“…Similarly, we found that many lncRNA associated mRNAs have binding functions such as nucleotide, small molecule, anion, and histone binding. This result directly suggests that the interaction of lncRNAs with target molecules is an important step in their transcriptional regulation of diverse biological processes, as shown recently (Shi et al, 2017).…”

Section: Discussionsupporting

confidence: 80%

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection withTomato yellow leaf curl virus

Zhou

Cho

Byun

et al. 2019

PeerJ

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Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.

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Section: Discussionsupporting

confidence: 80%

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection withTomato yellow leaf curl virus

Zhou

Cho

Byun

et al. 2019

PeerJ

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“…Chen et al (2015) performed a genome-wide identification of lncRNA in tension wood, opposite wood and normal wood xylem of P. tomentosa and identified 16 genes targeted by lncRNAs that are involved in wood formation processes, including lignin biosynthesis (Chen et al, 2015). In a similar study, the interaction of NEEDED FOR RDR2-INDEPENDENT DNA METHYLATION (NERD) and its regulatory lncRNA NERDL, which is partially located within the promoter region of NERD, is involved in the wood formation processes in Populus (Shi et al, 2017). In cotton, Dt subgenomespecific lncRNAs are enriched in lignin catabolic processes.…”

Section: Alternative Splicingmentioning

confidence: 99%

Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus

et al. 2020

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Lignin is a heterogeneous polymer of aromatic subunits derived from phenylalanine. It is polymerized in intimate proximity to the polysaccharide components in plant cell walls and provides additional rigidity and compressive strength for plants. Understanding the regulatory mechanisms of lignin biosynthesis is important for genetic modification of the plant cell wall for agricultural and industrial applications. Over the past 10 years the transcriptional regulatory model of lignin biosynthesis has been established in plants. However, the role of post-transcriptional regulation is still largely unknown. Increasing evidence suggests that lignin biosynthesis pathway genes are also regulated by alternative splicing, microRNA, and long non-coding RNA. In this review, we briefly summarize recent progress on the transcriptional regulation, then we focus on reviewing progress on the post-transcriptional regulation of lignin biosynthesis pathway genes in the woody model plant Populus.

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“…In P. tomentosa, 1377 lncRNAs were identified in the xylem of tension wood, contrast wood, and normal wood, and 15,691 lncRNAs were identified in the vascular cambium, developed xylem and mature xylem. Both UGTRL and NERDL might be involved in wood formation through regulation [16,17]. In E. grandis, lncRNA might act as a potential target or mimic to interact with miRNA, consistent with poplar lncRNA's interaction [47].…”

Section: Discussionmentioning

confidence: 55%

Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill

Zhan

Wang

Xie

et al. 2021

Forests

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Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of cellulose is a very complex process involving multiple genes and regulated by various biological networks. However, research on regulating associated genes and non-coding RNAs during cellulose synthesis in E. grandis remains lacking. In this study, the wood anatomical characteristics and chemical indexes of E. grandis were analyzed by taking three different parts (diameter at breast height (DBH), middle and upper part of the trunk) from the main stem of E. grandis as raw materials. The role of non-coding RNAs (Long non-coding RNA, lncRNA; Micro RNA, miRNA; Circle RNA, circRNA) on regulating candidate genes was presented, and the network map of ceRNA (Competing endogenous RNA) regulation during wood cellulose biosynthesis of E. grandis was constructed. The transcriptome sequencing of nine samples obtained from the trunk of the immature xylem in E. grandis at DBH, middle and upper parts had a 95.81 G clean reading, 57,480 transcripts, 7365 lncRNAs, and 5180 circRNAs. Each sample had 172–306 known miRNAs and 1644–3508 new miRNAs. A total of 190 DE-lncRNAs (Differentially expressed long non-coding RNAs), 174 DE-miRNAs (Differentially expressed micro RNAs), and 270 DE-circRNAs (Differentially expressed circle RNAs) were obtained by comparing transcript expression levels. Four lncRNAs and nine miRNAs were screened out, and the ceRNA regulatory network was constructed. LncRNA1 and lncRNA4 regulated the genes responsible for cellulose synthesis in E. grandis, which were overexpressed in 84K (Populus Alba × Populus glandulosa) poplar. The cellulose and lignin content in lncRNA4-oe were significantly higher than wild type 84K poplar and lncRNA1-oe. The average plant height, middle and basal part of the stem diameter in lncRNA4-oe were significantly higher than the wild type. However, there was no significant difference between the growth of lncRNA1-oe and the wild type. Further studies are warranted to explore the molecular regulatory mechanism of cellulose biosynthesis in Eucalyptus species.

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The Interactions between the Long Non-coding RNA NERDL and Its Target Gene Affect Wood Formation in Populus tomentosa

Cited by 13 publications

References 55 publications

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection withTomato yellow leaf curl virus

Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection withTomato yellow leaf curl virus

Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus

Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill

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