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Long non-coding RNAs and their biological roles in plants.

Liu X, Hao L, Li D, Zhu L, Hu S - Genomics Proteomics Bioinformatics (2015)

Bottom Line: In recent years, the lncRNAs have been considered as important regulators in many essential biological processes.In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited.Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

No MeSH data available.


Related in: MedlinePlus

The lncRNA-related regulatory networks for phosphate homeostasis in plantsA. miR399 can suppress the expression of its target gene, PHOSPHATE2 (PHO2), to control phosphate homeostasis [91,92]. miR399 is encoded by MIR399 genes, for which primary transcripts are lncRNAs. B. lncRNA IPS1 is induced under phosphate deficiency and acts as a target mimic for miR399 to regulate the phosphate homeostasis [61]. C.Cis-natural antisense RNA, cis-NATPHO1;2, can act as a translational enhancer for the expression of its sense gene, PHOSPHATE1;2 (PHO1;2), to control phosphate homeostasis in rice [89].
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f0005: The lncRNA-related regulatory networks for phosphate homeostasis in plantsA. miR399 can suppress the expression of its target gene, PHOSPHATE2 (PHO2), to control phosphate homeostasis [91,92]. miR399 is encoded by MIR399 genes, for which primary transcripts are lncRNAs. B. lncRNA IPS1 is induced under phosphate deficiency and acts as a target mimic for miR399 to regulate the phosphate homeostasis [61]. C.Cis-natural antisense RNA, cis-NATPHO1;2, can act as a translational enhancer for the expression of its sense gene, PHOSPHATE1;2 (PHO1;2), to control phosphate homeostasis in rice [89].

Mentions: Phosphate is an essential mineral nutrient for plant growth and development [87,88]. Several lines of evidence have suggested that lncRNAs are involved in the phosphate homeostasis [61,89]. First, some miRNAs have been reported to exert effects in regulating phosphate homeostasis [88,90,91]. The well-studied miR399 [91,92] can suppress the expression of its target gene, PHOSPHATE2 (PHO2), which encodes a ubiquitin-conjugating E2 enzyme (Figure 1A). PHO2 can interact with PHOSPHATE1 (PHO1), a membrane protein involved in phosphate loading to the xylem and a key regulator for phosphate homeostasis conserved in plants [93], to control phosphate homeostasis [92]. Since plant miRNAs are mainly encoded by lncRNAs [10,15], involvement of miRNAs in phosphate homeostasis is indicative of the involvement of lncRNAs in phosphate homeostasis. In addition, the aforementioned eTM-type lncRNAs IPS1 exemplifies the direct involvement of lncRNAs in phosphate homeostasis [61]. IPS1 is induced under phosphate deficiency and acts as a target mimic for miR399 (Figure 1B) [61]. Jabnoune et al. reported another layer of regulation in plants. They found that in rice, the cis-natural antisense RNA, cis-NATPHO1;2, can act as a translational enhancer for the expression of its sense gene, PHOSPHATE1;2 (PHO1;2) (Figure 1C) [89], the functional ortholog of PHO1 in Arabidopsis[94]. These findings reveal that there exists complex RNA regulatory network to control phosphate homeostasis in plants. Other lncRNAs related to phosphate homeostasis in tomato and rice are listed in Table 1, together with other important lncRNAs reported in plants [95–99].


Long non-coding RNAs and their biological roles in plants.

Liu X, Hao L, Li D, Zhu L, Hu S - Genomics Proteomics Bioinformatics (2015)

The lncRNA-related regulatory networks for phosphate homeostasis in plantsA. miR399 can suppress the expression of its target gene, PHOSPHATE2 (PHO2), to control phosphate homeostasis [91,92]. miR399 is encoded by MIR399 genes, for which primary transcripts are lncRNAs. B. lncRNA IPS1 is induced under phosphate deficiency and acts as a target mimic for miR399 to regulate the phosphate homeostasis [61]. C.Cis-natural antisense RNA, cis-NATPHO1;2, can act as a translational enhancer for the expression of its sense gene, PHOSPHATE1;2 (PHO1;2), to control phosphate homeostasis in rice [89].
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4563214&req=5

f0005: The lncRNA-related regulatory networks for phosphate homeostasis in plantsA. miR399 can suppress the expression of its target gene, PHOSPHATE2 (PHO2), to control phosphate homeostasis [91,92]. miR399 is encoded by MIR399 genes, for which primary transcripts are lncRNAs. B. lncRNA IPS1 is induced under phosphate deficiency and acts as a target mimic for miR399 to regulate the phosphate homeostasis [61]. C.Cis-natural antisense RNA, cis-NATPHO1;2, can act as a translational enhancer for the expression of its sense gene, PHOSPHATE1;2 (PHO1;2), to control phosphate homeostasis in rice [89].
Mentions: Phosphate is an essential mineral nutrient for plant growth and development [87,88]. Several lines of evidence have suggested that lncRNAs are involved in the phosphate homeostasis [61,89]. First, some miRNAs have been reported to exert effects in regulating phosphate homeostasis [88,90,91]. The well-studied miR399 [91,92] can suppress the expression of its target gene, PHOSPHATE2 (PHO2), which encodes a ubiquitin-conjugating E2 enzyme (Figure 1A). PHO2 can interact with PHOSPHATE1 (PHO1), a membrane protein involved in phosphate loading to the xylem and a key regulator for phosphate homeostasis conserved in plants [93], to control phosphate homeostasis [92]. Since plant miRNAs are mainly encoded by lncRNAs [10,15], involvement of miRNAs in phosphate homeostasis is indicative of the involvement of lncRNAs in phosphate homeostasis. In addition, the aforementioned eTM-type lncRNAs IPS1 exemplifies the direct involvement of lncRNAs in phosphate homeostasis [61]. IPS1 is induced under phosphate deficiency and acts as a target mimic for miR399 (Figure 1B) [61]. Jabnoune et al. reported another layer of regulation in plants. They found that in rice, the cis-natural antisense RNA, cis-NATPHO1;2, can act as a translational enhancer for the expression of its sense gene, PHOSPHATE1;2 (PHO1;2) (Figure 1C) [89], the functional ortholog of PHO1 in Arabidopsis[94]. These findings reveal that there exists complex RNA regulatory network to control phosphate homeostasis in plants. Other lncRNAs related to phosphate homeostasis in tomato and rice are listed in Table 1, together with other important lncRNAs reported in plants [95–99].

Bottom Line: In recent years, the lncRNAs have been considered as important regulators in many essential biological processes.In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited.Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.

No MeSH data available.


Related in: MedlinePlus