Abstract
Salvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.
Highlights
Salvia miltiorrhiza is one of the most widely used traditional medicines
In Arabidopsis thaliana, a cis-Natural antisense transcripts (NATs) producing from the opposite strand of MADS AFFECTING FLOWERING4 (MAF4) gene can positively regulate the expression of its sense transcripts (STs) MAF4, thereby affecting flowering time
To identify the NATs in S. miltiorrhiza, we carried out strand-specific RNA-seq analysis of 12 RNA samples extracted from three tissues, including roots (r), flowers (f), and leaves (l)
Summary
Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. In Arabidopsis thaliana, a cis-NAT producing from the opposite strand of MADS AFFECTING FLOWERING4 (MAF4) gene can positively regulate the expression of its ST MAF4, thereby affecting flowering time. It activates MAF4 by recruiting WDR5a to MAF4 to enhance histone 3 lysine 4 trimethylation (H3K4me3)[17]. Tanshinones is one of the major active compounds in S. miltiorrhiza and are used to treat cardiovascular diseases through anti-atherosclerosis[20], anti-oxidation[21], etc This plant produces many flavonoids[22], such as rutin, isoquercitrin, and astragalin. The results suggest that NATs might interact with different types of molecules such as the STs and miRNAs, and play an important role in a wide range of biological processes such as the biosynthesis of active compounds and glycosylation
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