Biogenesis, Mode of Action and the Interactions of Plant Non-Coding RNAs

Abstract

The central dogma of genetics, which outlines the flow of genetic information from DNA to RNA to protein, has long been the guiding principle in molecular biology. In fact, more than three-quarters of the RNAs produced by transcription of the plant genome are not translated into proteins, and these RNAs directly serve as non-coding RNAs in the regulation of plant life activities at the molecular level. The breakthroughs in high-throughput transcriptome sequencing technology and the establishment and improvement of non-coding RNA experiments have now led to the discovery and confirmation of the biogenesis, mechanisms, and synergistic effects of non-coding RNAs. These non-coding RNAs are now predicted to play important roles in the regulation of gene expression and responses to stress and evolution. In this review, we focus on the synthesis, and mechanisms of non-coding RNAs, and we discuss their impact on gene regulation in plants.

Keywords: biogenesis; growth; non-coding RNA; regulation; stress.

Figure 1

The central dogma and plant non-coding RNAs. As the primary transcription product, plant non-coding RNA transmits genetic information through biological macromolecules and plays a direct role in or outside the cell. Non-coding RNAs range from housekeeping RNAs that differ in expression and function to regulatory RNAs specifically expressed to help plants respond to changes in different habitats. Housekeeping RNAs consist of tRNAs and rRNAs, while regulatory RNAs can be categorized into circular RNA (circRNA), long intergenic non-coding RNA (lincRNA), microRNA (miRNA), and small interfering RNA (siRNA) according to different categories. The arrows represent the direction of biological process. M7G, a modification that a methyl group is added to the N⁷ position of guanine (G) of mRNA.

Figure 2

The biosynthesis and mechanism of micro RNAs (miRNAs). Many factors, such as transcription factors, mediators, and other protein complexes, affect the transcription of miRNA genes. Transcription factors (TFs) mediate POLII catalysis to unravel the miRNA gene (MIR). MIR is transcribed into stable pri-miRNA with stem-loop structure under the catalysis of DDL and CBC. TGH, SE, HYL1/DRB1, CPL1, and DCL proteins form a complex (D-body). DCL protein excises redundant sequences at the 5′ and 3′ terminals of the pri-miRNA stem base to form pre-miRNA. The DCL protein continues to cleave upward along the stem base of the pre-miRNA to form two complementary short double-stranded RNAs (dsRNAs). DsRNAs are methylated by HEN1 dsRNA terminal nucleotides and transported to the cytoplasm by HST. In the cytoplasm, SDN and HESO1 protein degrade one strand of dsRNA, while the other strand binds to AGO in RISC to form mature RISC. The fully functional RISC binds to the mRNA target sites under the guidance of miRNA and uses endonuclease activity to cleave the target mRNA. RISC can also prevent ribosome movement or promote ribosome shedding by binding mRNA to AMP1 on the endoplasmic reticulum. The RNA of the sheared mRNA fragment is degraded by an exonuclease and forms secondary small RNA. AMP1, ALTERED MERISTEM PROGRAM 1; CBC, nuclear cap-binding complex; CPL1, C-TERMINAL DOMAIN PHOSPHATASE-LIKE1; DCL, Dicer-like Protein; DDL, the phosphothreonine binding forkhead-associated domain protein DAWDLE; ER, endoplasmic reticulum; HESO1, the non-canonical poly (A) polymerase HEN1 SUPPRESSOR1; HYL1, HYPONASTIC LEAVES 1; m7G, a modification that a methyl group is added to the seventh N position of guanine (G) of mRNA; NOT2a/b, homologous proteins of the animal CCR4-NOT complex component NOT; POLII, RNA polymerase II; RDR6, RNA-dependent RNA polymerase 6; SDN, SMALL RNA DEGRADING NUCLEASE; SE, the zinc-finger protein SERRATE; TF, transcription factors; TGH, G-patch domain protein TOUGH.

Figure 3

The biogenesis and mechanism of small interfering RNAs (siRNAs). The biogenesis and mechanism of siRNAs begin with the cleavage of nucleic acid, RISC formation and product release. The exogenous dsRNAs from virus infection in the cytoplasm are cleaved by DCL to form vsiRNA and combined with a member of the AGO protein family to form a mature RISC (A). In the cytoplasm, the cleavage of the transcript by miRNA and AGO1 recruits SGS3 and RDR6. The RDR6 replicated SGS3 catalyzes transcript to form dsRNA, which will be cleaved by DCL and methylated by HEN1 to form a 21 nt tasiRNA that will bind to AGO1 to form a mature complex RISC (B). Under the co-catalysis of RDR, DCL and HEN1, the nucleic acid fragments produced by the miRNA-mediated mRNA cleavage process are transformed into 21 or 24 nt phasiRNA (C). Catalyzed by RDR, SGS3 and NRPD1, DCL1/2/3 cleaves NATs to produce 21 and 24 nt NatsiRNAs (D). After catalytic and cleavage by POLIV, RDR2 and DCL, 24 nt het-siRNAs load into AGO4 protein, which induced inhibitory chromatin modification and transcription gene silencing. In addition, SHH1 protein can recruit POLIV to synthesize siRNA at the transcription site of POLV (E). Mature RISC recognizes complementary target RNAs and cleaves them at positions between t10 and t11 (F). In some cases, highly purified RISCs cannot cleave their target mRNAs in a multi-conversion manner, suggesting the presence of external factors possibly driven by ATP hydrolysis (G). AGO, argonaute protein family; ATP, adenosine triphosphate; DCL, Dicer-like protein family; dsRNA, double-stranded RNA; HEN1, methyltransferase; het-siRNA, heterochromatic siRNA; m7G, a modification that a methyl group is added to the seventh N position of guanine (G) of mRNA; NATs, natural antisense transcripts; natsiRNA, natural antisense siRNA; NRPD1, DNA-directed RNA polymerase IV subunit 1; phasiRNA, phased small interfering RNA; POLIV, RNA polymerase IV; POLV, RNA polymerase V; RDR, RNA-dependent RNA polymerase; RdRP, RNA-dependent RNA polymerases; RISC, RNA-induced silencing complex; SGS3, SUPPRESSOR OF GENE SILENCING 3; SHH1, SAWADEE HOMEODOMAIN HOMOLOGUE 1; tasiRNA, trans-acting siRNA.

Figure 4

The biosynthesis and mechanism of circular RNAs (circRNAs). Different splicing of pre-mRNA produces different types and functions of circRNA. Exonic and intronic circRNAs are formed after pre-mRNA is cleaved at exon ends and flanking sequences containing long introns (multiple RBPS and IR or DR) (A). Cleavage of both ends of an exon at the pre-mRNA will result in the formation of linear RNA, exonic circRNA, and intronic circRNA (B). Exon–intron circRNA and intron–exon circRNA are generated when the cleavage initiation or termination site occurs within an exon of the pre-mRNA (C). When the exon of pre-mRNA is short, the longer linear RNA and exon circular RNA can be formed from the remaining sequences (D). The generated circRNA types have different functions; for example, exonic circRNAs can directly hybridize with target DNA to form a DNA:RNA structure, preventing the linear RNA formed by transcription from binding to DNA, resulting in transcriptional pause (E). CircRNAs can also act as miRNA sponges to regulate gene expression indirectly (F). CircRNAs have certain coding abilities and can also be translated into proteins (G). DR, direct repeat sequence; IR, reverse repeat sequence; RBP, RNA binding protein.

Figure 5

The biosynthesis and mechanism of long intergenic non-coding RNAs (lincRNAs). The synthesis of lincRNAs is similar to mRNA, in which DNA is transcribed into precursor RNA sequences catalyzed by TFs and RNA polymerase and transported to the cytoplasm for modification to perform different functions. LincRNAs can be classified according to different nuclear transcription sites: sense, antisense, bidirectional, intronic, and enhancer lincRNAs (A–E). The lincRNAs have several functions, such as decoy (F), where lincRNAs bind RNA-binding proteins (RBPs) to regulate gene expression. The lincRNAs can be a guide (G) to regulate gene expression by recruiting proteins to bind directly or form complexes with proteins that then bind to target gene-specific sites. The lincRNAs can act as a scaffold (H) by constituting the assembly sites of biological macromolecules and the necessary components for their function. Moreover, lincRNA can act as a molecular signal (I) to regulate gene expression at a specific time. m7G, a modification that a methyl group is added to the seventh N position of guanine (G) of mRNA; POLII, RNA polymerase II; POLIII, RNA polymerase III; POLIV, RNA polymerase IV; POLV, RNA polymerase V; TF, transcription factor.