Expression of microRNAs and its regulation in plants

Abstract

MicroRNAs (miRNAs) have emerged as an essential regulatory component in plants. Many of the known miRNAs are evolutionarily conserved across diverse plant species and function in the regulatory control of fundamentally important biological processes such as developmental timing, patterning, and response to environmental changes. Expression of miRNAs in plants involves transcription from MIRNA loci by RNA polymerase II (pol II), multi-step processing of the primary transcripts by the DICER-LIKE1 (DCL1) complex, and formation of effector complexes consisting of mature miRNAs and ARGONAUTE (AGO) family proteins. In this short review, we present the most recent advances in our understanding of the molecular machinery as well as the regulatory mechanisms involved in the expression of miRNAs in plants.

Figure 1. Transcriptional regulation of miRNA expression in Arabidopsis thaliana

A. Certain ARF family members are regulated by miRNAs, either directly (miR160 and miR167) or indirectly (miR390). B. A possible negative feedback regulatory loop involving miR160, miR167 and certain ARF family members. Numerous copies of ARF recognition motif (TGTCTC) are found in the putative promoter regions of MIR160b, MIR167a, MIR167b, and miR167d [12]. C. SPL-mediated cross talk between miR156 and miR172. miR156 targets mRNAs for 10 members of the SPL family of transcription factors including SPL9 and SPL10, both of which promote the expression of MIR156a [18]. miR156 also regulates the expression of miR172 through SPL9 and SPL10 which function redundantly in promoting the transcription of MR172b [18]. TOE1 and TOE2, two of the six AP2 family transcription factors that are known to be the regulatory targets of miR172, also appear to positively regulate the expression of MIR172b [18], although evidence for a direct interaction between these AP2-like TFs and the MIR172 promoter is currently lacking. D. Putative SPL7 recognition sequences are found in the promoter regions of several low-copper-inducible MIRNAs. Each vertical light blue bar represents the presence of a putative SPL7 recognition sequence motif (GTAC) [26], as revealed by a computational scan within the putative promoter regions for each of the MIRNAs. Up to 1,000bp of the the putative promoter sequence, arbitrarily defined as the sequence upstream of a curated miRNA hairpin precursor [5] was included in the analysis. Note that while the putative promoter regions were drawn to scale, the miRNA hairpin precursor regions (black boxes) were not.

Figure 2. miRNA biogenesis in plants

A. Multi-step processing of pri-miRNA and miRNA maturation in a plant cell. Expression of miRNAs in plants begins with the pol II transcription of a MIRNA locus that is typically located in a genomic region not occupied by protein-coding genes, previously known as intergenic regions (IGR). The primary transcripts of a miRNA (pri-miRNA), which bear a 5′cap and a 3′ poly (A) tail, are capable of forming a characteristic hairpin-like secondary structure. CBC, a heterodimer consisting of CBP80 and CBP20 subunits of the nuclear cap-binding complex has been shown to play a role in pri-miRNA processing, likely through its direct interaction with a nascent transcript. DDL, a forkhead-associated domain-containing protein that has been shown to physically interact with pri-miRNA in vitro, likely function to stabilize the hairpin structure and help recruit DCL1 to its substrate. DCL1 and two other factors, HYL1, a dsRNA-binding protein, and SE, a C2H2-type zinc-finger domain-containing protein physically interact with each other and form a processing complex (DCL1 complex) in subnuclear bodies. The stepwise processing of a pri-miRNA by the DCL1 complex ultimately gives rise to a miRNA: miRNA* duplex that is subsequently recognized and end-methylated by HEN1. Loading of the miRNA strand into an AGO protein to form a functional miRISC marks the end of miRNA biogenesis. B. Size distribution of predicted hairpin precursors for plant and animal miRNAs. For each of the five model organisms (Arabidopsis thaliana, Oryza sativa, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens), the size distribution of miRNA hairpin precursors was analyzed by plotting the size (as curated in miRBase [5]; release 14) versus its frequency of occurrence.