Prediction of Plant MicroRNA Targets

Abstract

We predict regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity. Complementary sites within predicted targets are conserved in rice. Of the 49 predicted targets, 34 are members of transcription factor gene families involved in developmental patterning or cell differentiation. The near-perfect complementarity between plant miRNAs and their targets suggests that many plant miRNAs act similarly to small interfering RNAs and direct mRNA cleavage. The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages.

Identification of Potential microRNAs and Their Targets in Brassica rapa L.

“…The targets of BrMiR 837 were pathogenesis-related protein genes such as low-molecular-weight cysteine-rich 69 (LCR69). Similar observations were made in several studies of other plants (Bonnet et al, 2004a;Rhoades et al, 2002;Zhang et al, 2006b). Our result supports the previous reports of extensive evolutionary and functional conservation of miRNAs in plant species.…”

“…The identification of target genes for miRNAs is an important step in understanding the regulation of miRNA by structural genes. It is well understood that miRNAs and their counterpart target genes have perfect or near-perfect complementarities; computational identification coupled with experimental results have been successful in proving this in plants (Llave et al, 2002a;Park et al, 2002;Reinhart et al, 2002;Rhoades et al, 2002;Song et al, 2009). BLAST search analysis allowing for 1-4 nt mismatches without gaps for 186 miRNA could identify a total of 66 candidate target genes in B. rapa for 33 miRNA families.…”

“…Recently, many miRNAs have been shown to regulate a wide range of biological functions of plants. A growing amount of experimental evidence shows that miRNAs are involved in the regulation of transcrip-tion factors and other genes that play important roles in developmental timing, including the transitions from juvenile to adult and from the vegetative to reproductive phase (Lauter et al, 2005;Schwab et al, 2005;Wu and Poethig, 2006), floral development (Chen, 2004;Rhoades et al, 2002), leaf formation (Palatnik et al, 2003), stem development (Mallory et al, 2004), root development (Guo et al, 2005), signal transduction , male and female reproductive development (Wu and Poethig, 2006), and many other cellular processes (Ambros and Chen, 2007;Carrington and Ambros, 2003;Zhang et al, 2007b). Changes in the expression levels of miRNAs in plant tissues subjected to biotic stresses such as viral, fungal, and bacterial infection are reported (Bazzini et al, 2007;Lu et al, 2007;Navarro et al, 2006).…”

Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

“…Mature miRNAs can downregulate gene expression by pairing with messages of protein-coding genes to promote mRNA cleavage, or repression of productive translation upon incorporation into a ribonucleoprotein complex (miRNP) similar to the RNA-induced silencing complex (RISC) [10][11][12][13][14]. Indeed, the vast majority of the predicted or verified miRNA targets encode members of large families of transcription factors that regulate development [15]. Mutants that lack miRNA pathway proteins, such as DICER-LIKE 1 (DCL1), ARGONAUTE 1 (AGO1) and HUA ENHANCER 1 (HEN1), exhibit morphological defects in Arabidopsis and rice, suggesting an important role for miRNA in plant development [8,14,[16][17][18][19][20].…”

Des microARN comme s’il en pleuvait…

“…Alors que leur nombre ne cesse de croître, la fonction biologique des miARN est très mal comprise. Chez les plantes, nombreux sont les miARN pré-sentant des complémentarités parfaites avec des ARNm ; c'est notamment le cas de ceux codant pour des facteurs de transcription impliqués dans le développement [9]. En revanche, chez les métazoaires, la recherche des gènes que contrôlent les miARN reste plus problématique.…”