5 publications mentioning ptc-MIR390c

Open access articles that are associated with the species Populus trichocarpa and mention the gene name MIR390c. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1

To validate the predicted target genes of miRNAs, degradome sequencing was performed, which confirmed LPCAT1/2, ACOX1/3, and IDH as targets of MIR156i/j, MIR396e/g, and MIR390c, respectively, in lipid metabolism or peroxidation (Supplementary Figure S4).

The IDH gene, a target of Ptc-miR390c, was highly expressed in cold stress.

Also, ISOCITRATE DEHYDROGENASE (IDH) participates in peroxisome biogenesis (a target gene of Ptc-miR390c; Biswas and Mano, 2015; Figure 4 and Excel S3).

Ptc-MIR390c showed [m]CG under heat stress and was unmethylated in cold -treated and control groups and also showed lower expression when modified with [m]CG, compared with the unmethylated control (Table 1; Figures 3B,C).

By contrast, under heat stress, these miRNA genes (except for Ptc-MIR390c) were methylated at CNG sites.

Thus, these miRNA genes showed different patterns of methylation, but most of the miRNA genes (except for Ptc-MIR156j and Ptc-MIR390c) were methylated at CG sites under cold stress.

Also, Ptc-MIR390c was unmethylated in the control group and cold -treated plants, but had [m]CG in heat -treated plants (Table 1).

This identified seven DMSs that mapped to conserved miRNA genes in the sequenced P. trichocarpa genome: Ptc-MIR156i, Ptc-MIR156j, Ptc-MIR167h, Ptc-MIR390c, Ptc-MIR393a, Ptc-MIR396e, and Ptc-MIR396g (Excel S2); these are homologs of the P. simonii miRNA genes.

Temperature stress also changed the methylation patterns of specific loci associated with miRNA genes responding to stress treatments, including Ptc-MIR156i and j, Ptc-MIR390c, and Ptc-MIR396e and g, which decrease the products of ACYL-COA OXIDASE (ACOX1 and ACOX3), PHOSPHOLIPID/GLYCEROL ACYLTRANSRASE FAMILY PROTEIN (LPCAT1 and LPCAT2), and ISOCITRATE DEHYDROGENASE (IDH) from Potri.

2

We also performed a search for predicted genomic target sites of miR390, miR475, miR476, miR482.2, and miR828 to examine whether any predicted targets matched the location of identified phased loci.

Despite the high level of conservation between the duplicated regions, there does not appear to have been conservation of the siRNA sequences themselves nor of the miR390 target sites.

Both [31] (Figure 4 of [31]) and [15] have previously shown conservation across a number of species for both the TAS3 miR390 target sites and two trans-acting siRNAs (TAS).

TAS1 and TAS2 transcripts are targeted by miR173, TAS3 by miR390 and TAS4 by miR828.

While miR390 and miR828 are conserved in Populus, there is no evidence of miR173 conservation.

3

In Arabidopsis, miR390 was reported to target TAS genes [66], while in P. trichocarpa, no TAS homologs have been found [26].

This may explain the regulatory mechanism of miR390 in poplars.

From our study, the degradome sequencing data proved the adjustment mechanism of Ptc-miR390 and lipoxygenases (LOXs).

4

No targets were found for 5 miRNA families, including pde-MIR390, pde-MIR1310, pde-MIR1311, pde-MIR3701 and pde-MIR3704.

It includes pde-MIR159, pde-MIR162, pde-MIR166, pde-MIR169, pde-MIR171, pde-MIR390, pde-MIR396 and pde-MIR399.

For example, the pde-MIR482 family has 4 members, whereas only one exists in 19 miRNA families (pde-MIR159, pde-MIR162, pde-MIR169, pde-MIR171, pde-MIR390, pde-MIR396, pde-MIR783, pde-MIR946, pde-MIR947, pde-MIR950, pde-MIR951, pde-MIR1310, pde-MIR1311, pde-MIR1312, pde-MIR1313, pde-MIR1314, pde-MIR1448, pde-MIR3701 and pde-MIR3712).

5

miR156, miR159, miR166, miR172, miR390, miR396, and miR5021 are the most expressed families in bud tissues.

Most of conserved families common to Arabidopsis and peach (miR156, miR159, miR160, miR164, miR166, miR171, miR172, miR319, miR390, miR395, and miR396) did not show significant size variation (Figure 4).