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5 publications mentioning mdm-MIR390e

Open access articles that are associated with the species Malus domestica and mention the gene name MIR390e. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 57
Other miRNAs from this paper: mdm-MIR390a, mdm-MIR390b, mdm-MIR390c, mdm-MIR390d, mdm-MIR390f
And after genome doubling, the upregulation of miR390 level (Figs 6c and 7a) leads to upregulation of MdTAS3s expression (Fig. 7b), which in turn causes downregulation of MdARF3 expression (Figs 4 and 5). [score:14]
Using the 2 x plant as a control, miR390 expression was found to be upregulated by 3.2-fold in 3-year-old 4 x apple plants and upregulated by 2.65-fold in 5-year-old 4 x apple plants. [score:9]
Only miR390, which regulates the formation of trans-acting siRNA (TAS3 ta-siRNA), was significantly upregulated, with a log [2](4 x/2 x) ratio of 1.02 (Fig. 6c). [score:5]
Assessment of differences in the expression of miR390 and MdTAS3 in apple by qRT-PCRIn apple, miR390 is an indirect negative regulator of MdARF3 via MdTAS3 ta-siRNAs 24. [score:5]
Interestingly, miR390 was upregulated in the microarray analysis of autotetraploid apple. [score:4]
Both miR390 and TAS3-1a were found to be significantly upregulated in the autotetraploids (Fig. 7). [score:4]
We used qRT-PCR to analyse the differences in miR390 and TAS3-1a expression between diploids and autotetraploids using 3-year-old and 5-year-old plants. [score:3]
In apple, miR390 is an indirect negative regulator of MdARF3 via MdTAS3 ta-siRNAs 24. [score:3]
Expression of miR390 and MdTAS3-1a in diploid and autotetraploid 3- and 5-year-old apple plants as determined by qRT-PCR. [score:3]
Assessment of differences in the expression of miR390 and MdTAS3 in apple by qRT-PCR. [score:3]
The reactions were incubated in a 96-well plate (Applied Biosystems) at 95 °C for 3 min, followed by 40 cycles of 95 °C/10 s and 60 °C/30 s. To detect the difference in expression of miR390 and MdTAS3-1 between diploids and autotetraploids, qRT-PCR was performed with an iQ5 Real-Time PCR system (Bio-Rad) in a final reaction volume of 20 μl containing 1 μl of RT product, 8 μl of 2.5 × RealMaster Mix (TianGen, Beijing, China), 1 μl of 20 × probe enhancer solution, 0.5 μl of 10 μm TaqMan Probe, and 1 μl of 10 μM forward and reverse primers (Table 1). [score:2]
The reactions were incubated in a 96-well plate (Applied Biosystems) at 95 °C for 3 min, followed by 40 cycles of 95 °C/10 s and 60 °C/30 s. To detect the difference in expression of miR390 and MdTAS3-1 between diploids and autotetraploids, qRT-PCR was performed with an iQ5 Real-Time PCR system (Bio-Rad) in a final reaction volume of 20 μl containing 1 μl of RT product, 8 μl of 2.5 × RealMaster Mix (TianGen, Beijing, China), 1 μl of 20 × probe enhancer solution, 0.5 μl of 10 μm TaqMan Probe, and 1 μl of 10 μM forward and reverse primers (Table 1). [score:2]
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2
[+] score: 33
Other miRNAs from this paper: mdm-MIR156a, mdm-MIR156b, mdm-MIR156c, mdm-MIR156d, mdm-MIR156e, mdm-MIR156f, mdm-MIR156g, mdm-MIR156h, mdm-MIR156i, mdm-MIR156j, mdm-MIR156k, mdm-MIR156l, mdm-MIR156m, mdm-MIR156n, mdm-MIR156o, mdm-MIR156p, mdm-MIR156q, mdm-MIR156r, mdm-MIR156s, mdm-MIR156t, mdm-MIR156u, mdm-MIR156v, mdm-MIR156w, mdm-MIR156x, mdm-MIR156y, mdm-MIR156z, mdm-MIR156aa, mdm-MIR156ab, mdm-MIR156ac, mdm-MIR156ad, mdm-MIR156ae, mdm-MIR159a, mdm-MIR159b, mdm-MIR162a, mdm-MIR162b, mdm-MIR164a, mdm-MIR164b, mdm-MIR164c, mdm-MIR164d, mdm-MIR164e, mdm-MIR164f, mdm-MIR167a, mdm-MIR167b, mdm-MIR167c, mdm-MIR167d, mdm-MIR167e, mdm-MIR167f, mdm-MIR167g, mdm-MIR167h, mdm-MIR167i, mdm-MIR167j, mdm-MIR168a, mdm-MIR168b, mdm-MIR172a, mdm-MIR172b, mdm-MIR172c, mdm-MIR172d, mdm-MIR172e, mdm-MIR172f, mdm-MIR172g, mdm-MIR172h, mdm-MIR172i, mdm-MIR172j, mdm-MIR172k, mdm-MIR172l, mdm-MIR172m, mdm-MIR172n, mdm-MIR172o, mdm-MIR319a, mdm-MIR319b, mdm-MIR390a, mdm-MIR390b, mdm-MIR390c, mdm-MIR390d, mdm-MIR390f, mdm-MIR396a, mdm-MIR396b, mdm-MIR396c, mdm-MIR396d, mdm-MIR396e, mdm-MIR396f, mdm-MIR396g, mdm-MIR399a, mdm-MIR399b, mdm-MIR399c, mdm-MIR399d, mdm-MIR399e, mdm-MIR399f, mdm-MIR399g, mdm-MIR399h, mdm-MIR399i, mdm-MIR399j, mdm-MIR2111a, mdm-MIR2111b, mdm-MIR3627a, mdm-MIR3627b, mdm-MIR3627c, mdm-MIR535a, mdm-MIR535b, mdm-MIR535c, mdm-MIR535d, mdm-MIR828a, mdm-MIR828b, mdm-MIR159c, mdm-MIR319c, mdm-MIR858, mdm-MIR3627d, mdm-MIR159d, mdm-MIR159e, mdm-MIR159f, mdm-MIR399k, mdm-MIR319d, mdm-MIR319e, mdm-MIR319f, mdm-MIR319g, mdm-MIR319h, mdm-MIR172p
The pairings between miR390 and its target sites are illustrated below. [score:3]
Moreover, these short TAS3 genes are absent in Arabidopsis but conserved in many dicots sharing the presence of the dual miR390 target sites and production of a single tasiARF (Figure 5c). [score:3]
In contrast to MdTAS3-1, MdTAS3-2 family transcripts encode only one tasiARF, and there was no mismatch in the tenth position of the 5' miR390 target site (Figure 5c). [score:3]
Interestingly, tasiRNAs from each member displayed leaf- and flower-biased accumulation despite the nearly exclusive expression of miR390 in flower (Figures 1a, 3c and 5d; Figure S4f in Additional file 2). [score:3]
Apple TAS gene families with unique features and target specificityIn Arabidopsis, four TAS families targeted by three miRNAs, including miR173, miR390 and miR828, have been characterized [5, 17- 20, 30, 63]. [score:3]
The parings between miR390 and its target sites are illustrated below. [score:3]
In Arabidopsis, the transcript from a trans-acting siRNA (TAS) gene is first cleaved by one of three specialized miRNAs (miR173, miR390 and miR828), and then either the 3'-cleaved (in the case of miRNA828, miR173) or the 5'-cleaved transcript fragments (in the case of miR390) are converted into double-stranded RNAs by RDR6 and subsequently diced into phased 21-nucleotide siRNAs by DCL4 to generate multiple but distinct tasiRNA species, some of which are found to further guide sequence-specific cleavage of their targeted gene transcripts through the RISC [5, 17- 20]. [score:3]
Both miR390 and miR828 were identified in apple (Figure 1a, b), and showed highest expression specifically in flower as detected by RNA blot and RNA sequencing methods (Figures 1a, b and 3C). [score:3]
The miR390- TAS3 pathway is highly conserved in the plant kingdom [20], and the miR828- TAS4 pathway is wi dely represented in dicot species [65], but no miR173- TAS1/ TAS2 pathway has been found in other species besides Arabidopsis. [score:1]
To date, only four TAS families (AtTAS1-4) and three miRNAs (miR173, miR828, and miR390) that target TAS transcripts and trigger tasiRNA production have been reported and well characterized in Arabidopsis [5, 18- 20, 30]. [score:1]
The discovery of an additional short MdTAS3 family suggests that miR390 and tasiARFs may play more complicated roles in the auxin signaling pathway. [score:1]
In this study, we showed that apple conserved the miR390- TAS3 and miR828- TAS4 pathways with expanded features. [score:1]
Our deep sequence data show that both MdTAS3-1a/b and MdTAS3-1c have two miR390 cleavage sites flanking phased-tasiRNA generation regions (Figure 5a). [score:1]
Based on the siRNA distribution pattern, the 3' site of miR390 is predicted to set the phase for siRNA generation (Figure S4c, d in Additional file 2). [score:1]
We found that while blotting results for some miRNAs - miR828, miR858, miR390 (Figure 3c) and miR4376 (Figure 1c) - were reflective of the relative abundances of sequenced RNAs from these four tissues, many others displayed varying degrees of divergence between the two analyses. [score:1]
Like the MdTAS3-1 family, both MdTAS3-2a and MdTAS3-2b transcripts have two miR390 cleavage sites flanking an approximate 190-nucleotide region for 21-nucleotide phased siRNA production (Figure S4c, d in Additional file 2). [score:1]
In Arabidopsis, four TAS families targeted by three miRNAs, including miR173, miR390 and miR828, have been characterized [5, 17- 20, 30, 63]. [score:1]
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3
[+] score: 26
Other miRNAs from this paper: mdm-MIR156a, mdm-MIR156b, mdm-MIR156c, mdm-MIR156d, mdm-MIR156e, mdm-MIR156f, mdm-MIR156g, mdm-MIR156h, mdm-MIR156i, mdm-MIR156j, mdm-MIR156k, mdm-MIR156l, mdm-MIR156m, mdm-MIR156n, mdm-MIR156o, mdm-MIR156p, mdm-MIR156q, mdm-MIR156r, mdm-MIR156s, mdm-MIR156t, mdm-MIR156u, mdm-MIR156v, mdm-MIR156w, mdm-MIR156x, mdm-MIR156y, mdm-MIR156z, mdm-MIR156aa, mdm-MIR156ab, mdm-MIR156ac, mdm-MIR156ad, mdm-MIR156ae, mdm-MIR159a, mdm-MIR159b, mdm-MIR160a, mdm-MIR160b, mdm-MIR160c, mdm-MIR160d, mdm-MIR160e, mdm-MIR162a, mdm-MIR162b, mdm-MIR164a, mdm-MIR164b, mdm-MIR164c, mdm-MIR164d, mdm-MIR164e, mdm-MIR164f, mdm-MIR166a, mdm-MIR166b, mdm-MIR166c, mdm-MIR166d, mdm-MIR166e, mdm-MIR166f, mdm-MIR166g, mdm-MIR166h, mdm-MIR166i, mdm-MIR167a, mdm-MIR167b, mdm-MIR167c, mdm-MIR167d, mdm-MIR167e, mdm-MIR167f, mdm-MIR167g, mdm-MIR167h, mdm-MIR167i, mdm-MIR167j, mdm-MIR168a, mdm-MIR168b, mdm-MIR169a, mdm-MIR169b, mdm-MIR169c, mdm-MIR169d, mdm-MIR171a, mdm-MIR171b, mdm-MIR171c, mdm-MIR171d, mdm-MIR171e, mdm-MIR171f, mdm-MIR171g, mdm-MIR171h, mdm-MIR171i, mdm-MIR171j, mdm-MIR171k, mdm-MIR171l, mdm-MIR171m, mdm-MIR171n, mdm-MIR172a, mdm-MIR172b, mdm-MIR172c, mdm-MIR172d, mdm-MIR172e, mdm-MIR172f, mdm-MIR172g, mdm-MIR172h, mdm-MIR172i, mdm-MIR172j, mdm-MIR172k, mdm-MIR172l, mdm-MIR172m, mdm-MIR172n, mdm-MIR172o, mdm-MIR390a, mdm-MIR390b, mdm-MIR390c, mdm-MIR390d, mdm-MIR390f, mdm-MIR393a, mdm-MIR393b, mdm-MIR393c, mdm-MIR394a, mdm-MIR394b, mdm-MIR396a, mdm-MIR396b, mdm-MIR396c, mdm-MIR396d, mdm-MIR396e, mdm-MIR396f, mdm-MIR396g, mdm-MIR397a, mdm-MIR397b, mdm-MIR398a, mdm-MIR398b, mdm-MIR398c, mdm-MIR399a, mdm-MIR399b, mdm-MIR399c, mdm-MIR399d, mdm-MIR399e, mdm-MIR399f, mdm-MIR399g, mdm-MIR399h, mdm-MIR399i, mdm-MIR399j, mdm-MIR403a, mdm-MIR403b, mdm-MIR408a, mdm-MIR408b, mdm-MIR408c, mdm-MIR408d, mdm-MIR159c, mdm-MIR393d, mdm-MIR393e, mdm-MIR393f, mdm-MIR171o, mdm-MIR169e, mdm-MIR169f, mdm-MIR159d, mdm-MIR159e, mdm-MIR159f, mdm-MIR166j, mdm-MIR399k, mdm-MIR169g, mdm-MIR169h, mdm-MIR169i, mdm-MIR169j, mdm-MIR171p, mdm-MIR393g, mdm-MIR393h, mdm-MIR171q, mdm-MIR169k, mdm-MIR169l, mdm-MIR169m, mdm-MIR169n, mdm-MIR172p, mdm-MIR169o
Several miRNAs were expressed to similar levels in all tissues tested, e. g. miR396 was highly expressed in all tissues and miR162 showed moderate to low levels of expression in all tissues; miR164 and miR393 were barely detectable in the shoot apex, whereas miR160, miR169 and miR390 were more abundant in the shoot apex than other tissues; miR398, miR403 and miR408 appeared up-regulated in leaf. [score:10]
Conservation status miRNA family Arabidopsis Oryza(rice) Populus(poplar) Predicted target gene(s) miR156 √ √ √Squamosa promoter -binding proteins[57] miR159/319 √ √ √GAMYB transcription factors[57] miR160 √ √ √Auxin response factors (ARF) [57] miR162 √ √ √DICER-LIKE 1 (DCL1) [57] miR164 √ √ √NAC domain transcription factors[57] miR156/166 √ √ √HD-ZIP transcription factors[57] miR167 √ √ √Auxin response factors (ARF) [57] miR168 √ √ √ARGONAUTE 1 (AGO1) [57] miR169 √ √ √HAP2-like transcription factors[57] miR171 √ √ √Scarecrow-like transcription factors[57] miR172 √ √ √APETALA 2 transcription factors[58] miR390 √ √ √TAS3[59] miR393 √ √ √F-box transcription factors (TIR1) [60] miR394 √ √ √F-box transcription factors[60] miR396 √ √ √GRF, rhodenase[60] miR397 √ √ √laccase[60] miR398 √ √ √Copper superoxid dismutase, CytC oxidase[60] miR403 √ √ √ARGONAUTE 2 (AGO2)[20] miR408 √ √Peptide chain release factor, laccase[20] miR475 √PPR proteins[8] miR476 √PPR proteins[8] Figure 1 Differential expression of miRNAs in apple tissues. [score:5]
Conservation status miRNA family Arabidopsis Oryza(rice) Populus(poplar) Predicted target gene(s) miR156 √ √ √Squamosa promoter -binding proteins[57] miR159/319 √ √ √GAMYB transcription factors[57] miR160 √ √ √Auxin response factors (ARF) [57] miR162 √ √ √DICER-LIKE 1 (DCL1) [57] miR164 √ √ √NAC domain transcription factors[57] miR156/166 √ √ √HD-ZIP transcription factors[57] miR167 √ √ √Auxin response factors (ARF) [57] miR168 √ √ √ARGONAUTE 1 (AGO1) [57] miR169 √ √ √HAP2-like transcription factors[57] miR171 √ √ √Scarecrow-like transcription factors[57] miR172 √ √ √APETALA 2 transcription factors[58] miR390 √ √ √TAS3[59] miR393 √ √ √F-box transcription factors (TIR1) [60] miR394 √ √ √F-box transcription factors[60] miR396 √ √ √GRF, rhodenase[60] miR397 √ √ √laccase[60] miR398 √ √ √Copper superoxid dismutase, CytC oxidase[60] miR403 √ √ √ARGONAUTE 2 (AGO2)[20] miR408 √ √Peptide chain release factor, laccase[20] miR475 √PPR proteins[8] miR476 √PPR proteins[8] Figure 1 Differential expression of miRNAs in apple tissues. [score:5]
C, Stem-loop RT-PCR analyses using 10 ng total RNA of miR160, miR162, miR164, miR168, miR169, miR171, miR390, miR393, miR394, miR396, miR397, miR398, miR403, miR408, miR475, and miR476 expression. [score:3]
In particular, accumulation of miR156, miR167, miR169, miR390, and miR398 was more than ten-fold higher in the phloem sap than in the vascular tissue, suggesting a possibility of an active mechanism regulating their presence in the phloem sap. [score:2]
Using this approach miR156, miR159, miR160, miR162, miR167, miR169, miR396 and miR398 were clearly detectable; miR172, miR390 and miR393 produced a weak amplification signal; miR166 and miR397 amplification did not produce the expected product, but resulted in a smear not detected in the minus-RT control; miR164, miR168, miR171, miR394, miR403, miR408 and the miRNAs specific to poplar (miR475 and miR476) were not detected (Figure 4). [score:1]
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4
[+] score: 17
Other miRNAs from this paper: mdm-MIR482a, mdm-MIR156a, mdm-MIR156b, mdm-MIR156c, mdm-MIR156d, mdm-MIR156e, mdm-MIR156f, mdm-MIR156g, mdm-MIR156h, mdm-MIR156i, mdm-MIR156j, mdm-MIR156k, mdm-MIR156l, mdm-MIR156m, mdm-MIR156n, mdm-MIR156o, mdm-MIR156p, mdm-MIR156q, mdm-MIR156r, mdm-MIR156s, mdm-MIR156t, mdm-MIR156u, mdm-MIR156v, mdm-MIR156w, mdm-MIR156x, mdm-MIR156y, mdm-MIR156z, mdm-MIR156aa, mdm-MIR156ab, mdm-MIR156ac, mdm-MIR156ad, mdm-MIR156ae, mdm-MIR159a, mdm-MIR159b, mdm-MIR162a, mdm-MIR162b, mdm-MIR164a, mdm-MIR164b, mdm-MIR164c, mdm-MIR164d, mdm-MIR164e, mdm-MIR164f, mdm-MIR167a, mdm-MIR167b, mdm-MIR167c, mdm-MIR167d, mdm-MIR167e, mdm-MIR167f, mdm-MIR167g, mdm-MIR167h, mdm-MIR167i, mdm-MIR167j, mdm-MIR171a, mdm-MIR171b, mdm-MIR171c, mdm-MIR171d, mdm-MIR171e, mdm-MIR171f, mdm-MIR171g, mdm-MIR171h, mdm-MIR171i, mdm-MIR171j, mdm-MIR171k, mdm-MIR171l, mdm-MIR171m, mdm-MIR171n, mdm-MIR172a, mdm-MIR172b, mdm-MIR172c, mdm-MIR172d, mdm-MIR172e, mdm-MIR172f, mdm-MIR172g, mdm-MIR172h, mdm-MIR172i, mdm-MIR172j, mdm-MIR172k, mdm-MIR172l, mdm-MIR172m, mdm-MIR172n, mdm-MIR172o, mdm-MIR319a, mdm-MIR319b, mdm-MIR390a, mdm-MIR390b, mdm-MIR390c, mdm-MIR390d, mdm-MIR390f, mdm-MIR393a, mdm-MIR393b, mdm-MIR393c, mdm-MIR395a, mdm-MIR395b, mdm-MIR395c, mdm-MIR395d, mdm-MIR395e, mdm-MIR395f, mdm-MIR395g, mdm-MIR395h, mdm-MIR395i, mdm-MIR396a, mdm-MIR396b, mdm-MIR396c, mdm-MIR396d, mdm-MIR396e, mdm-MIR396f, mdm-MIR396g, mdm-MIR398a, mdm-MIR398b, mdm-MIR398c, mdm-MIR399a, mdm-MIR399b, mdm-MIR399c, mdm-MIR399d, mdm-MIR399e, mdm-MIR399f, mdm-MIR399g, mdm-MIR399h, mdm-MIR399i, mdm-MIR399j, mdm-MIR408a, mdm-MIR3627a, mdm-MIR3627b, mdm-MIR3627c, mdm-MIR477b, mdm-MIR477a, mdm-MIR482b, mdm-MIR482c, mdm-MIR535a, mdm-MIR535b, mdm-MIR535c, mdm-MIR535d, mdm-MIR408b, mdm-MIR408c, mdm-MIR408d, mdm-MIR2118a, mdm-MIR2118b, mdm-MIR2118c, mdm-MIR482d, mdm-MIR5225c, mdm-MIR159c, mdm-MIR7124a, mdm-MIR7124b, mdm-MIR5225a, mdm-MIR5225b, mdm-MIR319c, mdm-MIR393d, mdm-MIR393e, mdm-MIR393f, mdm-MIR171o, mdm-MIR1511, mdm-MIR3627d, mdm-MIR159d, mdm-MIR159e, mdm-MIR159f, mdm-MIR399k, mdm-MIR319d, mdm-MIR319e, mdm-MIR319f, mdm-MIR319g, mdm-MIR395j, mdm-MIR171p, mdm-MIR393g, mdm-MIR393h, mdm-MIR395k, mdm-MIR319h, mdm-MIR171q, mdm-MIR172p, mdm-MIR395l
Of the DE-miRNAs detected, miR164 targets NAC (NAM, ATAF, CUC) genes, miR167 targets AUXIN RESPONSIVE FACTOR6/8 (ARF6/8), miR390 targets trans-acting small interfering RNA3 (TAS3) transcripts to produce ta-siRNAs, which in turn regulates plant development by repressing ARF2/3/4, and miR393 targets TIR1 genes. [score:11]
In Arabidopsis, miR167 -targeted ARF6/8 are activators of auxin-responsive genes and could accelerate flowering timing (Nagpal et al., 2005); while the miR390-TAS3-repressed ARF2/3/4 are known to be repressors of auxin-responsive genes and flowering (Fahlgren et al., 2006). [score:3]
Interestingly, the majority of DE-miRNAs identified in our study (miR162, miR167, miR390, miR393, miR396, miR398, miR408, miR535, miR1511, miR2118, miR3627, and miR7124) showed opposite expression patterns compared to the ones in the previous study on phase transition in apple trees (Xing et al., 2014). [score:2]
miR164, miR167, miR390, and miR393 were found to involve in auxin signaling. [score:1]
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5
[+] score: 3
Three Md-miRNAs were listed in the Predicted miRNA/Target Pairs analysis among the genes included in this LG10 QTL confidence interval: Md-miR390 (6 isogenes), Md-miR7124 (2 isogenes) and Md-miR482a-p (list in Table S3 and S4). [score:3]
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