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36 publications mentioning ath-MIR399a

Open access articles that are associated with the species Arabidopsis thaliana and mention the gene name MIR399a. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 78
The expression level of IPS1 was reported to be up-regulated under P– condition, although miR399 was induced as well. [score:6]
The lncRNAs whose expression levels were negatively correlated with miR399 were shown in Table  2. Three lncRNAs (XLOC_020833, XLOC_001691 and XLOC_013661) were revealed to be potential targets of both PHR1 and miR399, indicating their feasible functions involved in the Pi starvation regulatory network (Tables  1 and 2, Fig.   6, and Additional file 7). [score:6]
We predicted 16 lncRNAs and 26 protein-coding genes as miR399 potential targets by integrating the sequence and expression relevance (Table  2). [score:5]
We combined expression correlations of miR399 and its potential targets to obtain a competing endogenous RNA (ceRNA) network for miR399. [score:5]
Furthermore, 104 and 16 lncRNAs were predicted as potential regulatory targets of PHR1 and miR399, respectively. [score:4]
Moreover, we identified 16 candidate lncRNAs as potential targets of miR399, another key regulator of plant Pi homeostasis. [score:4]
Integrating the above information, we proposed a Pi starvation signaling network illustrating the regulatory relationship among PHR1, miR399, PHO2, and their targets (Fig.   6). [score:4]
In addition, miR399 itself can be up-regulated by PHR1 [55]. [score:4]
IPS1–miR399 matching would therefore lead to the inhibition of miR399 -mediated cleavage of PHO2 transcripts, thus influencing downstream Pi uptake and translocation [27]. [score:3]
Pi starvation-responsive lncRNAs targeted by miR399. [score:3]
There were a total of 42 potential targets of miR399 (Table  2), of which 16 were lncRNAs. [score:3]
The expression of miR399 is highly induced in both shoots and roots by a decrease in external Pi levels [23, 24]. [score:3]
Our prediction recovered PHO2, the well-known target of miR399 [55, 75]. [score:3]
Two Pi starvation -induced long non-coding RNAs, IPS1 and AT4, further modulate the activity of miRNA399, through a mechanism called ‘target mimicry’ [27]. [score:3]
In total, we have predicted 10 potential target mimics of Pi starvation responsive miRNAs (miR399, miR156 and miR169). [score:3]
On the other hand, at the post-transcriptional level, miRNA399 has been identified as a key regulator of Pi homeostasis in post-transcriptional regulation [22]. [score:3]
Many other protein-coding genes and lncRNAs showed potential to be regulated by PHR1 and miR399 With the advance of next-generation sequencing technology, many novel non-coding RNA transcripts have been found in different species. [score:2]
Furthermore, our study provided many candidate lncRNAs that could be simultaneously regulated by PHR1 and miR399 (Tables  1 and 2, and Additional file 7). [score:2]
PHR1 and miRNA399 are two central transcriptional and post-transcriptional signal transducers in the regulatory network of Pi starvation responses. [score:2]
We also globally analyzed the regulatory network of miR399. [score:2]
We extended the regulatory network of PHR1 and miR399 by P1BS motif enrichment prediction and ceRNA network construction. [score:2]
Many other protein-coding genes and lncRNAs showed potential to be regulated by PHR1 and miR399 To systematically identify lncRNAs that responded to Pi starvation, we performed strand-specific poly(A) + and poly(A)– RNA sequencing of 10-day-old Arabidopsis seedlings grown under P+ and P– conditions. [score:2]
MiR399 has previously been shown to be a crucial post-transcriptional regulator [54], and has been demonstrated to bind the mRNAs of the PHO2 and AT4/IPS1 lncRNA family [27, 55]. [score:1]
Two lncRNAs, IPS1 and At4, have been found to act as decoys of miR399 during Pi starvation [27, 76]. [score:1]
Here, we calculated correlation coefficient of miR399 and its target genes using 8 matched small RNA-seq and long RNA-seq datasets from different samples, including two replicates of P+ in roots and shoots, and two replicates of P– in roots and shoots. [score:1]
In addition, we proposed the coding–non-coding network of Pi starvation responses, based on the PHR1–miR399–PHO2 pathway. [score:1]
[1 to 20 of 26 sentences]
2
[+] score: 64
Expression of (a) NF-YA8 -target of miR169; (b) PPR superfamily- target of miR161.1; (c) PHO2- target of miR399; (d) AGL16- target of miR824; (e) CIP4.1 or CIP4- target of miR834; (f) R3H- target of miR854. [score:15]
Throughout the germination stages miR399a and miR399b/c expression levels were upregulated in comparison to DS and the target PHO2 expression level was downregulated, except 48 h/4 °C (Fig.   6c). [score:13]
Availability of phytate and orthophosphate (Pi) in germinating seeds may regulate miR399 expression, which is known to be regulated by Pi availability, during germination [47]. [score:5]
PHO2 (PHOSPHATE 2) expression correlation was validated as the target of miR399 (Fig.   6c). [score:5]
Highest expression of miR399a (Fig.   3d) was at 24 h/RT and then 48 h/4 °C, whereas highest expression of miR399b/c (Fig.   3e) was at 12 h/4 °C and then 24 h/RT. [score:5]
miR399 is involved in orthophosphate (Pi) deficiency signalling pathway targets PHOSPHATE2 (PHO2) gene encoding E2 enzyme that negatively regulates phosphate uptake and root-to-shoot allocation 47, 48. [score:4]
This indicates that cold imbibition plays significant role in miR399 expression during seed germination. [score:3]
Previous reports also indicated the expression of miR399 in seeds of maize [20] and Nelumbo nucifera [22]. [score:3]
Interestingly, in spite of single nucleotide difference in miR399a and miR399b/c, we observed a significant variation in their expression levels at different germination stages. [score:3]
Expression of miR399a and miR399b/c were analyzed independently, since their mature sequence differed. [score:3]
The miR399a and miR399b/c (miR399b and miR399c have same mature sequence in Arabidopsis) has single nucleotide difference in the 13 [th] position from 5’ end. [score:1]
The other miRNAs for validation were miR165/166 (Fig.   2a), miR172a (Fig.   2b), miR390b (Fig.   2c), miR160a (Fig.   2d), miR156h (Fig.   2e), miR164a (Fig.   3a), miR169b (Fig.   3b), miR161.1 (Fig.   3c), miR399a (Fig.   3d), miR824 (Fig.   3f), miR834 (Fig.   3g), miR854 (Fig.   3h) and miR2112-5p (Fig.   3i). [score:1]
DS and they are miR161.2; miR169b, d, e; miR399a, b; miR824 and miR854a, c, e. Similarly, 8 miRNA genes were common in IS-4 °C vs. [score:1]
The Arabidopsis genome encodes six miR399 genes (miR399a -f), which are all induced by Phosphorus starvation to different extents [47]. [score:1]
Interestingly, all the miR399 (a, b and c) were induced in case of cold imbibition (4 °C) rather than RT. [score:1]
[1 to 20 of 15 sentences]
3
[+] score: 63
Other miRNAs from this paper: ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f
Furthermore, the expression of PHO2 was downregulated while the expression of miRNA399a and miRNA399d, which target to PHO2, was upregulated in bik1 plants, compared to the wild type plants, when grown under Pi deficient condition. [score:12]
Data presented are the means ± SD from three independent experiments and different letters above the columns indicate significant differences at p < 0.05 levelIt was found that expression of PHO2, encoding a ubiquitin-conjugating E2 enzyme, was suppressed by miRNA399, which controls Pi homeostasis in plants and whose expression is up-regulated by Pi starvation [48– 52]. [score:10]
Data presented are the means ± SD from three independent experiments and different letters above the columns indicate significant differences at p < 0.05 level It was found that expression of PHO2, encoding a ubiquitin-conjugating E2 enzyme, was suppressed by miRNA399, which controls Pi homeostasis in plants and whose expression is up-regulated by Pi starvation [48– 52]. [score:10]
These regulatory mechanisms include transcriptional regulation by transcription factors such as PHR1, WRKY6, WRKY42, WRKY45, WRKY75, ZAT6, bHLH32, ERF070 and MYB62 [37– 47], posttranscriptional regulation by microRNAs including miRNA399 [48– 53], posttranslational regulation by protein modifications such as sumoylation of SIZ1 [54], phosphorylation of Pht1.1 and activation of MKK9-MPK3/MPK6 module [55, 56], deubiquitination of UBP14 [57] and chromatin histone modification and epigenetic [46, 58]. [score:7]
Furthermore, altered expression patterns of PHO2 and miRNA399a/d, which are thought to be involved in systemic signaling of Pi starvation response and Pi distribution in plants [49, 52], were also observed in bik1 plants grown under + Pi and –Pi conditions (Fig.   6b). [score:3]
To examine whether PHO2/ miRNA399 links to increased accumulation of Pi in bik1 plants, we analyzed the changes in levels of PHO2 expression and two miRNA399 primary transcripts, miRNA399a and miRNA399d, in bik1 seedlings grown under + Pi and –Pi conditions. [score:3]
b Expression patterns of PHO2 and miRNA399 in WT and bik1 seedlings grown under + Pi and –Pi conditions. [score:3]
Altered expression of Pi starvation -induced genes and miRNA399 in bik1 plants. [score:3]
The expression level of PHO2 and the transcript levels of miRNA399a and miRNA399d were comparable in WT and bik1 seedlings grown under + Pi condition. [score:3]
A further reduction in the expression of PHO2 and a further increase in the transcripts of miRNA399a and miRNA399d in bik1 seedlings was observed as compared with those in WT seedlings grown under –Pi condition (Fig.   6b). [score:2]
However, the expression levels of PHO in WT and bik1 seedlings under –Pi condition were significantly reduced whereas the transcript levels of miRNA399a and miRNA399d in WT and bik1 seedlings grown under –Pi condition were markedly increased, as compared with the corresponding seedlings under + Pi condition (Fig.   6b). [score:2]
Together, these data indicate that the PHO2/ miRNA399 plays a role in regulating Pi accumulation in bik1 plants under –Pi condition. [score:2]
Data presented are the means ± SD from three independent experiments and different letters above the columns indicate significant differences at p < 0.05 level between WT and bik1 plants grwon under same condition Altered expression of Pi starvation -induced genes and miRNA399 in bik1 plantsExpression of some well-characterized Pi starvation -induced genes was analyzed and compared between WT and bik1 seedlings that had been transferred into medium with Pi (+Pi) or without Pi (−Pi) for 5 days. [score:2]
Pri-miRNA399a-1F, 5′-TGG CAG GAA ACC ATT ACT TAG ATC T-3′; Pri-miRNA399a-1R, 5′-TCA CTA ATT AAA AGC AAT GCA TAA AGA GA-3′; Pri-miRNA399d-1F, 5′-TTA CTG GGC GAA TAC TCC TAT GG-3′; Pri-miRNA399d-1R, 5′-ATT TTA CTT GCA TAT CTA GCC AAT GC-3′; PHO2-q-1F, 5′-AGG TTT GAA GCT CCA CCC TCA-3′; PHO2-q-1R, 5′-CCC AAG ATG TGA TTG GAG TTC C-3′; UBQ10-q-1F, 5′-GGC CTT GTA TAA TCC CTG ATG AAT AAG-3′; UBQ10-q-1R, 5′-AAA GAG ATA ACA GGA ACG GAA ACA TAG T-3′. [score:1]
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4
[+] score: 53
It could explain the increased expression of PHT1-8 and PHT1-9 in pho2 mutant plants (Bari et al., 2006), and the decreased expression of PHO2 and of the PHT1-8 and PHT1-9 Pi transporter genes in miR399 over -expressing transgenic lines (Aung et al., 2006). [score:7]
PHO2 expression is itself post-transcriptionally repressed by miR399, a small non-coding RNA up-regulated by Pi deficiency at the transcriptional level through PHR1/PHL1 activity (Fujii et al., 2005; Aung et al., 2006; Bari et al., 2006; Chiou et al., 2006; Liu et al., 2014; Figure 2). [score:6]
IPS1-miR399 matching would therefore lead to the inhibition of the miR399 RNA activity (Franco-Zorrilla et al., 2007) known to target PHO2 (Figure 2). [score:5]
It demonstrated the transport of this small RNA from leaves to root within the phloem sap, explaining why specific overexpression of the miR399 in leaves led to decrease the expression of PHO2 in roots (Pant et al., 2008). [score:5]
miR399 -dependent inhibition of PHO2 can be titrated under high Pi through RNA mimicry via its appariement to IPS1, a non-coding RNA positively regulated by PHR1 under Pi deficiency. [score:4]
As mentioned above, in response to Pi starvation PHR1 controls the transcription of post-transcriptional and post-translational regulators such as miR399, IPS1, and PHO2 (Figure 2). [score:4]
Among them the miRNA miR399 negatively regulates the ubiquitin E2 conjugase PHO2 responsible of the ubiquitination of PHT1 and PHO1 proteins in order to target them for proteasome degradation. [score:4]
So far, the major regulations of the expression of numerous Pi deficiency -induced genes was attributed to PHR1, via the PHR1-PHO2–miRNA399 pathway described below (Figure 2). [score:4]
At a molecular level, the PHR1 transcription factor was initially identified as a key regulator of the expression of phosphate starvation induced (PSI) genes, including phosphate transporters PHT1;1, PHO1;H 1, and genes involved in phosphate deficiency sensing and signaling including SPX1, miR399, and miR827. [score:4]
pho2 a phosphate overaccumulator, is caused by a nonsense mutation in a microRNA399 target gene. [score:3]
As aforementioned, PHR1 was already known as a major regulator of Pi deficiency signaling through its involvement in the PHR1-miR399-PHO2 regulatory pathway (Bari et al., 2006). [score:3]
IPS1 encodes a non-coding RNA whose sequence is in part complementary of the microRNA miR399, enabling post-transcriptional regulation via RNA mimicry (Liu et al., 2014). [score:2]
Finally the systemic effect of miR399 was evidenced by grafting experiments. [score:1]
MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. [score:1]
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5
[+] score: 43
However, it has been shown that while miR399 and PHO2 are co-expressed in vascular tissue, miR399 alone is expressed in mesophyll cells, where it may have a currently unidentified target (Aung et al. 2006), which could be repressed during senescence. [score:7]
Both miR399, which targets the negative repressor of phosphate transport, PHOSPHATE2 (PHO2, AT2G33770) and miR827, which targets the nitrogen/phosphate balance regulator NITROGEN LIMITATION ADAPTATION (NLA, AT1G02860), are well known to be strongly induced by low phosphate conditions (Chiou et al. 2006; Kant et al. 2011). [score:6]
The incoherent regulation of miR399 and miR827's target genes, which does not occur under whole-plant nutrient starvation, implies that nutrient-responsive miRNAs and their target genes may play additional roles in adaptation to shifting nutrient balance during natural senescence. [score:6]
Both miR399, which targets PHO2, and miR827, which targets NLA, were strongly induced during senescence in leaves (Fig.   2). [score:5]
Additionally, Arabidopsis expresses target mimics that sequester miR399, which could explain how both miR399 and PHO2 levels could increase under the same conditions (Franco-Zorrilla et al. 2007). [score:5]
miR399 and miR827 were both strongly induced during senescence in leaves but showed more complex pattern of regulation in siliques, where their expression was initially lower in early senescence (Fig.   2). [score:4]
In leaves, PHO2 gradually increased during senescence, showing incoherent regulation with miR399 and an opposite expression change than has been reported in non-senescence -induced phosphate deficiency. [score:4]
In keeping with the nutrient remobilization hypothesis, five out of the seven miRNAs (miR408, miR399, miR827, miR447 and miR398), which were senescence regulated, have been previously reported to be nutrient responsive (Fujii et al. 2005; Ab del-Ghany & Pilon 2008; Dugas & Bartel 2008; Pant et al. 2009; Kant et al. 2011), indicating that they may play a currently underappreciated role in controlling the flow of nutrients from vegetative to reproductive tissue. [score:2]
In siliques, PHO2 and NLA showed mostly coherent regulation, increasing to their highest levels in early senescence as miR399 and miR827 decreased. [score:2]
Like miR399 and miR827, this miRNA may also play a different role in senescence than it does in whole-plant nutrient deficiency and oxidative stress. [score:1]
miR399, on the other hand, was strongly increased at the end of senescence. [score:1]
[1 to 20 of 11 sentences]
6
[+] score: 41
The expression of TaPHO2 was presented as percentage of that in the control leaves which were transformed with TaPHO2-A1, -B1 or -D1 alone, the relative expression levels of tae-miR399-A1 and TaIPS1 were normalized using the expression of NtACTIN. [score:7]
The relative expression levels of TaPHO2 (a), tae-miR399-A1 (b) and TaIPS1 (c) in the tobacco leaves transiently overexpressed the indicated gene(s). [score:5]
Previously, the miR399 activity in cleaving PHO2 has been found to be reduced by IPS1 according to the target mimicry mechanism in Arabidopsis 14. [score:3]
Each of them contained 10 exons (including 2 untranslated exons in the 5′-UTR), and had five putative miR399 -binding sites in the second exon (Fig. 1a). [score:3]
The degradation of the TaPHO2s by tae-miR399-A1 was able to be inhibited by TaIPS1.1 (Fig. 2). [score:3]
These results indicated that all the three TaPHO2 genes were able to be degraded by tae-miR399, and TaIPS1.1 inhibited this degradation. [score:3]
Indeed, it has been reported that the miR399- PHO2 module regulates the flowering time in response to different ambient temperatures in Arabidopsis 30. [score:2]
The regulation of the TaPHO2 transcripts by tae-miR399 and TaIPS1. [score:2]
Regulation of TaPHO2 by tae-miR399 and TaIPS1. [score:2]
Regulation of TaPHO2 by tae-miR399 and TaIPS1Sequence analysis revealed that there were five putative miR399 -binding sites in 5′-UTRs of the three TaPHO2 genes (Supplemental Fig. S4). [score:2]
As such, the IPS1-miR399- PHO2 signaling cascade is conserved in plants. [score:1]
As all the three TaIPS1 genes conferred the conserved complementary sequences with tae-miR399, only TaIPS1.1 was chosen to check if it affected the degradation of TaPHO2-A1, -B1 or -D1 by tae-miR399. [score:1]
When TaPHO2-A1, -B1 or -D1 was co-transformed with tae-miR399-A1 in the tobacco leaves, the mRNA levels of all three TaPHO2 genes were significantly lower than that transformed with TaPHO2 gene alone (Fig. 2a). [score:1]
Sequence analysis revealed that there were five putative miR399 -binding sites in 5′-UTRs of the three TaPHO2 genes (Supplemental Fig. S4). [score:1]
In order to investigate whether TaPHO2 could be degraded by tae-miR399, we used tobacco transient expression system to analyze this possibility. [score:1]
Moreover, sequence analysis of TaIPS1s also found that three TaIPS1 genes all contained a motif with sequence complementarity to tae-miR399 (Supplemental Fig. S4). [score:1]
TaPHO2 mRNA levels in the tobacco leaves transformed with TaPHO2, tae-miR399-A1 and TaIPS1.1 were higher than that transformed with TaPHO2 and tae-miR399-A1 (Fig. 2a). [score:1]
The full length of tae-miR399 and TaIPS1.1 were also cloned into pRI101-AN vector. [score:1]
The blue ticks in the second exon depict the position of five putative miR399 binding sites. [score:1]
[1 to 20 of 19 sentences]
7
[+] score: 40
The sequencing analysis showed that in both callus and leaf tissues, various stress regulated-miRNAs were differentially expressed and real time PCR validated the expression profile of miR156, miR158, miR159, miR169, miR393, miR398, miR399 and miR408 along with their target genes. [score:8]
In the callus tissue two miRNAs (miR396 and miR399) and their corresponding target genes (growth regulating factor 4 and ubiquitin-protein ligase respectively) showed no agreement in their expression profile as expected. [score:6]
The H-T sequencing results showed that miR399 was only expressed in the callus tissue (Table  1) but the qPCR revealed that it was not differentially expressed in both tissues (Figure  5A, B). [score:5]
The expression data was then compared against the H-T sequencing data analysis which revealed that five (miR156, miR169, miR398, miR399 and miR408) of the nine miRNAs in callus tissue and six (miR158, miR159, miR169, miR393, miR396 and miR408) of the nine miRNAs in leaf tissue showed expression patterns that were similar to those observed with the H-T sequencing data. [score:4]
To validate the sequencing results with the bioinformatics -based analysis and based on their key function in gene regulation, the following mature miRNA were selected for expression profile analysis: miR156, mi158, miR159, miR169, miR393, miR396, miR398, miR399 and miR408. [score:4]
Furthermore, in the callus tissue, miR399 and three miRNAs in the leaf tissue (miR159, miR396 and miR399) were not differentially expressed between the untreated and treated samples. [score:3]
Experimental studies in Arabidopsis and other plants have shown that abiotic and biotic stresses induce differential expression of a set of miRNAs such as: miR156, miR159, miR165, miR167, miR168, miR169, miR319, miR393, miR395, miR396, miR398, miR399, and miR402 [7, 18- 23]. [score:3]
This was also the case in the leaf tissue for miR156, miR159, miR399 with their corresponding target genes; squamosa promoter -binding-like protein, Myb domain protein 101 and ubiquitin-protein ligase respectively. [score:3]
A putative target of miR399 encodes ubiquitin-protein ligase [60]. [score:3]
A similar observation was done for miR399 in the leaf tissue. [score:1]
[1 to 20 of 10 sentences]
8
[+] score: 32
We revealed that both miR399 and miR827 were expressed at low levels under N-starvation conditions, with concomitant increase in expression of their targets, PHO2 and NLA (Figure 3). [score:7]
Under N-starvation conditions, miR399, miR395, miR850, miR857, miR863, and miR827 were significantly down-regulated, whereas miR160, miR826, miR839, and miR846 were dramatically up-regulated. [score:7]
For example, miR395 is induced by sulfate starvation and regulates sulfate accumulation and allocation by targeting APSs (ATP Sulfurylase) and SULTR2;1 (SULFATE TRANSPORTER 2;1), respectively [10]; miR399 is up-regulated by phosphate limitation and controls phosphate transport and redistribution by repressing PHO2 (PHOSPHATE 2) [11]. [score:7]
pho2 mutant plants showed phosphate-toxic phenotypes similar to miR399 over -expressing plants [11]. [score:3]
For miR156, miR160, miR169, miR171, miR172, miR395, miR397, miR398, miR399, miR408, miR775, miR780.1, miR827, miR842, miR846, miR857, and miR2111, their targets have been predicted and most of them were validated previously (Table 2). [score:3]
For example, miR399 was induced under low-phosphate conditions, and moves from shoots to roots in Arabidopsis [32]. [score:1]
Three miRNAs (miR399, miR827, and miR2111) were identified to function in P homeostasis. [score:1]
Recent sequence analysis of miRNAs from Brassica napus [31] revealed that miR395 and miR399 are abundant in the phloem under low-sulfate and low-phosphate conditions, respectively. [score:1]
miR399 is specifically induced by P starvation and promotes phosphate uptake by cleavage of PHO2 transcripts. [score:1]
P-starvation -induced miRNAs (miR399, miR827, and miR2111) are involved in ubiquitin -mediated protein degradation [11]– [13], [27] and all of them were repressed greatly by N starvation. [score:1]
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9
[+] score: 28
Other miRNAs from this paper: ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f
PHO2 is a target of miR399 repression (Aung et al., 2006; Bari et al., 2006), and represses itself the expression a set of P starvation-inducible (PSI) genes under P-sufficient conditions (Bari et al., 2006). [score:5]
The pho2 mutant and miR399 overexpresser (miR399-OX) show a range of indistinguishable visible, physiological, and molecular phenotypes (Aung et al., 2006; Bari et al., 2006; Pant et al., 2009), such as the constitutive expression of PSI transcripts in P-replete conditions. [score:5]
In order to assess if miR399 and PHO2 are involved in the P starvation -dependent regulation of lipid metabolism, the expression of lipid-remo deling genes and lipid composition were analysed in the pho2 null mutant and in miR399d-OX. [score:4]
The function of miR399 as a phloem-mobile long-distance signal that reports P status between organs was revealed when miR399-OX shoots were grafted to wild-type roots, and miR399 was able to suppress PHO2 in the roots but not in the grafted shoots themselves (Pant et al., 2008). [score:3]
Aung K Lin SI Wu CC Huang YT Su CL Chiou TJ 2006 pho2, a phosphate overaccumulator, is caused by a nonsense mutation in a MicroRNA399 target gene. [score:3]
As PHO2 is strongly repressed during P starvation, only P-replete conditions were analysed for gene expression in both pho2 and miR399-OX lines. [score:3]
In miR399d-OX P-replete shoots, several species of TAG accumulated, suggesting that at least part of the TAG phenotype is dependent on miR399 (Supplementary Fig. S4). [score:1]
Six miR399 genes exist in Arabidopsis. [score:1]
PHR1, together with miR399 and PHO2, constitutes a systemic signalling pathway that communicates shoot P status to the root. [score:1]
PHR1 does not only affect local responses; together with microRNA399 (miR399) and PHO2, an E2 ubiquitin-conjugase, PHR1 constitutes a systemic signalling pathway that communicates shoot Pi status to the root (Bari et al., 2006; Pant et al., 2008). [score:1]
Pant BD Buhtz A Kehr J Scheible W-R 2008 MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. [score:1]
[1 to 20 of 11 sentences]
10
[+] score: 17
Other miRNAs from this paper: ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f
The mature miR399 can move from shoot to root via the phloem, where it targets the transcript of the E2-conjugase PHO2, leading to expression of Pi transporters (Lin et al., 2008; Pant et al., 2009). [score:5]
The increase in miR399 accumulation upon Pi deprivation is strongly suppressed in the phr1 mutant that lacks a MYB transcription factor (Bari et al., 2006). [score:3]
PHR1 is a master gene controlling the expression of numerous genes under Pi -deficient conditions, including the so-called ‘PHR1–miR399–PHO2’ Pi-starvation-signalling pathway (Rubio et al., 2001; Franco-Zorrilla et al., 2004, 2007; Aung et al., 2006; Bari et al., 2006; Chiou et al., 2006; Lin et al., 2008; Pant et al., 2008; Bustos et al., 2010). [score:3]
To explore whether the PHR1–miR399–PHO2 signalling pathway is part of the Zn-deficiency response in Arabidopsis, this work analysed the transcript abundance of several genes involved in this pathway, namely PHR1, miR399b, miR399d, PHO2, and two Pi-starvation-responsive genes that are dependent on PHR1, namely AT4 and IPS1 (Martín et al., 2000; Shin et al., 2006). [score:1]
Altogether, these results revealed that PHR1 plays a role in Zn–Pi interaction but ruled out the involvement of the already known PHR1–miR399–PHO2 Pi-starvation signalling cascade in this process. [score:1]
Nature Chemical Biology 5, 333– 340 Pant BD Buhtz A Kehr J Scheible WR 2008 MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. [score:1]
Fig. 2. mRNA accumulation of PHR1, AT4, IPS1, miR399, PHO2, and ZIP5 in response to the availability of Pi and Zn in shoots (A) and roots (B). [score:1]
This defined a Pi-signalling cascade, in which miR399 and PHO2 operate downstream of PHR1 (Franco-Zorrilla et al., 2004; Aung et al., 2006; Bari et al., 2006; Chiou et al., 2006; Doerner, 2008; Lin et al., 2008; Pant et al., 2009). [score:1]
The PHR1–miR399–PHO2 signalling pathway is not involved in the Pi response to Zn deficiency. [score:1]
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11
[+] score: 17
Other miRNAs from this paper: ath-MIR156a, ath-MIR156b, ath-MIR156c, ath-MIR156d, ath-MIR156e, ath-MIR156f, ath-MIR157d, ath-MIR158a, ath-MIR159a, ath-MIR160a, ath-MIR160b, ath-MIR160c, ath-MIR161, ath-MIR162a, ath-MIR162b, ath-MIR163, ath-MIR164a, ath-MIR164b, ath-MIR165a, ath-MIR165b, ath-MIR166a, ath-MIR166b, ath-MIR166c, ath-MIR166d, ath-MIR166e, ath-MIR166f, ath-MIR166g, ath-MIR167a, ath-MIR167b, ath-MIR169a, ath-MIR170, ath-MIR172a, ath-MIR172b, ath-MIR173, ath-MIR159b, ath-MIR319a, ath-MIR319b, ath-MIR167d, ath-MIR169b, ath-MIR169c, ath-MIR169d, ath-MIR169e, ath-MIR169f, ath-MIR169g, ath-MIR169h, ath-MIR169i, ath-MIR169j, ath-MIR169k, ath-MIR169l, ath-MIR169m, ath-MIR169n, ath-MIR171b, ath-MIR172c, ath-MIR172d, ath-MIR391, ath-MIR395a, ath-MIR395b, ath-MIR395c, ath-MIR395d, ath-MIR395e, ath-MIR395f, ath-MIR397a, ath-MIR397b, ath-MIR398a, ath-MIR398b, ath-MIR398c, ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f, ath-MIR400, ath-MIR408, ath-MIR156g, ath-MIR156h, ath-MIR158b, ath-MIR159c, ath-MIR319c, ath-MIR164c, ath-MIR167c, ath-MIR172e, ath-MIR447a, ath-MIR447b, ath-MIR447c, ath-MIR773a, ath-MIR775, ath-MIR822, ath-MIR823, ath-MIR826a, ath-MIR827, ath-MIR829, ath-MIR833a, ath-MIR837, ath-MIR841a, ath-MIR842, ath-MIR843, ath-MIR845a, ath-MIR848, ath-MIR852, ath-MIR824, ath-MIR854a, ath-MIR854b, ath-MIR854c, ath-MIR854d, ath-MIR857, ath-MIR864, ath-MIR2111a, ath-MIR2111b, ath-MIR773b, ath-MIR841b, ath-MIR854e, ath-MIR833b, ath-MIR156i, ath-MIR156j, ath-MIR826b
miR399, miR827, and miR2111 were upregulated by –P, but downregulated by –C, –N, and –S. [score:7]
Both miR399 and miR827 were suppressed by –C, –N, and –S, and their targets, PHO2 and NLA, were induced correspondingly (Fig. 3E,H). [score:5]
miR399 targets PHO2 which encodes a ubiquitin E2 conjugase and regulates the allocation of phosphate 22 34. [score:4]
Interestingly, the three miRNA families (miR399, miR827, and miR2111) induced by phosphate starvation (–P) were also repressed by other nutrient deficiencies (–C, –N, and –S). [score:1]
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12
[+] score: 15
While the expressions of 14 families (miR156/miR157, miR158, miR160, miR162, miR165/miR166, miR168, miR169, miR171, miR390, miR393, miR394, miR396, miR398, and miR399) were dramatically reduced, 3 families (miR159, miR167, and miR172) were up-regulated in CsCl -treated seedlings. [score:6]
In our analysis, we detected the expression levels of only 5 genes (miR399a, b, c, d, and f) which were significantly suppressed in both CsCl -treated (5-fold) and KCl -treated seedlings (3.2-fold) (Fig 3B, number 57–61). [score:5]
MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. [score:1]
Likewise, the miR399 family consists of 15 genes (miR399a - miR399o) and mostly contributes to the maintenance of phosphate homeostasis [34, 35]. [score:1]
In the case of KCl treatment, the miRNA counts of 4 families (miR156/miR157, miR169, miR394, and miR399) were reduced, whereas 9 families (miR159, miR164, miR165/miR166. [score:1]
Several miRNA families were significantly lower in both CsCl -treated and KCl -treated seedlings (miR156, miR169, miR170/miR171, and miR399). [score:1]
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13
[+] score: 12
Sequestration of RISC [miR399] by the natural target mimic IPS1 prevents miR399 -guided cleavage of PHO2 mRNA, thus increasing PHO2 mRNA levels [18]. [score:3]
Although such an effect has not been observed in case of the endogenous IPS1-miR399 interaction [18], a similar reduction in small RNA levels triggered by a target mimic has been reported in bacteria [24], [25]. [score:3]
To obtain additional evidence for such interactions, we embedded a functional MIM159 site in the 3′-UTR of a triple- Enhanced Yellow Fluorescent Protein (EYFP) reporter; stable recruitment of RISC [miR399] to the mimic site could be expected to interfere with EYFP translation. [score:3]
This results in sequestration of RISC [miR399], leading to a reduction of miR399 activity. [score:1]
As described [18], we modified the 23 nucleotide, miR399-complementary motif in IPS1. [score:1]
IPS1 (INDUCED BY PHOSPHATE STARVATION 1) encodes a non-coding RNA with a short motif that is highly complementary to the sequence of miR399, which like IPS1 is involved in the response to phosphate starvation [19]– [23]. [score:1]
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14
[+] score: 9
The absence of these classes in our dataset, together with the general trend of our data and the expression profile of P [i]-starvation responsive noncoding RNAs IPS1, miR399, and miR827 (see Additional file 4), confirmed that a 3-day period in P [i] sufficient media was a suitable choice for the recovery period. [score:3]
By a mechanism known as target -mimicry, IPS1 is resistant against the activity of RISC -loaded miRNA399 due to its partial sequence complementarity to the mature miR399. [score:3]
This property enables IPS1 the ability to quench the miR399 signal without being cleaved by the latter [42]. [score:1]
Click here for file P [i] marker genes, RT-PCR of P [i] -starvation responsive non-coding RNAs IPS, miR399, and miR827 at 10-days P [i] -replete and -starved, and 3-days recovery. [score:1]
P [i] marker genes, RT-PCR of P [i] -starvation responsive non-coding RNAs IPS, miR399, and miR827 at 10-days P [i] -replete and -starved, and 3-days recovery. [score:1]
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15
[+] score: 9
While miR168a targets ARGONAUTE 1 (AGO1) acting as a negative-feedback mediator to control AGO1 expression, miR399a is stress-inducible and targets PHO2 transcripts which encode E2 ubiquitin-conjugating enzymes (Lin et al., 2008; Li et al., 2012). [score:7]
Regulatory network of microRNA399 and PHO2 by systemic signaling. [score:1]
A number of miRNA genes showed tandem duplication patterns in E. salsugineum, including MIR168a and MIR399a which were tandemly duplicated four times on EsChr7 and EsChr1, respectively (Figure 8 and Table S2 in). [score:1]
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16
[+] score: 8
Other miRNAs from this paper: ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f
This regulation occurs through the action of the microRNA miR399 that targets and cleaves PHO2 mRNA in the roots. [score:4]
The expression of miR399 in the shoots depends on PHR1 and its transfer to the roots maintains an appropriate Pi‐homeostasis under Pi‐sufficient conditions. [score:3]
This shoot–roots movement makes of miR399 the first component of a systemic signal specifically controlling Pi‐homeostasis. [score:1]
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17
[+] score: 7
PHR1 is a transcription factor that positively regulates the expression of numerous genes upon Pi deficiency and that forms, along with PHO2 and the microRNA miR399, an important branch in the long-distance Pi signaling pathway [25, 29, 32- 35]. [score:4]
PHR1 has also been shown to influence the expression of microRNA miR399, and forms, along with PHO2, an important branch in the long-distance Pi signaling pathway [25, 29, 32- 35]. [score:3]
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18
[+] score: 6
Other miRNAs from this paper: ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f
Such an assignment could not be made for pri-miR399d (red dotted lines) in roots of Pi-deprived seedlings, indicating our imperfect understanding of the regulation of pri-miR399 expression. [score:4]
The loss of AtPHT1;9 also had an indirect effect on the transcript abundance of genes involved in systemic signalling mediated by the PHO2/mir399 network. [score:2]
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19
[+] score: 5
In addition, phosphate starvation induced the expression of miR399, which targets an E2 conjugase PHOSPHATE2, that functions upstream of a subset of phosphate starvation -induced genes [11– 13]. [score:5]
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[+] score: 4
Unlike other non-coding RNAs, the mechanisms and functions of lncRNAs can range wildly – from epigenetic regulation, as exemplified by mouse Xist and human XIST [6, 7], to small RNA target mimics, as seen with IPS1 and ath-miR399 in Arabidopsis thaliana [8]. [score:4]
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[+] score: 4
In this way, IPS1 serves as a decoy for miR399 and interferes with the binding of miR399 to its target. [score:3]
Here, an endogenous long non-coding RNA (IPS1, Induced by Phosphate Starvation1) binds to miR399 but the pairing is interrupted by a mismatched loop at the expected miRNA cleavage site, which abolishes the cleavage effect (Franco-Zorrilla et al. 2007). [score:1]
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[+] score: 4
The presence of miR399, which targets transcripts of the E2-ubiquitin conjugating enzyme family, also supports the idea that small RNA regulation of the protein degradation pathways is important in late pollen. [score:4]
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[+] score: 3
Other miRNAs from this paper: ath-MIR156a, ath-MIR156b, ath-MIR156c, ath-MIR156d, ath-MIR156e, ath-MIR156f, ath-MIR166a, ath-MIR166b, ath-MIR166c, ath-MIR166d, ath-MIR166e, ath-MIR166f, ath-MIR166g, ath-MIR169a, ath-MIR171a, ath-MIR169b, ath-MIR169c, ath-MIR169d, ath-MIR169e, ath-MIR169f, ath-MIR169g, ath-MIR169h, ath-MIR169i, ath-MIR169j, ath-MIR169k, ath-MIR169l, ath-MIR169m, ath-MIR169n, ath-MIR171b, ath-MIR171c, ath-MIR395a, ath-MIR395b, ath-MIR395c, ath-MIR395d, ath-MIR395e, ath-MIR395f, ath-MIR396a, ath-MIR396b, ath-MIR408, ath-MIR156g, ath-MIR156h, gma-MIR156d, gma-MIR156e, gma-MIR156c, gma-MIR166a, gma-MIR166b, gma-MIR156a, gma-MIR396a, gma-MIR396b, gma-MIR156b, gma-MIR169a, ath-MIR848, gma-MIR169b, gma-MIR169c, gma-MIR171a, gma-MIR171b, gma-MIR1527, gma-MIR1533, gma-MIR396c, pvu-MIR166a, pvu-MIR399a, gma-MIR396d, gma-MIR156f, gma-MIR169d, gma-MIR171c, gma-MIR169e, gma-MIR156g, gma-MIR396e, gma-MIR156h, gma-MIR156i, gma-MIR166c, gma-MIR166d, gma-MIR166e, gma-MIR166f, gma-MIR166g, gma-MIR166h, gma-MIR169f, gma-MIR169g, gma-MIR171d, gma-MIR171e, gma-MIR171f, gma-MIR171g, gma-MIR408d, ath-MIR5021, gma-MIR171h, gma-MIR171i, gma-MIR169h, gma-MIR169i, gma-MIR396f, gma-MIR396g, gma-MIR171j, gma-MIR395a, gma-MIR395b, gma-MIR395c, gma-MIR408a, gma-MIR408b, gma-MIR408c, gma-MIR156j, gma-MIR156k, gma-MIR156l, gma-MIR156m, gma-MIR156n, gma-MIR156o, gma-MIR166i, gma-MIR166j, gma-MIR169j, gma-MIR169k, gma-MIR169l, gma-MIR169m, gma-MIR169n, gma-MIR171k, gma-MIR396h, gma-MIR396i, gma-MIR171l, ath-MIR156i, ath-MIR156j, gma-MIR399a, gma-MIR156p, gma-MIR171m, gma-MIR171n, gma-MIR156q, gma-MIR171o, gma-MIR169o, gma-MIR171p, gma-MIR169p, gma-MIR156r, gma-MIR396j, gma-MIR171q, gma-MIR156s, gma-MIR169r, gma-MIR169s, gma-MIR396k, gma-MIR166k, gma-MIR156t, gma-MIR171r, gma-MIR169t, gma-MIR171s, gma-MIR166l, gma-MIR171t, gma-MIR171u, gma-MIR395d, gma-MIR395e, gma-MIR395f, gma-MIR395g, gma-MIR166m, gma-MIR169u, gma-MIR156u, gma-MIR156v, gma-MIR156w, gma-MIR156x, gma-MIR156y, gma-MIR156z, gma-MIR156aa, gma-MIR156ab, gma-MIR166n, gma-MIR166o, gma-MIR166p, gma-MIR166q, gma-MIR166r, gma-MIR166s, gma-MIR166t, gma-MIR166u, gma-MIR169v, gma-MIR395h, gma-MIR395i, gma-MIR395j, gma-MIR395k, gma-MIR395l, gma-MIR395m, gma-MIR169w
Fig. 4 Secondary structure of a pre-miR (pvu-miR399a) showing the mature miRNA sequence highlighted in blue The distribution of 208 newly predicted miRNAs in P vulgaris varies among the 118 miRNA families (Table  2). [score:1]
Fig.   4 shows a particular miRNA ‘pvu-miR399a’ that fulfils all the seven criteria used for the prediction. [score:1]
Fig. 4 Secondary structure of a pre-miR (pvu-miR399a) showing the mature miRNA sequence highlighted in blueThe distribution of 208 newly predicted miRNAs in P vulgaris varies among the 118 miRNA families (Table  2). [score:1]
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[+] score: 3
Other miRNAs from this paper: ath-MIR156a, ath-MIR156b, ath-MIR156c, ath-MIR156d, ath-MIR156e, ath-MIR156f, ath-MIR159a, ath-MIR160a, ath-MIR160b, ath-MIR160c, ath-MIR162a, ath-MIR162b, ath-MIR164a, ath-MIR164b, ath-MIR166a, ath-MIR166b, ath-MIR166c, ath-MIR166d, ath-MIR166e, ath-MIR166f, ath-MIR166g, ath-MIR167a, ath-MIR167b, ath-MIR168a, ath-MIR168b, ath-MIR169a, ath-MIR172a, ath-MIR172b, ath-MIR159b, osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR160a, osa-MIR160b, osa-MIR160c, osa-MIR160d, osa-MIR162a, osa-MIR164a, osa-MIR164b, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR167a, osa-MIR167b, osa-MIR167c, osa-MIR169a, ath-MIR167d, ath-MIR169b, ath-MIR169c, ath-MIR169d, ath-MIR169e, ath-MIR169f, ath-MIR169g, ath-MIR169h, ath-MIR169i, ath-MIR169j, ath-MIR169k, ath-MIR169l, ath-MIR169m, ath-MIR169n, ath-MIR172c, ath-MIR172d, ath-MIR395a, ath-MIR395b, ath-MIR395c, ath-MIR395d, ath-MIR395e, ath-MIR395f, ath-MIR396a, ath-MIR396b, ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f, osa-MIR395b, osa-MIR395d, osa-MIR395e, osa-MIR395g, osa-MIR395h, osa-MIR395i, osa-MIR395j, osa-MIR395k, osa-MIR395l, osa-MIR395s, osa-MIR395t, osa-MIR395c, osa-MIR395a, osa-MIR395f, osa-MIR395u, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR399a, osa-MIR399b, osa-MIR399c, osa-MIR399d, osa-MIR399e, osa-MIR399f, osa-MIR399g, osa-MIR399h, osa-MIR399i, osa-MIR399j, osa-MIR399k, ath-MIR408, ath-MIR156g, ath-MIR156h, ath-MIR159c, ath-MIR164c, ath-MIR167c, ath-MIR172e, osa-MIR156k, osa-MIR156l, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR160e, osa-MIR160f, osa-MIR162b, osa-MIR164c, osa-MIR164d, osa-MIR164e, osa-MIR166k, osa-MIR166l, osa-MIR167d, osa-MIR167e, osa-MIR167f, osa-MIR167g, osa-MIR167h, osa-MIR167i, osa-MIR168a, osa-MIR168b, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR172a, osa-MIR172b, osa-MIR172c, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR408, osa-MIR172d, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, zma-MIR156d, zma-MIR156f, zma-MIR156g, zma-MIR156b, zma-MIR156c, zma-MIR156e, zma-MIR156a, zma-MIR156h, zma-MIR156i, zma-MIR160a, zma-MIR160c, zma-MIR160d, zma-MIR160b, zma-MIR164a, zma-MIR164d, zma-MIR164b, zma-MIR164c, zma-MIR169a, zma-MIR169b, zma-MIR167a, zma-MIR167b, zma-MIR167d, zma-MIR167c, zma-MIR160e, zma-MIR166a, zma-MIR162, zma-MIR166h, zma-MIR166e, zma-MIR166i, zma-MIR166f, zma-MIR166g, zma-MIR166b, zma-MIR166c, zma-MIR166d, zma-MIR172a, zma-MIR172d, zma-MIR172b, zma-MIR172c, osa-MIR396e, zma-MIR395b, zma-MIR395c, zma-MIR395a, zma-MIR396b, zma-MIR396a, zma-MIR399a, zma-MIR399c, zma-MIR399b, zma-MIR399d, zma-MIR399e, zma-MIR399f, zma-MIR156j, zma-MIR159a, zma-MIR159b, zma-MIR159c, zma-MIR159d, zma-MIR166k, zma-MIR166j, zma-MIR167e, zma-MIR167f, zma-MIR167g, zma-MIR167h, zma-MIR167i, zma-MIR168a, zma-MIR168b, zma-MIR169c, zma-MIR169f, zma-MIR169g, zma-MIR169h, zma-MIR169i, zma-MIR169k, zma-MIR169j, zma-MIR169d, zma-MIR169e, zma-MIR172e, zma-MIR166l, zma-MIR166m, zma-MIR171h, zma-MIR408a, zma-MIR156k, zma-MIR160f, osa-MIR529a, osa-MIR395m, osa-MIR395n, osa-MIR395o, osa-MIR395p, osa-MIR395q, osa-MIR395v, osa-MIR395w, osa-MIR395r, osa-MIR529b, osa-MIR169r, osa-MIR396f, zma-MIR396c, zma-MIR396d, osa-MIR2118a, osa-MIR2118b, osa-MIR2118c, osa-MIR2118d, osa-MIR2118e, osa-MIR2118f, osa-MIR2118g, osa-MIR2118h, osa-MIR2118i, osa-MIR2118j, osa-MIR2118k, osa-MIR2118l, osa-MIR2118m, osa-MIR2118n, osa-MIR2118o, osa-MIR2118p, osa-MIR2118q, osa-MIR2118r, osa-MIR2275a, osa-MIR2275b, zma-MIR2118a, zma-MIR2118b, zma-MIR2118c, zma-MIR2118d, zma-MIR2118e, zma-MIR2118f, zma-MIR2118g, zma-MIR2275a, zma-MIR2275b, zma-MIR2275c, zma-MIR2275d, osa-MIR396g, osa-MIR396h, osa-MIR396d, zma-MIR156l, zma-MIR159e, zma-MIR159f, zma-MIR159g, zma-MIR159h, zma-MIR159i, zma-MIR159j, zma-MIR159k, zma-MIR160g, zma-MIR164e, zma-MIR164f, zma-MIR164g, zma-MIR164h, zma-MIR166n, zma-MIR167j, zma-MIR169l, zma-MIR169m, zma-MIR169n, zma-MIR169o, zma-MIR169p, zma-MIR169q, zma-MIR169r, zma-MIR395d, zma-MIR395e, zma-MIR395f, zma-MIR395g, zma-MIR395h, zma-MIR395i, zma-MIR395j, zma-MIR395k, zma-MIR395l, zma-MIR395m, zma-MIR395n, zma-MIR395o, zma-MIR395p, zma-MIR396e, zma-MIR396f, zma-MIR396g, zma-MIR396h, zma-MIR399g, zma-MIR399h, zma-MIR399i, zma-MIR399j, zma-MIR408b, zma-MIR529, osa-MIR395x, osa-MIR395y, osa-MIR2275c, osa-MIR2275d, ath-MIR156i, ath-MIR156j
There were extremely low frequencies of miR395, miR399, miR2275, miRs12, and miRs19, possibly because these families are expressed in a tissue-specific manner. [score:3]
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25
[+] score: 2
Other miRNAs from this paper: ath-MIR159a, ath-MIR162a, ath-MIR162b, ath-MIR166a, ath-MIR166b, ath-MIR166c, ath-MIR166d, ath-MIR166e, ath-MIR166f, ath-MIR166g, ath-MIR169a, ath-MIR171a, ath-MIR159b, ath-MIR319a, ath-MIR319b, osa-MIR162a, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR169a, osa-MIR171a, ath-MIR169b, ath-MIR169c, ath-MIR169d, ath-MIR169e, ath-MIR169f, ath-MIR169g, ath-MIR169h, ath-MIR169i, ath-MIR169j, ath-MIR169k, ath-MIR169l, ath-MIR169m, ath-MIR169n, ath-MIR171b, ath-MIR171c, ath-MIR390a, ath-MIR390b, ath-MIR396a, ath-MIR396b, ath-MIR398a, ath-MIR398b, ath-MIR398c, ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f, osa-MIR396a, osa-MIR396b, osa-MIR396c, osa-MIR398a, osa-MIR398b, osa-MIR399a, osa-MIR399b, osa-MIR399c, osa-MIR399d, osa-MIR399e, osa-MIR399f, osa-MIR399g, osa-MIR399h, osa-MIR399i, osa-MIR399j, osa-MIR399k, ath-MIR408, ath-MIR159c, ath-MIR319c, osa-MIR156k, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR319a, osa-MIR319b, osa-MIR162b, osa-MIR166k, osa-MIR166l, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR171b, osa-MIR171c, osa-MIR171d, osa-MIR171e, osa-MIR171f, osa-MIR171g, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR408, osa-MIR171i, osa-MIR166m, osa-MIR166j, ath-MIR414, osa-MIR414, osa-MIR390, osa-MIR396e, ptc-MIR156k, ptc-MIR159a, ptc-MIR159b, ptc-MIR159d, ptc-MIR159e, ptc-MIR159c, ptc-MIR162a, ptc-MIR162b, ptc-MIR166a, ptc-MIR166b, ptc-MIR166c, ptc-MIR166d, ptc-MIR166e, ptc-MIR166f, ptc-MIR166g, ptc-MIR166h, ptc-MIR166i, ptc-MIR166j, ptc-MIR166k, ptc-MIR166l, ptc-MIR166m, ptc-MIR166n, ptc-MIR166o, ptc-MIR166p, ptc-MIR166q, ptc-MIR169a, ptc-MIR169aa, ptc-MIR169ab, ptc-MIR169ac, ptc-MIR169ad, ptc-MIR169ae, ptc-MIR169af, ptc-MIR169b, ptc-MIR169c, ptc-MIR169d, ptc-MIR169e, ptc-MIR169f, ptc-MIR169g, ptc-MIR169h, ptc-MIR169i, ptc-MIR169j, ptc-MIR169k, ptc-MIR169l, ptc-MIR169m, ptc-MIR169n, ptc-MIR169o, ptc-MIR169p, ptc-MIR169q, ptc-MIR169r, ptc-MIR169s, ptc-MIR169t, ptc-MIR169u, ptc-MIR169v, ptc-MIR169w, ptc-MIR169x, ptc-MIR169y, ptc-MIR169z, ptc-MIR171a, ptc-MIR171b, ptc-MIR171c, ptc-MIR171d, ptc-MIR171e, ptc-MIR171f, ptc-MIR171g, ptc-MIR171h, ptc-MIR171i, ptc-MIR319a, ptc-MIR319b, ptc-MIR319c, ptc-MIR319d, ptc-MIR319e, ptc-MIR319f, ptc-MIR319g, ptc-MIR319h, ptc-MIR319i, ptc-MIR390a, ptc-MIR390b, ptc-MIR390c, ptc-MIR390d, ptc-MIR396a, ptc-MIR396b, ptc-MIR396c, ptc-MIR396d, ptc-MIR396e, ptc-MIR396f, ptc-MIR396g, ptc-MIR398a, ptc-MIR398b, ptc-MIR398c, ptc-MIR399a, ptc-MIR399b, ptc-MIR399d, ptc-MIR399f, ptc-MIR399g, ptc-MIR399h, ptc-MIR399i, ptc-MIR399j, ptc-MIR399c, ptc-MIR399e, ptc-MIR408, ptc-MIR482a, ptc-MIR171k, osa-MIR169r, ptc-MIR171l, ptc-MIR171m, ptc-MIR171j, ptc-MIR1448, osa-MIR396f, osa-MIR2118a, osa-MIR2118b, osa-MIR2118c, osa-MIR2118d, osa-MIR2118e, osa-MIR2118f, osa-MIR2118g, osa-MIR2118h, osa-MIR2118i, osa-MIR2118j, osa-MIR2118k, osa-MIR2118l, osa-MIR2118m, osa-MIR2118n, osa-MIR2118o, osa-MIR2118p, osa-MIR2118q, osa-MIR2118r, osa-MIR396g, osa-MIR396h, osa-MIR396d, ptc-MIR482d, ptc-MIR169ag, ptc-MIR482b, ptc-MIR482c, pde-MIR159, pde-MIR162, pde-MIR166a, pde-MIR166b, pde-MIR169, pde-MIR171, pde-MIR390, pde-MIR396, pde-MIR482a, pde-MIR482b, pde-MIR482c, pde-MIR482d, pde-MIR946, pde-MIR947, pde-MIR949a, pde-MIR950, pde-MIR951, pde-MIR952a, pde-MIR952b, pde-MIR952c, pde-MIR1311, pde-MIR1312, pde-MIR1313, pde-MIR1314, pde-MIR3701, pde-MIR3704a, pde-MIR3704b, pde-MIR3712
In addition, seven contig sequences identical to or highly homologous to osa-miR156k, osa-miR399a, osa-miR414, pta-miR948, cre-miR1171, pta-miR1309 and pta-miR1316 were also found in the database (Additional file 5). [score:1]
It includes pde-MIR159, pde-MIR162, pde-MIR166, pde-MIR169, pde-MIR171, pde-MIR390, pde-MIR396 and pde-MIR399. [score:1]
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26
[+] score: 2
PHR1, a well-known transcription factor in the CC-type MYB family, is an important regulator in the Pi-starvation response that controls Pi homeostasis by enhancing PHO2 cleavage by miR399 [51]. [score:2]
[1 to 20 of 1 sentences]
27
[+] score: 1
For miRNAs that are induced by nutritional stresses, such as phosphate deficiency (miR399) copper deficiency (miR398), and sulfate deficiency (miR395), their abundance were low in all lines and were not significantly changed in our OE lines [22, 30- 32]. [score:1]
[1 to 20 of 1 sentences]
28
[+] score: 1
Abundant miRNAs on chromosome A3 included miR2111 and miR399. [score:1]
[1 to 20 of 1 sentences]
29
[+] score: 1
Other miRNAs from this paper: ath-MIR156a, ath-MIR156b, ath-MIR156c, ath-MIR156d, ath-MIR156e, ath-MIR156f, ath-MIR159a, ath-MIR172a, ath-MIR172b, ath-MIR159b, ath-MIR319a, ath-MIR319b, ath-MIR172c, ath-MIR172d, ath-MIR390a, ath-MIR390b, ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f, ath-MIR156g, ath-MIR156h, ath-MIR159c, ath-MIR319c, ath-MIR172e, gma-MIR156d, gma-MIR156e, gma-MIR156c, gma-MIR159a, gma-MIR172a, gma-MIR172b, gma-MIR319a, gma-MIR319b, gma-MIR156a, gma-MIR319c, gma-MIR156b, gma-MIR159b, gma-MIR159c, gma-MIR390a, gma-MIR390b, gma-MIR172c, gma-MIR172d, gma-MIR172e, gma-MIR156f, gma-MIR172f, gma-MIR156g, gma-MIR159d, gma-MIR156h, gma-MIR156i, gma-MIR319d, gma-MIR319e, gma-MIR319f, gma-MIR390c, gma-MIR156j, gma-MIR156k, gma-MIR156l, gma-MIR156m, gma-MIR156n, gma-MIR156o, gma-MIR159e, gma-MIR159f, gma-MIR172g, gma-MIR172h, gma-MIR172i, gma-MIR172j, gma-MIR319g, gma-MIR319h, gma-MIR319i, gma-MIR319j, gma-MIR319k, gma-MIR319l, gma-MIR319m, ath-MIR156i, ath-MIR156j, gma-MIR399a, gma-MIR156p, gma-MIR172k, gma-MIR156q, gma-MIR172l, gma-MIR319n, gma-MIR156r, gma-MIR399b, gma-MIR156s, gma-MIR156t, gma-MIR399c, gma-MIR399d, gma-MIR399e, gma-MIR399f, gma-MIR399g, gma-MIR399h, gma-MIR156u, gma-MIR156v, gma-MIR156w, gma-MIR156x, gma-MIR156y, gma-MIR156z, gma-MIR156aa, gma-MIR156ab, gma-MIR390d, gma-MIR390e, gma-MIR390f, gma-MIR390g, gma-MIR319o, gma-MIR319p, gma-MIR399i, gma-MIR319q, gma-MIR399j, gma-MIR399k, gma-MIR399l, gma-MIR399m, gma-MIR399n, gma-MIR399o
In addition, the miR319, miR390 and miR399 families also play a role in the control of flowering time [8, 9, 10, 11]. [score:1]
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30
[+] score: 1
Other miRNAs from this paper: ath-MIR156a, ath-MIR156b, ath-MIR156c, ath-MIR156d, ath-MIR156e, ath-MIR156f, ath-MIR157a, ath-MIR157b, ath-MIR157c, ath-MIR157d, ath-MIR159a, ath-MIR165a, ath-MIR165b, ath-MIR166a, ath-MIR166b, ath-MIR166c, ath-MIR166d, ath-MIR166e, ath-MIR166f, ath-MIR166g, ath-MIR169a, ath-MIR170, ath-MIR171a, ath-MIR172a, ath-MIR172b, ath-MIR159b, ath-MIR319a, ath-MIR319b, osa-MIR156a, osa-MIR156b, osa-MIR156c, osa-MIR156d, osa-MIR156e, osa-MIR156f, osa-MIR156g, osa-MIR156h, osa-MIR156i, osa-MIR156j, osa-MIR166a, osa-MIR166b, osa-MIR166c, osa-MIR166d, osa-MIR166e, osa-MIR166f, osa-MIR169a, osa-MIR171a, ath-MIR169b, ath-MIR169c, ath-MIR169d, ath-MIR169e, ath-MIR169f, ath-MIR169g, ath-MIR169h, ath-MIR169i, ath-MIR169j, ath-MIR169k, ath-MIR169l, ath-MIR169m, ath-MIR169n, ath-MIR171b, ath-MIR171c, ath-MIR172c, ath-MIR172d, ath-MIR395a, ath-MIR395b, ath-MIR395c, ath-MIR395d, ath-MIR395e, ath-MIR395f, ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f, osa-MIR395b, osa-MIR395d, osa-MIR395e, osa-MIR395g, osa-MIR395h, osa-MIR395i, osa-MIR395j, osa-MIR395k, osa-MIR395l, osa-MIR395s, osa-MIR395t, osa-MIR395c, osa-MIR395a, osa-MIR395f, osa-MIR395u, osa-MIR399a, osa-MIR399b, osa-MIR399c, osa-MIR399d, osa-MIR399e, osa-MIR399f, osa-MIR399g, osa-MIR399h, osa-MIR399i, osa-MIR399j, osa-MIR399k, ath-MIR401, ath-MIR156g, ath-MIR156h, ath-MIR159c, ath-MIR319c, ath-MIR172e, osa-MIR156k, osa-MIR156l, osa-MIR159a, osa-MIR159b, osa-MIR159c, osa-MIR159d, osa-MIR159e, osa-MIR159f, osa-MIR319a, osa-MIR319b, osa-MIR166k, osa-MIR166l, osa-MIR169b, osa-MIR169c, osa-MIR169d, osa-MIR169e, osa-MIR169f, osa-MIR169g, osa-MIR169h, osa-MIR169i, osa-MIR169j, osa-MIR169k, osa-MIR169l, osa-MIR169m, osa-MIR169n, osa-MIR169o, osa-MIR169p, osa-MIR169q, osa-MIR171b, osa-MIR171c, osa-MIR171d, osa-MIR171e, osa-MIR171f, osa-MIR171g, osa-MIR172a, osa-MIR172b, osa-MIR172c, osa-MIR166g, osa-MIR166h, osa-MIR166i, osa-MIR171h, osa-MIR172d, osa-MIR171i, osa-MIR166m, osa-MIR166j, ath-MIR413, ath-MIR414, ath-MIR415, ath-MIR416, ath-MIR417, osa-MIR413, osa-MIR414, osa-MIR415, osa-MIR416, osa-MIR417, ath-MIR426, osa-MIR426, osa-MIR438, osa-MIR444a, ptc-MIR156a, ptc-MIR156b, ptc-MIR156c, ptc-MIR156d, ptc-MIR156e, ptc-MIR156f, ptc-MIR156g, ptc-MIR156h, ptc-MIR156i, ptc-MIR156j, ptc-MIR156k, ptc-MIR159a, ptc-MIR159b, ptc-MIR159d, ptc-MIR159e, ptc-MIR159c, ptc-MIR166a, ptc-MIR166b, ptc-MIR166c, ptc-MIR166d, ptc-MIR166e, ptc-MIR166f, ptc-MIR166g, ptc-MIR166h, ptc-MIR166i, ptc-MIR166j, ptc-MIR166k, ptc-MIR166l, ptc-MIR166m, ptc-MIR166n, ptc-MIR166o, ptc-MIR166p, ptc-MIR166q, ptc-MIR169a, ptc-MIR169aa, ptc-MIR169ab, ptc-MIR169ac, ptc-MIR169ad, ptc-MIR169ae, ptc-MIR169af, ptc-MIR169b, ptc-MIR169c, ptc-MIR169d, ptc-MIR169e, ptc-MIR169f, ptc-MIR169g, ptc-MIR169h, ptc-MIR169i, ptc-MIR169j, ptc-MIR169k, ptc-MIR169l, ptc-MIR169m, ptc-MIR169n, ptc-MIR169o, ptc-MIR169p, ptc-MIR169q, ptc-MIR169r, ptc-MIR169s, ptc-MIR169t, ptc-MIR169u, ptc-MIR169v, ptc-MIR169w, ptc-MIR169x, ptc-MIR169y, ptc-MIR169z, ptc-MIR171a, ptc-MIR171b, ptc-MIR171c, ptc-MIR171d, ptc-MIR171e, ptc-MIR171f, ptc-MIR171g, ptc-MIR171h, ptc-MIR171i, ptc-MIR172a, ptc-MIR172b, ptc-MIR172c, ptc-MIR172d, ptc-MIR172e, ptc-MIR172f, ptc-MIR172g, ptc-MIR172h, ptc-MIR172i, ptc-MIR319a, ptc-MIR319b, ptc-MIR319c, ptc-MIR319d, ptc-MIR319e, ptc-MIR319f, ptc-MIR319g, ptc-MIR319h, ptc-MIR319i, ptc-MIR395a, ptc-MIR395b, ptc-MIR395c, ptc-MIR395d, ptc-MIR395e, ptc-MIR395f, ptc-MIR395g, ptc-MIR395h, ptc-MIR395i, ptc-MIR395j, ptc-MIR399a, ptc-MIR399b, ptc-MIR399d, ptc-MIR399f, ptc-MIR399g, ptc-MIR399h, ptc-MIR399i, ptc-MIR399j, ptc-MIR399c, ptc-MIR399e, ptc-MIR481a, ptc-MIR482a, osa-MIR395m, osa-MIR395n, osa-MIR395o, osa-MIR395p, osa-MIR395q, osa-MIR395v, osa-MIR395w, osa-MIR395r, ptc-MIR171k, osa-MIR169r, osa-MIR444b, osa-MIR444c, osa-MIR444d, osa-MIR444e, osa-MIR444f, ptc-MIR171l, ptc-MIR171m, ptc-MIR171j, osa-MIR395x, osa-MIR395y, ath-MIR156i, ath-MIR156j, ptc-MIR482d, ptc-MIR156l, ptc-MIR169ag, ptc-MIR482b, ptc-MIR395k, ptc-MIR482c
In Oryza and Populus, we find no new miSquare families, but three new members of known miRBase families (oza-MIR399, ptc-MIR166, and ptc-MIR395; see Table 2). [score:1]
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31
[+] score: 1
Among these families, the miR156 family had the most family members (13), with 93.7% of all conserved miRNA reads, followed by miR166 (6), miR168 (5), miR167 (4), miR397 (4), miR390 (3), and miR399 (3) etc. [score:1]
[1 to 20 of 1 sentences]
32
[+] score: 1
mir399 [87], [88] PHO2, an E2-UBC that negatively affects shoot phosphate content. [score:1]
[1 to 20 of 1 sentences]
33
[+] score: 1
Indeed, research data in the past twenty years indicate that 21 miRNA families, such as miR156 and miR399, are conserved in sequence across monocots and dicots 25. [score:1]
[1 to 20 of 1 sentences]
34
[+] score: 1
miR399 and miR395 have been identified as being involved in sulfate- and phosphate-starvation responses [16, 17]. [score:1]
[1 to 20 of 1 sentences]
35
[+] score: 1
Other miRNAs from this paper: ath-MIR399b, ath-MIR399c, ath-MIR399d, ath-MIR399e, ath-MIR399f
Only 4 miRNAs belonging to 2 families (MIR399 and MIR827_3) can bind to the 5'UTR region. [score:1]
[1 to 20 of 1 sentences]
36
[+] score: 1
Failure to identify miR398a, miR399a, miR399d, miR399e, miR399f and miR447c was due to a lack of sequence reads. [score:1]
[1 to 20 of 1 sentences]