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9 publications mentioning bra-MIR167d

Open access articles that are associated with the species Brassica rapa and mention the gene name MIR167d. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

[+] score: 81
Other miRNAs from this paper: bna-MIR156a, bna-MIR171g, bna-MIR396a, bra-MIR824, bna-MIR824, bna-MIR397a, bna-MIR397b, bna-MIR390a, bna-MIR390b, bna-MIR390c, bna-MIR171a, bna-MIR171b, bna-MIR171c, bna-MIR171d, bna-MIR171e, bna-MIR171f, bna-MIR169a, bna-MIR169b, bna-MIR169c, bna-MIR169d, bna-MIR169e, bna-MIR169f, bna-MIR169g, bna-MIR169h, bna-MIR169i, bna-MIR169j, bna-MIR169k, bna-MIR169l, bna-MIR169m, bna-MIR168a, bna-MIR167a, bna-MIR167b, bna-MIR167c, bna-MIR166a, bna-MIR166b, bna-MIR166c, bna-MIR166d, bna-MIR164a, bna-MIR159, bna-MIR156b, bna-MIR156c, bra-MIR1885a, bra-MIR157a, bra-MIR159a, bra-MIR160a, bra-MIR164a, bra-MIR167a, bra-MIR167b, bra-MIR167c, bra-MIR171a, bra-MIR171b, bra-MIR171c, bra-MIR171d, bra-MIR171e, bra-MIR172a, bra-MIR172b, bna-MIR2111b, bna-MIR2111a, bra-MIR2111a, bra-MIR1885b, bna-MIR156d, bna-MIR156e, bna-MIR156f, bna-MIR156g, bna-MIR160a, bna-MIR160b, bna-MIR160c, bna-MIR160d, bna-MIR164b, bna-MIR164c, bna-MIR164d, bna-MIR166f, bna-MIR166e, bna-MIR167d, bna-MIR168b, bna-MIR169n, bna-MIR172d, bna-MIR172b, bna-MIR172c, bna-MIR172a, bna-MIR394a, bna-MIR394b, bna-MIR395a, bna-MIR395b, bna-MIR395c, bna-MIR395d, bna-MIR395e, bna-MIR395f, bna-MIR403, bna-MIR860, bna-MIR2111d, bna-MIR2111c, bra-MIR408, bra-MIR158, bra-MIR156a, bra-MIR156b, bra-MIR156c, bra-MIR156d, bra-MIR156e, bra-MIR156f, bra-MIR156g, bra-MIR168b, bra-MIR168c, bra-MIR168a, bra-MIR319, bra-MIR390, bra-MIR391, bra-MIR395d, bra-MIR395b, bra-MIR395c, bra-MIR395a, bra-MIR396, bra-MIR400, bra-MIR403, bra-MIR860, bra-MIR164b, bra-MIR164d, bra-MIR164c, bra-MIR164e, bra-MIR172c, bra-MIR2111, bra-MIR172d
Comparing our putative targets to Xu et al. [16] and Zhou et al. [15], we found significant overlap among them based on the annotations of target genes, including miR156 targets (SPLs), miR167 targets (ARFs), miR159 targets (MYBs), miR169 targets (NF-Y subunits), miR164 targets (NAC-domain proteins) and miR172 targets (AP2-like transcription factors). [score:17]
Homologous EST contigs of many known miRNA target genes including most SPLs (targets of miR156), MYB101 (target of miR159), ARF6 and ARF8 (targets of miR167) and numerous others either showed negative expression patterns or were expressed at very low levels throughout seed maturation. [score:13]
In addition, we also predict that miR173, miR400 and miR396 "co-target" pentatricopeptide (PPR) repeat-containing proteins; miR156, miR394, miR319 "co-target" F-box family proteins and miR160, miR167, miR390 and miR156 "co-target" various auxin response factors (ARFs). [score:7]
Comparison of the expression of the 90 known miRNAs in Zhou et al. [15] and this study revealed many commonly expressed miRNAs despite the very different conditions and stages, especially for the most highly expressed miRNAs such as miR156, miR167, miR158 and miR166. [score:7]
The relative abundance as well as specific temporal and spatial expression patterns of these miRNAs and their targets suggested that miR156, miR159, miR172, miR167, miR158 and miR166 are the major contributors to the network controlling seed development and maturation through their pivotal roles in plant development. [score:7]
There are two peaks of miR167 reads at 25 and 40 DAF and expression of miR167 was negatively correlated with that of its targets ARF6 and ARF8. [score:5]
miR167 is one of the most abundant miRNAs during seed development and is preferentially expressed in the seed coat and endosperm. [score:4]
miRNAs in group A4, represented by miR172, miR157, miR167, miR396 and several miR156 variants, were preferentially expressed in flower buds and, to a much lesser extent, in seed developmental stages. [score:4]
The high abundance and specific expression of miR165/166, miR167, miR160 and miR164 indicate that these miRNAs play important roles in maintaining proper auxin signaling homeostasis in seed development. [score:4]
miR160 and miR167 are predicted to target AUXIN RESPONSE FACTORs (ARFs), specifically ARF17, ARF8 and ARF6. [score:3]
Most miRNA family members showed similar expression patterns such as miR159 (A2, B1), miR319 (B2), miR172 (A3, B3), miR167 (A3, B3), miR824 (A1) and miR160 (A1). [score:3]
miR156, miR159, miR172, miR167, miR158 and miR166 are the major contributors to the network controlling seed development and maturation through their pivotal roles in plant development. [score:3]
The miRNA156 family was the most abundant in seed followed by the miR159, miR172, miR167 and miR158 families. [score:1]
For example, ath-miR156a, ath-miR159a, ath-miR172c, ath-miR167a and bna-miR158b were the predominant variants in the miR156, miR159, miR172, miR167 and miR158 families. [score:1]
For example, there were 115, 75, 47, 31 and 28 unique variant sequences (with reads >300) in the miR156, miR159, miR167, miR172 and miR166 families respectively, but only one miRNA sequence in the miR845, miR170, miR173 and miR391 families. [score:1]
Most of the miRNAs with stem-loop structures and typical mapping patterns are highly conserved in the plant kingdom including miR156, miR159, miR160, MiR166, miR167, miR172, miR319 and miR395 [26]. [score:1]
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[+] score: 26
CT The predicted miRNA's mode of action SWISS-PROT annotation bra-miR167 4.37 Bra015704 0.86 Translation inhibitionTM1L2_XENLA TOM1-like protein 2 OS= Xenopus laevis GN=tom1l2 PE=2 SV=1 bra-miR167 4.37 Bra002277 −1.25 mRNA cleavage TDRD3_CHICK Tudor domain-containing protein 3 OS=Gallus gallus GN=TDRD3 PE=2 SV=1bra-miR167 [*] 5.29 Bra025064 5.84 mRNA cleavageGDL82_ARATH GDSL esterase/lipase At5g45670 OS= Arabidopsis thaliana GN=At5g45670 PE=2 SV=1bra-miR167 [*] 5.29 Bra005019 2.28 Translation inhibition RCA_ARATH Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic OS=Arabidopsis bra-miR168 6.48 Bra032254 −1.56 mRNA cleavageAGO1_ARATH Protein argonaute OS= Arabidopsis thaliana GN=AGO1 PE=1 SV=1 bra-miR171a-1 14.89 Bra039431 0.79 Translation inhibition PRS6A_BRACM 26S protease regulatory subunit 6A homolog OS=Brassica campestris GN=TBP1 PE=2 SV=1Gene target prediction for miRNAs was done using the psRNATarget program for the Brassica rapa CDS library v 1.1 (Dai and Zhao, 2011). [score:18]
CT q-value bra-miR167 bra-miR167d Pollen 1.19 5.00E-02 Endosperm 4.37 5.00E-02 Progeny −3.29 1.30E-01 bra-miR390 bra-miR390a-1 Pollen 2.32 2.00E-02 Endosperm 3.78 1.90E-01 Progeny −2.69 4.00E-04 bra-miR168 bra-miR168a-1 Pollen 1.18 4.00E-02 bra-miR168a-3 Endosperm 6.48 5.00E-02 bra-miR168a-1 Progeny −1.57 1.90E-01 The differentially expressed smRNAs mapped to conservative mature miRNAs (TR vs. [score:3]
We observed a unique pattern of tissue response to stress (Figure 7A), with only a few overlapping differentially expressed mature miRNAs among pollen, endosperm and leaf tissues of the progeny belonging to three microRNA gene families: bra-miR167, bra-miR390, and bra-miR168 (Figure 7B, Table 2). [score:3]
The members of miR167 and miR390 gene families have been implemented in the regulation of auxin response factors (ARFs) in Arabidopsis which are transcription factors that bind to auxin response elements in the promoters of early auxin response genes (Tiwari et al., 2003; Mallory et al., 2005; Montgomery et al., 2008). [score:2]
[1 to 20 of 4 sentences]
[+] score: 18
Most of these putative target genes encode transcription factors such as SPL (targets of miR156, miR157 and miR1088), Auxin response factor (ARF) (targets of miR160 and miR167), Myeloblastosis (MYB) (targets of miR159 and miR828), Basic leucine zipper (bZIP) (BrmiRC0651, and BrmiRC0940), AGAMOUS-like (AGL) (targets of miR824 and BrmiRC0607), WRKY (targets of BrmiRC0049, BrmiRC0149, BrmiRC0177 and BrmiRC0181) and APETALA2 (AP2) (targets of miR172), which have known or putative functions in a wide variety of biological processes. [score:15]
In our light -induced RNA library, BrmiR391, BrmiR2111, BrmiR5083 and BrmiRC0132, BrmiRC0448, BrmiRC0491 were induced by both blue light and UV-A. Furthermore, miR156/157, miR159/319, miR160, miR165/166, miR167, miR169, miR170/171, miR172, miR393, miR398 and miR401, which are responsive to UV-B in Arabidopsis [34], were all detected in light -treated seedlings of Brassica rapa, but most had no obvious difference in transcription level. [score:1]
Four miRNAs (miR160, miR165/166, miR167 and miR393) also respond to UV-B and might be involved in auxin signaling pathways of Arabidopsis [23]. [score:1]
Among these families, miR156, miR157, miR167, miR168 were abundant, accounting for more than 90 % of the total conserved and novel miRNA reads in dark-, blue-light- and UV-A-responsive sRNA libraries. [score:1]
[1 to 20 of 4 sentences]
[+] score: 7
miR167 targets IAA-amino acid hydrolase 3 (IAR3), which encodes an auxin conjugate hydrolase that contributes to the jasmonate pathway (Kinoshita et al., 2012; Widemann et al., 2013). [score:3]
IAA-Ala Resistant3, an evolutionarily conserved target of miR167, mediates Arabidopsis root architecture changes during high osmotic stress. [score:3]
By expending the members to the existing B. rapa miRNA families, bra-miR156 was now the largest family (harboring 21 members), followed by bra-miR171 (11 members), bra-miR167 (8 members), bra-miR172 (8 members), bra-miR164 (7 members), bra-miR168 (7 members), bra-miR2111 (7 members), bra-miR157 (6 members), bra-miR160 (6 members), bra-miR390 (6 members), and bra-miR395 (6 members). [score:1]
[1 to 20 of 3 sentences]
[+] score: 7
Conversely, mir894, mir535a, mir166a, mir166h, mir167, mir168, mir397 and mir2950 showed higher expression levels in P. indica infected Oncidium root tissue (Figure 3). [score:3]
We could not detect the two ARFs, type 6 and 8, targets of mir167, in our qPCR assay, suggesting that the transcript abundance is low. [score:2]
Others are related to auxin signaling, such as mir164 and mir167 (Table 3). [score:1]
The miRNAs involved in auxin signalling functions were easily detectable in our experiment, including miR160, mir164, mir167, mir393, miR394 and mir5293. [score:1]
[1 to 20 of 4 sentences]
[+] score: 5
For example, both miR160 and miR167 target auxin response factor (ARF) transcription factors (Mallory et al., 2005; Wu et al., 2006), miR156/miR157 and miR162 target squamosa promoter -binding-like protein (SPL) and Dicer-liker (DCL) protein in Arabidopsis and B. napus. [score:5]
[1 to 20 of 1 sentences]
[+] score: 2
In addition, most of the petiole-specific miRNAs were members of the conserved miRNA families miR164 and miR167, although there was one novel miRNA (bra-miR6104). [score:1]
Both the miR164 and miR167 families were identified as stem-specific miRNAs from A. thaliana and tobacco [50, 51]. [score:1]
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[+] score: 1
In addition, we found that some conserved miRNAs (miR156, miR159, miR166, miR167, miR168, miR172, miR393, miR1885, miR5654 and miR5718) were produced by lncRNAs in either B. rapa or B. oleracea as well as in B. napus. [score:1]
[1 to 20 of 1 sentences]
[+] score: 1
Eight cis-NATs were coincidently the precursors of miR162, miR167, miR171, miR172, miR398 and miR408 (Table  3). [score:1]
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