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3 publications mentioning bdi-MIR390a

Open access articles that are associated with the species Brachypodium distachyon and mention the gene name MIR390a. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1
[+] score: 56
Other miRNAs from this paper: ath-MIR390a, ath-MIR390b, osa-MIR390
Four different ami RNA sequences designed to target specifically endogenous genes and expressed from Os MIR390‐based vectors were validated in transgenic Brachypodium distachyon plants. [score:5]
To test amiRNA expression from OsMIR390 precursors, transformed B.  distachyon calli containing amiRNA constructs expressing miR390 or modified versions of several miRNAs from Arabidopsis (amiR173‐21, amiR472‐21 or amiR828‐21) (Cuperus et al., 2010) were analyzed (Figure  2a). [score:5]
Here, a series of expression vectors based on Oryza sativa MIR390 (Os MIR390) precursor was developed for high‐throughput cloning and high expression of ami RNAs in monocots. [score:5]
Surprisingly, ami RNAs accumulated to higher levels and were processed more accurately when expressed from chimeric Os MIR390‐based precursors that include distal stem–loop sequences from Arabidopsis thaliana MIR390a (At MIR390a). [score:3]
These included a series of eudicot amiRNA vectors based on Arabidopsis thaliana MIR390a (AtMIR390a) precursor, whose relatively short distal stem–loop allows the cost‐effective synthesis and cloning of the amiRNA inserts into ‘B/c’ expression vectors (Carbonell et al., 2014). [score:3]
Mean (n = 3) relative ami RNA levels + standard deviation (SD) when expressed from the Os MIR390 (light grey, ami RNA level = 1.0). [score:3]
Figure 5Mapping of ami RNA reads from Os MIR390‐AtL‐ or Os MIR390‐based precursors expressed in Brachypodium T0 transgenic plants. [score:3]
Figure 6Transcriptome analysis of transgenic Brachypodium plants expressing ami RNAs from chimeric Os MIR390‐AtL precursors. [score:3]
MA plots show log2 fold change versus mean expression of genes for each 35S:Os MIR390‐AtL ami RNA line compared with the control lines (35S: GUS). [score:2]
These vectors contain a truncated sequence from Oryza sativa MIR390 (OsMIR390) precursor in a configuration that allows the direct cloning of amiRNAs. [score:2]
Surprisingly, miR390 accumulated to highest levels when expressed from the chimeric OsMIR390‐AtL precursor compared with each of the other three precursors (P ≤ 0.001 for all pairwise t‐test comparisons; Figure  2b). [score:2]
Unexpectedly, ami RNAs produced from chimeric Os MIR390‐based precursors including Arabidopsis thaliana MIR390a distal stem‐loop sequences accumulated elevated levels of highly effective and specific ami RNAs in transgenic Brachypodium distachyon plants. [score:1]
Figure 2Comparative analysis of accumulation and processing of several ami RNAs produced from At MIR390a, At MIR390a‐OsL, Os MIR390 and Os MIR390‐AtL precursors in Brachypodium transgenic calli. [score:1]
OsMIR390‐based amiRNAs were generally more accurately processed and accumulated to higher levels in transgenic Brachypodium distachyon (Brachypodium) when processed from chimeric precursors (OsMIR390‐AtL) containing Arabidopsis thaliana (Arabidopsis) MIR390a (AtMIR390a) distal stem–loop sequences. [score:1]
miR390 and miR390* nucleotides are highlighted in blue and green, respectively. [score:1]
Moreover, OsMIR390 contains the shortest distal stem–loop of all 51 sequenced MIR390 precursors from 36 species (median length = 47 nt; Figure  1b and Table S2), including those from maize (ZmaMIR390a and ZmaMIR390b), sorghum (SbiMIR390a) and B. distachyon (BdiMIR390) with lengths of 137, 148, 134 and 107 nt respectively. [score:1]
Nucleotides from the At MIR390a or Os MIR390 precursors are in black and grey, respectively, except those that were modified to preserve the corresponding authentic precursor secondary structure (in red). [score:1]
Nucleotides corresponding to the mi RNA guide and mi RNA* strands are in blue and green, respectively; nucleotides from At MIR390a or Os MIR390 precursors are in black or grey, respectively, except those that were modified to preserve authentic At MIR390a or Os MIR390 precursor secondary structures (in red). [score:1]
The MIR390 family is among the most deeply conserved miRNA families in plants (Axtell et al., 2006; Cuperus et al., 2011). [score:1]
Approximately 70% of reads mapping to the OsMIR390 foldback correspond to the authentic 21‐nt miR390 guide strand (Figure  1c). [score:1]
Other nucleotides from At MIR390a and Os MIR390 precursors are in black and grey, respectively. [score:1]
MiRbase locus identifiers of plant MIR390 precursors. [score:1]
Shapes of At MIR390a and Os MIR390 precursors are in black and grey, respectively. [score:1]
Figure 1 Oryza sativa MIR390 (Os MIR390) is an accurately processed, conserved MIRNA precursor with a particularly short distal stem–loop. [score:1]
Figure 3Functionality of ami RNAs produced from authentic Os MIR390‐ or chimeric Os MIR390‐AtL‐based precursors in Brachypodium T0 transgenic plants. [score:1]
org) (Kozomara and Griffiths‐Jones, 2014) locus identifiers of the conserved rice MIRNA precursors and plant MIR390 precursors (Figure  1b) are detailed in Tables S1 and S2, respectively. [score:1]
Box‐plot showing the distal stem–loop length of O. sativa conserved MIRNA precursors and all catalogued MIR390 precursors. [score:1]
miR390 and each amiRNA derived from authentic AtMIR390a or chimeric AtMIR390a‐OsL precursors accumulated to low or non‐detectable levels, indicating that the AtMIR390a stem is suboptimal for the accumulation and/or processing of amiRNAs in Brachypodium. [score:1]
A series of ami RNA vectors based on Oryza sativa MIR390 (Os MIR390) precursor were developed for simple, cost‐effective and large‐scale synthesis of ami RNA constructs to silence genes in monocots. [score:1]
The distal stem–loop length of Os MIR390 is highlighted with an orange dot and indicated with an orange arrow. [score:1]
Proportion of small RNA reads for the entire Os MIR390 precursor are plotted as stacked bar graphs. [score:1]
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[+] score: 5
Only about half of the phased loci were accounted for by miR390, miR2118 and miR2275. [score:1]
Other than the tasiRNAs generated by the 21-nucleotide miR390 [25], most of the other tasiRNAs (or phasiRNAs) are generated by 22-nucleotide-long miRNAs [26- 29]. [score:1]
Examples of miRNAs initiating 21-nucleotide phased loci are miR173 [19], miR390 [25] and miR2118 [30], whereas miR2275 [30] is the only miRNA currently known that initiates 24-nucleotide phased loci. [score:1]
Since Brachypodium produces miR390, miR2118 and miR2275, all known for initiating phased loci, these miRNAs may initiate some or all of these previously reported loci. [score:1]
The PARE sequences within five phase periods of these loci were pulled from the BDI25 PARE library and scored for complementarity to Bdi-miR390, Bdi-miR2118, Bdi-2275 and the 22-nucleotide small RNAs listed in Additional file 1: Table S2. [score:1]
[1 to 20 of 5 sentences]
3
[+] score: 3
Other miRNAs from this paper: 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, osa-MIR171a, osa-MIR393a, osa-MIR394, 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-MIR397a, osa-MIR397b, osa-MIR398a, osa-MIR398b, osa-MIR156k, osa-MIR156l, osa-MIR319a, osa-MIR319b, 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-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-MIR393b, osa-MIR172d, osa-MIR171i, osa-MIR167j, osa-MIR166m, osa-MIR166j, osa-MIR164f, osa-MIR390, osa-MIR396e, osa-MIR528, osa-MIR529a, osa-MIR395m, osa-MIR395n, osa-MIR395o, osa-MIR395p, osa-MIR395q, osa-MIR395v, osa-MIR395w, osa-MIR395r, osa-MIR529b, osa-MIR169r, osa-MIR827, osa-MIR396f, bdi-MIR171a, bdi-MIR167a, bdi-MIR397a, bdi-MIR156a, bdi-MIR172d, bdi-MIR166a, bdi-MIR171c, bdi-MIR169b, osa-MIR396g, osa-MIR396h, osa-MIR396d, osa-MIR395x, osa-MIR395y, bdi-MIR169d, bdi-MIR169i, bdi-MIR395a, bdi-MIR169j, bdi-MIR166f, bdi-MIR171b, bdi-MIR160a, bdi-MIR528, bdi-MIR395b, bdi-MIR166d, bdi-MIR171d, bdi-MIR167b, bdi-MIR166b, bdi-MIR160b, bdi-MIR164b, bdi-MIR167c, bdi-MIR396d, bdi-MIR169k, bdi-MIR168, bdi-MIR160c, bdi-MIR396c, bdi-MIR167d, bdi-MIR156b, bdi-MIR169g, bdi-MIR160d, bdi-MIR160e, bdi-MIR396e, bdi-MIR156c, bdi-MIR172a, bdi-MIR396a, bdi-MIR166e, bdi-MIR166c, bdi-MIR169e, bdi-MIR394, bdi-MIR398a, bdi-MIR164a, bdi-MIR393a, bdi-MIR169a, bdi-MIR172b, bdi-MIR156d, bdi-MIR393b, bdi-MIR169h, bdi-MIR396b, bdi-MIR169c, bdi-MIR395c, bdi-MIR827, bdi-MIR166g, bdi-MIR319a, bdi-MIR395d, bdi-MIR398b, bdi-MIR164c, bdi-MIR169f, bdi-MIR162, bdi-MIR164e, bdi-MIR164f, bdi-MIR395m, bdi-MIR395e, bdi-MIR395f, bdi-MIR395g, bdi-MIR395h, bdi-MIR395j, bdi-MIR395k, bdi-MIR395l, bdi-MIR395n, bdi-MIR529, bdi-MIR319b, bdi-MIR397b, bdi-MIR156e, bdi-MIR156f, bdi-MIR156g, bdi-MIR156h, bdi-MIR156i, bdi-MIR166h, bdi-MIR166i, bdi-MIR167e, bdi-MIR395o, bdi-MIR395p, bdi-MIR156j, bdi-MIR160f, bdi-MIR166j, bdi-MIR167f, bdi-MIR167g, bdi-MIR169l, bdi-MIR169m, bdi-MIR169n, bdi-MIR171e, bdi-MIR171f, bdi-MIR395q
The miR160a, miR164d, miR169f, miR172a, miR172b, miR319, miR390, miR393, miR394, miR395a, miR397a, miR529 and miR827 were moderately expressed, and were represented by the number of sequences varying between 10 and 100. [score:3]
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