3 publications mentioning bdi-MIR169d

Open access articles that are associated with the species Brachypodium distachyon and mention the gene name MIR169d. Click the [+] symbols to view sentences that include the gene name, or the word cloud on the right for a summary.

1

Other miRNAs included in this study (miR169, miR5085, miR6220, miR2118) may also be expressed, under stress conditions, in other wheat tissues and/or at different developmental stages.

In order to show expression of selected pre-miRNAs (pre-miR2118, pre-miR169, pre-miR5085, pre-miR6220, pre-miR5070), RT-PCR and qRT-PCR was performed using Chinese Spring cDNA.

0069801.g002 Figure 2PCR screening of pre-miRNA coding sequences in flow sorted 5D short and long chromosome arms (5DS and 5DL); Triticum aestivum L. cv Chinese Spring (CS) and nullitetrasomic lines (N5D-T5A and N5D-T5B) (A) pre-miR169 (B) pre-miR5085 (C) pre miR5070 (D) pre-miR6220 (E) pre-miR2118.

PCR screening of pre-miRNA coding sequences in flow sorted 5D short and long chromosome arms (5DS and 5DL); Triticum aestivum L. cv Chinese Spring (CS) and nullitetrasomic lines (N5D-T5A and N5D-T5B) (A) pre-miR169 (B) pre-miR5085 (C) pre miR5070 (D) pre-miR6220 (E) pre-miR2118.

0069801.g004 Figure 4q-RT PCR (A) Five miRNA coding regions (pre-miR169, pre-miR5085, pre-miR6220 and pre-miR5070) in Triticum aestivum L. cv Chinese Spring (CS) B) Levels of non 5D-specific miR5070, detected by qRT-PCR in nullitetrasomic line (N5D-T5A) and Triticum aestivum L. cv Chinese Spring (CS).

miR2118 was shown to be located on both arms of the 5D chromosome (5D specific), while miR5085 and miR169 were found to be specific to the long arm (Figure 2).

In this study, five pre-miRNA (miR169, miR5085, miR2118, miR6220, miR2118) coding sequences were verified to be located to the 5D chromosome (Figure 2).

q-RT PCR (A) Five miRNA coding regions (pre-miR169, pre-miR5085, pre-miR6220 and pre-miR5070) in Triticum aestivum L. cv Chinese Spring (CS) B) Levels of non 5D-specific miR5070, detected by qRT-PCR in nullitetrasomic line (N5D-T5A) and Triticum aestivum L. cv Chinese Spring (CS).

PCR screening of 5DL specific pre-miRNA coding sequences (A) pre-miR169 (B) pre-miR5085 in Triticum aestivum L. cv Chinese Spring (CS) deletion lines (5DS-2, 5DS-5, 5DL-5, 5DL7) (C) Fraction length values of deletion lines.

2.5 mM MgCl [2] (stock concentration : 25 mM) was used for the amplification of miR6220, miR5070 and miR2118 and this value was optimized to 2 mM and 3 mM for the miR5085 and miR169 amplicons.

Three of these pre-miRNAs (miR169, miR5085, miR2118) were shown to be 5D specific (Figure 2).

Independent studies in different plant species including A. thaliana, O. sativa,and Populus trichocarpashowed drought stress responsiveness of miR160,miR167, miR169, miR1125, and miR398, which were also found in wheat chromosome 5D [55]– [57].

Coding regions of both 5DL specific pre-miRNAs (pre-miR5085, pre-miR169) were found to be located between the breakpoint of 5DL-7 (FL : 0.29) and the centromere (Figure 3).

To experimentally validate 5D chromosome localization of selected pre-miRNAs (miR169, miR5085, miR2118, miR5070, miR6220), PCR screening was carried out using DNA from flow-sorted 5D chromosome arms.

0069801.g003 Figure 3PCR screening of 5DL specific pre-miRNA coding sequences (A) pre-miR169 (B) pre-miR5085 in Triticum aestivum L. cv Chinese Spring (CS) deletion lines (5DS-2, 5DS-5, 5DL-5, 5DL7) (C) Fraction length values of deletion lines.

Our experimental results supported our in silico predictions: 5DS was verified to harbour regions coding for pre-miR2118 and pre-miR5070, and 5DL was confirmeded to contain both of the above plus pre-miR6220, pre-miR5085 and miR169 coding regions.

For instance, in several reports, miR169 was implicated in a broad range of stress responsive mechanisms including nitrogen starvation, arsenic, salt and drought stresses and response to virus infection [69]– [73].

pre-miR169, pre-miR5085 and pre-miR2118 coding regions were found to be 5D chromosome-specific.

Quantification with real-time PCR using CS gDNA suggested that coding regions of the selected pre-miRNAs had variable copy number: pre-miR169, pre-miR5085 and pre-miR5070 were shown to have approximately 8.6, 2.2 and 1.5 fold more copies than pre-miR6220.

5DL specific pre-miRNA (miR169, miR5085) coding sequences were shown to be located between the centromer and the breakpoint present in 5DL-7 (FL : 0.29) deletion line (Figure 3).

2

The expression of miR169e was difficult to be detected due to its sequence similarity to other members in the miR169 family and low expression level.

MiR169 and miR397 were also shown to be cold -upregulated in Populus [19].

MiR164, miR166 and miR172 were represented by two variants and miR169 was represented by four variants in the library (Table 2).

Then, miR169 and miR172 were found to be responsive to cold stress in Arabidopsis both through a computational, transcriptome -based approach and by microarray analysis almost simultaneously [17, 18].

3

Downregulation of miR169 can lead to NF-YA upregulation under very specific environmental conditions, such as drought or nitrogen starvation [21], [77].

In Arabidopsis the accumulation of most NF-YA transcripts is regulated by the micro RNA miR169 [76].

Based on the conservation of miR169 in Brachypodium [78], it is likely that similar mechanisms control the accumulation of BdNF-YA mRNA and protein.