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Adenylation of plant miRNAs.

Lu S, Sun YH, Chiang VL - Nucleic Acids Res. (2009)

Bottom Line: We also show that a significant portion of the isolated miRNAs contains, at the 3'-end, one or a few post-transcriptionally added adenylic acid residues, which are distinct in length from the polyadenylate tail added to other plant RNAs for exosome-mediated degradation.It indicates that addition of adenylic acid residues on the 3'-end plays a negative role in miRNA degradation.Our results provide new information for understanding the mechanism of miRNA degradation.

View Article: PubMed Central - PubMed

Affiliation: Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA. slu@unity.ncsu.edu

ABSTRACT
The modification or degradation of RNAs including miRNAs may play vital roles in regulating RNA functions. The polyadenylation- and exosome-mediated RNA decay is involved in the degradation of plant RNAs including the primary miRNA processing intermediates. However, plant miRNA levels are not affected by exosome depletion. Here, we report the cloning of a large number of 5' and/or 3' truncated versions of the known miRNAs from various tissues of Populus trichocarpa (black cottonwood). It suggests that plant miRNAs may be degraded through either 5' to 3' or 3' to 5' exonucleolytic digestion. We also show that a significant portion of the isolated miRNAs contains, at the 3'-end, one or a few post-transcriptionally added adenylic acid residues, which are distinct in length from the polyadenylate tail added to other plant RNAs for exosome-mediated degradation. Using an in vitro miRNA degradation system, where synthesized miRNA oligos were degraded in extracts of P. trichocarpa cells, we revealed that the adenylated miRNAs were degraded slower than others without adenylation. It indicates that addition of adenylic acid residues on the 3'-end plays a negative role in miRNA degradation. Our results provide new information for understanding the mechanism of miRNA degradation.

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Related in: MedlinePlus

Percentages of adenylated miRNAs isolated from shoot tips (ST), root tips (RT) and tissues of the stem cambial zone (CZ). Percentages of adenylated miRNAs from each family and from all of the 12 families are shown. The 12 miRNA families include ptc-MIR159, ptc-MIR166, ptc-MIR167, ptc-MIR172, ptc-MIR319, ptc-MIR396, ptc-MIR397, ptc-MIR475, ptc-MIR1444, ptc-MIR1447, ptc-MIR1448 and ptc-MIR1450.
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Figure 4: Percentages of adenylated miRNAs isolated from shoot tips (ST), root tips (RT) and tissues of the stem cambial zone (CZ). Percentages of adenylated miRNAs from each family and from all of the 12 families are shown. The 12 miRNA families include ptc-MIR159, ptc-MIR166, ptc-MIR167, ptc-MIR172, ptc-MIR319, ptc-MIR396, ptc-MIR397, ptc-MIR475, ptc-MIR1444, ptc-MIR1447, ptc-MIR1448 and ptc-MIR1450.

Mentions: In order to know the tissue-dependency of miRNA adenylation, miRNAs isolated from ST, CZ and RT were analyzed individually. Again, we focused on the 12 miRNA families having percentages of adenylated miRNAs >5%. We found that the adenylated miRNA percentage isolated from CZ (∼19%) is about twice as high as that from ST (∼9%) (Figure 4). Among the 12 miRNA families examined, 10 show the greatest adenylation percentage for miRNAs isolated from CZ of P. trichocarpa (Figure 4). It includes an miRNA (ptc-miR475) expressed highly in CZ and nine having lower expression levels in CZ than in ST and RT (Table 1 and Figure 4), suggesting that the percentage of adenylated miRNA is independent with the expression level of miRNA. Thus, miRNA adenylation seems tissue-dependent. The high percentage of adenylated miRNAs isolated from CZ could be associated with the active metabolism of cells in and around the cambial zone of P. trichocarpa in the fast-growing season, when the tissues were collected. Further study to find the reason causing high percentage of adenylated miRNAs in CZ may help to add new insights into the regulatory mechanism of miRNA degradation.Figure 4.


Adenylation of plant miRNAs.

Lu S, Sun YH, Chiang VL - Nucleic Acids Res. (2009)

Percentages of adenylated miRNAs isolated from shoot tips (ST), root tips (RT) and tissues of the stem cambial zone (CZ). Percentages of adenylated miRNAs from each family and from all of the 12 families are shown. The 12 miRNA families include ptc-MIR159, ptc-MIR166, ptc-MIR167, ptc-MIR172, ptc-MIR319, ptc-MIR396, ptc-MIR397, ptc-MIR475, ptc-MIR1444, ptc-MIR1447, ptc-MIR1448 and ptc-MIR1450.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665221&req=5

Figure 4: Percentages of adenylated miRNAs isolated from shoot tips (ST), root tips (RT) and tissues of the stem cambial zone (CZ). Percentages of adenylated miRNAs from each family and from all of the 12 families are shown. The 12 miRNA families include ptc-MIR159, ptc-MIR166, ptc-MIR167, ptc-MIR172, ptc-MIR319, ptc-MIR396, ptc-MIR397, ptc-MIR475, ptc-MIR1444, ptc-MIR1447, ptc-MIR1448 and ptc-MIR1450.
Mentions: In order to know the tissue-dependency of miRNA adenylation, miRNAs isolated from ST, CZ and RT were analyzed individually. Again, we focused on the 12 miRNA families having percentages of adenylated miRNAs >5%. We found that the adenylated miRNA percentage isolated from CZ (∼19%) is about twice as high as that from ST (∼9%) (Figure 4). Among the 12 miRNA families examined, 10 show the greatest adenylation percentage for miRNAs isolated from CZ of P. trichocarpa (Figure 4). It includes an miRNA (ptc-miR475) expressed highly in CZ and nine having lower expression levels in CZ than in ST and RT (Table 1 and Figure 4), suggesting that the percentage of adenylated miRNA is independent with the expression level of miRNA. Thus, miRNA adenylation seems tissue-dependent. The high percentage of adenylated miRNAs isolated from CZ could be associated with the active metabolism of cells in and around the cambial zone of P. trichocarpa in the fast-growing season, when the tissues were collected. Further study to find the reason causing high percentage of adenylated miRNAs in CZ may help to add new insights into the regulatory mechanism of miRNA degradation.Figure 4.

Bottom Line: We also show that a significant portion of the isolated miRNAs contains, at the 3'-end, one or a few post-transcriptionally added adenylic acid residues, which are distinct in length from the polyadenylate tail added to other plant RNAs for exosome-mediated degradation.It indicates that addition of adenylic acid residues on the 3'-end plays a negative role in miRNA degradation.Our results provide new information for understanding the mechanism of miRNA degradation.

View Article: PubMed Central - PubMed

Affiliation: Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, NC 27695, USA. slu@unity.ncsu.edu

ABSTRACT
The modification or degradation of RNAs including miRNAs may play vital roles in regulating RNA functions. The polyadenylation- and exosome-mediated RNA decay is involved in the degradation of plant RNAs including the primary miRNA processing intermediates. However, plant miRNA levels are not affected by exosome depletion. Here, we report the cloning of a large number of 5' and/or 3' truncated versions of the known miRNAs from various tissues of Populus trichocarpa (black cottonwood). It suggests that plant miRNAs may be degraded through either 5' to 3' or 3' to 5' exonucleolytic digestion. We also show that a significant portion of the isolated miRNAs contains, at the 3'-end, one or a few post-transcriptionally added adenylic acid residues, which are distinct in length from the polyadenylate tail added to other plant RNAs for exosome-mediated degradation. Using an in vitro miRNA degradation system, where synthesized miRNA oligos were degraded in extracts of P. trichocarpa cells, we revealed that the adenylated miRNAs were degraded slower than others without adenylation. It indicates that addition of adenylic acid residues on the 3'-end plays a negative role in miRNA degradation. Our results provide new information for understanding the mechanism of miRNA degradation.

Show MeSH
Related in: MedlinePlus