Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jun 9;1(1):12.
doi: 10.1186/1758-907X-1-12.

Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity

H Alexander Ebhardt  1 , Amber Fedynak, Richard P Fahlman
Affiliations

Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity

H Alexander Ebhardt et al. Silence. .

Abstract

Background: Micro(mi)RNAs are short RNA sequences, ranging from 16 to 35 nucleotides (miRBase; http://www.mirbase.org). The majority of the identified sequences are 21 or 22 nucleotides in length. Despite the range of sequence lengths for different miRNAs, individual miRNAs were thought to have a specific sequence of a particular length. A recent report describing a longer variant of a previously identified miRNA in Arabidopsis thaliana prompted this investigation for variations in the length of other miRNAs.

Results: In this paper, we demonstrate that a fifth of annotated A. thaliana miRNAs recorded in miRBase V.14 have stable miRNA isoforms that are one or two nucleotides longer than their respective recorded miRNA. Further, we demonstrate that miRNA isoforms are co-expressed and often show differential argonaute complex association. We postulate that these extensions are caused by differential cleavage of the parent precursor miRNA.

Conclusions: Our systematic analysis of A. thaliana miRNAs reveals that miRNA length isoforms are relatively common. This finding not only has implications for miRBase and miRNA annotation, but also extends to miRNA validation experiments and miRNA localization studies. Further, we predict that miRNA isoforms are present in other plant species also.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Two mature micro(mi)RNA sequences derived from the ath-MIR156h pre-miRNA hairpin. The primary hairpin ath-MIR156h gives rise to two mature isoforms of ath-MIR156h, which differ by one nucleotide on the 5' terminus.
Figure 2
Figure 2
AGO association of ath-MIR156h isoforms. Mature miRNA ath-MIR156h resides mostly in the argonaute (AGO)1 effector complex, whereas the majority of ath-MIR156h+1 resides in the AGO5 effector complex. The cloning ratios are given in percentage and absolute numbers. Statistical analysis on the AGO association frequencies using the Freeman-Halton extension of the Fisher exact probability test [33] revealed a highly significant result (P = 2.5 × 10-5) for the observed difference in AGO association. Data originated from the AGO association datasets [11].
Figure 3
Figure 3
Frequency of extra 5' nucleotides. Several small Arabidopsis thaliana RNA datasets were analyzed for the occurrence of miRNAs with extra 5' nucleotides. From these datasets, 61% of the A. thaliana miRNAs listed in miRBase had no significant occurrence of extra nucleotides, 20% of the annotated miRNAs were not observed in the datasets at all, and 19% of miRNA had a significant proportion of either one (+1 MIR) or two (+2 MIR) nucleotides.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Carthew RW. Gene regulation by microRNAs. Curr Opin Genet Dev. 2006;16:203–208. doi: 10.1016/j.gde.2006.02.012. - DOI - PubMed
    1. Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAS and their regulatory roles in plants. Ann Rev Plant Biol. 2006;57:19–53. doi: 10.1146/annurev.arplant.57.032905.105218. - DOI - PubMed
    1. Hagen JW, Lai EC. microRNA control of cell-cell signaling during development and disease. Cell Cycle. 2008;7:2327–2332. - PMC - PubMed
    1. Williams AE. Functional aspects of animal microRNAs. Cell Mol Life Sci. 2008;65:545–562. doi: 10.1007/s00018-007-7355-9. - DOI - PMC - PubMed
    1. Yang B, Lu Y, Wang Z. Control of cardiac excitability by microRNAs. Cardiovasc Res. 2008;79:571–580. doi: 10.1093/cvr/cvn181. - DOI - PubMed

LinkOut - more resources