A genome-wide screen for non-template nucleotides and isomiR repertoires in miRNAs indicates dynamic and versatile microRNAome
Abstract
miRNA variants (termed isomiRs) have been reported as potential functional molecules that may affect miRNA stability or target selection. The aims of the present study were to comprehensively survey and characterize non-template nucleotides (NTNs) and isomiR repertoires in miRNAs. Over 50 % of the NTNs were located in the 3' ends (also termed 3' additions), followed by the 5' ends and adjacent positions to 5' and 3' ends. The similar distributions of NTNs and isomiR repertoires might be detected between homologous or clustered miRNAs. miRNA might be stably expressed based on the typical analysis, but its isomiRs might be strongly up- or down-regulated. IsomiRs with novel seed sequences were mainly derived from "seed shifting" events in 5' isomiRs, NTNs in 5' ends or in seed sequences. IsomiRs from a miRNA locus or homologous miRNA loci maybe have the same seed sequences, but they would have various enrichment levels and 3' ends. Interestingly, isomiR species with novel seed sequences via NTNs in the seed region were always stably expressed. These novel seed sequences could lead to novel functional roles through driving the potential novel target mRNAs. Integrated predicted target mRNAs and further microarray validation showed that these isomiRs have versatile biological roles. Collectively, multiple isomiR products and miRNA maturation processes provide opportunities to perform versatile roles in the regulatory network, which further enriches and complicates the regulation of…
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This could explain some of the variability of microRNA expression across methods demonstrated by the miRQC project.
“This could explain some of the variability of microRNA expression across methods demonstrated by the miRQC project (particularly between RNA-seq and hybridization approaches) (Mestdagh et al. 2014) and impact the biologic activity of mimics and inhibitors relative to the true microRNA 5p end (Guo et al. 2014).”
From Toward the human cellular microRNAome (2017) · cites this paper as Guo et al. 2014
Cites
A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing
Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A. O., Landthaler, M., et al. (2007) · Cell · doi:10.1016/j.cell.2007.04.040 · Cited by 3,626 · see citing works
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Toward the human cellular microRNAome
McCall, M. N., Kim, M.-S., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., et al. (2017) · Genome Research · doi:10.1101/gr.222067.117 · Cited by 151 · see citing works
- Authors
- Guo, L., Zhao, Y., Yang, S., Zhang, H., & Chen, F.
- Venue
- Molecular Biology Reports
- Published
- 2014-07-04
- Volume
- 41
- Issue
- 10
- Pages
- 6649-6658
- ISSN
- 0301-4851
- 1573-4978
- Cited by
- 20
- References
- 1
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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