Abstract
BackgroundmiRNAs are key players in gene expression regulation. To fully understand the complex nature of cellular differentiation or initiation and progression of disease, it is important to assess the expression patterns of as many miRNAs as possible. Thereby, identifying novel miRNAs is an essential prerequisite to make possible a comprehensive and coherent understanding of cellular biology.Methodology/Principal FindingsBased on two extensive, but previously published, small RNA sequence datasets from human embryonic stem cells and human embroid bodies, respectively [1], we identified 112 novel miRNA-like structures and were able to validate miRNA processing in 12 out of 17 investigated cases. Several miRNA candidates were furthermore substantiated by including additional available small RNA datasets, thereby demonstrating the power of combining datasets to identify miRNAs that otherwise may be assigned as experimental noise.Conclusions/SignificanceOur analysis highlights that existing datasets are not yet exhaustedly studied and continuous re-analysis of the available data is important to uncover all features of small RNA sequencing.
Highlights
MiRNAs are small,22 nt non-coding RNA sequences
Considering the complex combinatorial regulatory functions ascribed to miRNAs today, it is of great importance to find and validate all genomic miRNAs in humans and other organisms to uncover the complexity of gene regulation during cellular differentiation, homeostasis and disease
By re-inspection of published small RNA sequence datasets [1,13,14,15,16,17,18], we here put forth an extensive list of yet 112 un-annotated miRNA candidates with 12 of 17 putative miRNAs being validated by northern blotting giving a preliminary 70% success rate of our prediction
Summary
MiRNAs are small ,22 nt non-coding RNA sequences. The miRNA is produced by the cellular RNAi machinery from large hairpin structured transcript (pri-miRNA) into the mature form (miRNA) in a two-step process having a precursor miRNA (premiRNA) intermediate (reviewed in [2]). By re-inspection of published small RNA sequence datasets [1,13,14,15,16,17,18], we here put forth an extensive list of yet 112 un-annotated miRNA candidates with 12 of 17 putative miRNAs being validated by northern blotting giving a preliminary 70% success rate of our prediction.
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