The sufficient minimal set of miRNA seed types
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MOTIVATION: Pairing between the target sequence and the 6-8 nt long seed sequence of the miRNA presents the most important feature for miRNA target site prediction. Novel high-throughput technologies such as Argonaute HITS-CLIP afford meanwhile a detailed study of miRNA:mRNA duplices. These interaction maps enable a first discrimination between functional and non-functional target sites in a bulky fashion. Prediction algorithms apply different seed paradigms to identify miRNA target sites. Therefore, a quantitative assessment of miRNA target site prediction is of major interest. RESULTS: We identified a set of canonical seed types based on a transcriptome wide analysis of experimentally verified functional target sites. We confirmed the specificity of long seeds but we found that the majority of functional target sites are formed by less specific seeds of only 6 nt indicating a crucial role of this type. A substantial fraction of genuine target sites arenon-conserved. Moreover, the majority of functional sites remain uncovered by common prediction methods.
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In animals, microRNA binding to a 3'UTR depends on 6-8 nucleotides at the 5' end (seed region) and typically leads to translation repression without mRNA cleavage.
“In animals, binding of a microRNA with a 3′UTR is based on 6–8 nucleotides at the 5’ end of the microRNA, called the seed region. Such an interaction typically leads to translation repression without mRNA cleavage [7].”
From MicroRNAs as Regulators of Phagocytosis (2022) · cites this paper as [7]
The Introduction (page unavailable) describes the seed as a 6–8-nucleotide sequence near the miRNA’s 5′ end, and the Results discuss seed matches in 3′UTRs. The paper mentions regulation of translation and mRNA decay, but does not establish that these interactions typically repress translation without mRNA cleavage. (LLM, conf=0.85)
Experimental — accuracy not yet measuredIn many cases, a functional miRNA:MRE interaction occurs via the 5' seed region (nucleotides 2-8).
“In many cases, a functional miRNA:MRE interaction occurs via the 5' seed region (nucleotides 2–8) (42, 51).”
From Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation (2018) · cites this paper as [51]
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- Authors
- Ellwanger, D. C., Büttner, F. A., Mewes, H.-W., & Stümpflen, V.
- Affiliations
- Helmholtz Munich (DE)
- Corresponding author
- Büttner, Florian A.
- Stümpflen, Volker
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-03-26
- Volume
- 27
- Issue
- 10
- Pages
- 1346-1350
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3087955
- OpenAlex
- W2155785723
- Cited by
- 112
- References
- 31
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 4 · 2023: 5 · 2022: 6 · 2021: 6 · 2020: 8 · 2019: 12 · 2018: 15 · 2017: 5 · 2016: 7 · 2015: 7 · 2014: 8 · 2013: 7 · 2012: 11
- FWCI
- 2.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Site cant be reached (submittedVersion)
- Funders
- Bundesministerium für Bildung und Forschung (0315494A)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- microRNA, miRNA seed sequence
- MeSH terms
- Algorithms, Animals, Base Sequence, Humans, Oligonucleotides, RNA, Messenger, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, MicroRNAs, Eukaryotic Initiation Factors, Mice
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