Background: Same-nucleotide repeats (iterons) are strongly expressed in many DNA regions and RNA classes. These repeats serve importantly in association of polynucleotides and proteins, but have not been characterized in miRNAs.
Methods: Iterons and nucleotide strings were quantified in currently known human miRNAs, including some comparisons with miRNAs of other species.
Results: Human 5p miRNAs have significantly more G iterons than other miRNA groups. The 3p miRNAs have an inverse excess of C iterons. The miRNAs lacking functional counter-stems (which we differentiate as 5n or 3n by position in pre-miRNAs) also have a large excess of G iterons. In 5p miRNAs G and C iterons have much higher density in the seed compared to the post-seed region. This difference is lower in 5n and 3n sequences, and much lower in 3p sequences. In all groups the contiguous GC strings constitute a larger part of sequences than the AU strings. A surplus of G or C iterons and of GC strings should enable a more stable association with the target mRNAs.
Conclusion: From the available evidence, the G iteron- and GC-rich miRNAs should also interact more readily with miRNA-processing and similar proteins.