Open Access Highly Accessed Open Badges Research article

Sequence features associated with microRNA strand selection in humans and flies

Hai Yang Hu12, Zheng Yan1, Ying Xu1, Hao Hu13, Corinna Menzel3, Yan Hong Zhou2, Wei Chen4* and Philipp Khaitovich15*

Author Affiliations

1 Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, PR China

2 Hubei Bioinformatics and Molecular Imaging Key Laboratory, 1037 Luoyu Road, Wuhan, 430074, PR China

3 Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany

4 Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany

5 Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany

For all author emails, please log on.

BMC Genomics 2009, 10:413  doi:10.1186/1471-2164-10-413

Published: 4 September 2009



During microRNA (miRNA) maturation in humans and flies, Drosha and Dicer cut the precursor transcript, thereby producing a short RNA duplex. One strand of this duplex becomes a functional component of the RNA-Induced Silencing Complex (RISC), while the other is eliminated. While thermodynamic asymmetry of the duplex ends appears to play a decisive role in the strand selection process, the details of the selection mechanism are not yet understood.


Here, we assess miRNA strand selection bias in humans and fruit flies by analyzing the sequence composition and relative expression levels of the two strands of the precursor duplex in these species. We find that the sequence elements associated with preferential miRNA strand selection and/or rejection differ between the two species. Further, we identify another feature that distinguishes human and fly miRNA processing machinery: the relative accuracy of the Drosha and Dicer enzymes.


Our result provides clues to the mechanistic aspects of miRNA strand selection in humans and other mammals. Further, it indicates that human and fly miRNA processing pathways are more distinct than currently recognized. Finally, the observed strand selection determinants are instrumental in the rational design of efficient miRNA-based expression regulators.