Open Access Highly Accessed Research article

Comprehensive survey of human brain microRNA by deep sequencing

Ning-Yi Shao12, Hai Yang Hu1, Zheng Yan1, Ying Xu1, Hao Hu13, Corinna Menzel3, Na Li4, Wei Chen34* and Philipp Khaitovich15*

Author Affiliations

1 Partner Institute for Computational Biology, 320 Yueyang Road, 200031, Shanghai, China

2 Graduate School of Chinese Academy of Sciences, 19 Yuquan Road, 100039, Beijing, China

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

4 Max-Delbrück-Centrum für Molekulare Medizin, Berlin Institute for Medical Systems Biology, Robert-Rössle-str 10, D-13092, 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 2010, 11:409  doi:10.1186/1471-2164-11-409

Published: 30 June 2010



MicroRNA (miRNA) play an important role in gene expression regulation. At present, the number of annotated miRNA continues to grow rapidly, in part due to advances of high-throughput sequencing techniques. Here, we use deep sequencing to characterize a population of small RNA expressed in human and rhesus macaques brain cortex.


Based on a total of more than 150 million sequence reads we identify 197 putative novel miRNA, in humans and rhesus macaques, that are highly conserved among mammals. These putative miRNA have significant excess of conserved target sites in genes' 3'UTRs, supporting their functional role in gene regulation. Additionally, in humans and rhesus macaques respectively, we identify 41 and 22 conserved putative miRNA originating from non-coding RNA (ncRNA) transcripts. While some of these molecules might function as conventional miRNA, others might be harmful and result in target avoidance.


Here, we further extend the repertoire of conserved human and rhesus macaque miRNA. Even though our study is based on a single tissue, the coverage depth of our study allows identification of functional miRNA present in brain tissue at background expression levels. Therefore, our study might cover large proportion of the yet unannotated conserved miRNA present in the human genome.