Open Access Highly Accessed Research article

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

Stefan E Seemann12, Susan M Sunkin3, Michael J Hawrylycz3, Walter L Ruzzo145 and Jan Gorodkin12*

Author Affiliations

1 Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark

2 , IBHV, University of Copenhagen, Denmark

3 Allen Institute for Brain Science, , USA

4 Computer Science and Engineering and Genome Sciences, Univ. of Washington, USA

5 Fred Hutchinson Cancer Research Center, , USA

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BMC Genomics 2012, 13:214  doi:10.1186/1471-2164-13-214

Published: 31 May 2012



Post-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) of mRNAs, in collaboration with specific binding proteins and RNAs. In several well characterized cases, these RNA elements are known to form stable secondary structures. RNA secondary structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance of lncRNAs in brain development and function. However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts.


By comprehensive spatial expression analysis of the adult mouse in situ hybridization data of the Allen Mouse Brain Atlas, we show that transcripts (coding as well as non-coding) associated with in silico predicted structured probes are highly and significantly enriched in almost all analyzed brain regions. Functional implications of these RNA structures and their role in the brain are discussed in detail along with specific examples. We observe that mRNAs with a structure prediction in their UTRs are enriched for binding, transport and localization gene ontology categories. In addition, after manual examination we observe agreement between RNA binding protein interaction sites near the 3’ UTR structures and correlated expression patterns.


Our results show a potential use for RNA structures in expressed coding as well as noncoding transcripts in the adult mouse brain, and describe the role of structured RNAs in the context of intracellular signaling pathways and regulatory networks. Based on this data we hypothesize that RNA structure is widely involved in transcriptional and translational regulatory mechanisms in the brain and ultimately plays a role in brain function.