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Open Access Open Badges Research article

Comparative analysis of neural transcriptomes and functional implication of unannotated intronic expression

Yazhou Sun134, Yaqiong Wang25, Yi Hu13, Gong Chen134 and Hong Ma12345*

Author Affiliations

1 Department of Biology, Pennsylvania State University, University Park, PA 16802, USA

2 State Key Laboratory of Genetic Engineering and Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, P. R. China

3 The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA

4 Intercollege Graduate Program in Genetics, Pennsylvania State University, University Park, PA 16802, USA

5 Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China

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BMC Genomics 2011, 12:494  doi:10.1186/1471-2164-12-494

Published: 10 October 2011



The transcriptome and its regulation bridge the genome and the phenome. Recent RNA-seq studies unveiled complex transcriptomes with previously unknown transcripts and functions. To investigate the characteristics of neural transcriptomes and possible functions of previously unknown transcripts, we analyzed and compared nine recent RNA-seq datasets corresponding to tissues/organs ranging from stem cell, embryonic brain cortex to adult whole brain.


We found that the neural and stem cell transcriptomes share global similarity in both gene and chromosomal expression, but are quite different from those of liver or muscle. We also found an unusually high level of unannotated expression in mouse embryonic brains. The intronic unannotated expression was found to be strongly associated with genes annotated for neurogenesis, axon guidance, negative regulation of transcription, and neural transmission. These functions are the hallmarks of the late embryonic stage cortex, and crucial for synaptogenesis and neural circuit formation.


Our results revealed unique global and local landscapes of neural transcriptomes. It also suggested potential functional roles for previously unknown transcripts actively expressed in the developing brain cortex. Our findings provide new insights into potentially novel genes, gene functions and regulatory mechanisms in early brain development.

neural transcriptomes; stem cell; intronic expression; embryonic brain cortex; neonatal brain cortex