Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing

Genome-wide characterization of the retinal transcriptome is central to understanding development, physiology and disorders of the visual system. Massively parallel, short-read sequencing of mRNA libraries was used to generate an extensive map of the transcriptome of the adult, murine neural retina. RNA-seq data strongly corroborates prior transcriptome studies by microarray and SAGE. However, several novel features of the retinal transcriptome were discovered. For example, retinal disease genes were discovered to be among the most highly expressed in the transcriptome. We also demonstrate other interesting features of the retinal transcriptome, for example, that the retina appears to employ a very specific and restricted set of synaptic vesicle genes, and also that there is persistence of expression of a majority of “neurodevelopmental” genes into adulthood. Retina transcriptome studies utilizing novel sequencing methods have been highly informative and these data may also serve as a resource for the community of researchers.

► Using RNA-seq, we have generated an extensive map of the transcriptome of the adult, murine neural retina. ► 15,251 genes were found to be expressed with greater than 3655 alternatively spliced genes. ► New insights into architecture of disease genes. ► Gene expression of developmental genes persists into adulthood. ► Retina uses a specific and restricted subset of synaptic vesicle genes.