Open Access Highly Accessed Research article

miRNeye: a microRNA expression atlas of the mouse eye

Marianthi Karali1, Ivana Peluso1, Vincenzo A Gennarino13, Marchesa Bilio1, Roberta Verde14, Giampiero Lago1, Pascal Dollé2 and Sandro Banfi1*

  • * Corresponding author: Sandro Banfi

  • † Equal contributors

Author Affiliations

1 Telethon Institute for Genetics and Medicine, Via P. Castellino 111, 80131 Naples, Italy

2 IGBMC (Institute de Génétique et de Biologie Moléculaire et Cellulaire); UMR 7104 CNRS; U 964 INSERM; BP 10142, 67404 Illkirch, France

3 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA

4 ICB (Istituto di Chimica Biomolecolare), CNR, Via Campi Flegrei 34, 80078 Naples, Italy

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BMC Genomics 2010, 11:715  doi:10.1186/1471-2164-11-715

Published: 20 December 2010



MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution.


In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina.


This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures.