THE JOURNAL OF COMPARATIVE NEUROLOGY 509:225–238 (2008) The Transcriptome of Retinal Mu¨ ller Glial Cells KARIN ROESCH,1 ASHUTOSH P. JADHAV,1 JEFFREY M. TRIMARCHI,1 MICHAEL B. STADLER,3 BOTOND ROSKA,3 BEN B. SUN,1,4 AND CONSTANCE L. CEPKO1,2* 1Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 2Howard Hughes Medical Institute, Boston, Massachusetts 02115 3Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland 4Canaccord Adams, Boston, Massachusetts 02110 ABSTRACT Mu¨ ller glial cells are the major type of glia in the mammalian retina. To identify the molecular machinery that deﬁnes M u¨ller glial cell identity and function, single cell gene expression proﬁling was performed on Affymetrix microarrays. Identiﬁcation of a cluster of genes expressed at high levels suggests a M u¨ller glia core transcriptome, which likely underlies many of the functions of M u¨ller glia. Expression of components of the cell cycle machinery and the Notch pathway, as well as of growth factors, chemokines, and lipoproteins might allow communication between M u¨ller glial cells and the neurons that they support, including modulation of neuronal activity. This approach revealed a set of transcripts that were not previously characterized in (M u¨ller) glia; validation of the expression of some of these genes was performed by in situ hybridization. Genes expressed exclusively by M u¨ller glia were identiﬁed as novel markers. In addition, a novel BAC transgenic mouse that expresses Cre in Mu¨ ller glia cells was generated. The molecular ﬁngerprint of M u¨ller glia provides a foundation for further studies of Mu¨ ller glia development and function in normal and diseased states. J. Comp. Neurol. 509:225–238, 2008. © 2008 Wiley-Liss, Inc. Indexing terms: murine retina; Mu¨ ller glia; microarray; molecular markers; BAC transgenic mouse; transcriptome Glial cells are found throughout the central nervous system. In the mammalian retina, three types of glia have been identiﬁed: Mu¨ ller glia, astrocytes, and microglia. As- trocytes originate in the more medial aspects of the brain, and enter into the retina through the developing optic nerve (Stone and Dreher, 1987; Watanabe and Raff, 1988). Microglial cells are thought to be of mesodermal origin (Chan-ling, 1994). The only glial cells derived from the retinal neuroepithelium are the M u¨ller glia. They arise late in development from multipotent progenitor cells (Sidman, 1961; Young, 1985; Turner and Cepko, 1987). In the mature retina, they are normally not mitotic but can re-enter the cell cycle under certain circumstances (Sahel et al., 1990; Dyer and Cepko, 2000). Mu¨ ller glial cells are radial and form the outer and inner limiting membranes. They surround neuronal cell bodies and processes within the retina and perform a wide range of functions, including structural stabilization, reg- ulation of ion homeostasis, neurotransmitter recycling, and neuronal survival (Newman and Reichenbach, 1996; Bringmann et al., 2000; Mata et al., 2002). Recently it was © 2008 WILEY-LISS, INC. shown that their speciﬁc cylindrical shape, their regular and parallel orientation within the retina, and the high refractive index of their stalk allow them to capture and transfer light efﬁciently through the retina (Franze et al., 2007). Mu¨ ller glia can undergo reactive gliosis, when they divide and upregulate glial ﬁbrillary acidic protein This article includes Supplementary Material available via the Internet at http://www.interscience.wiley.com/jpages/0021-9967/suppmat. Grant sponsor: National Institutes of Health; Grant numbers: T32EY007110 (to A.P.J.), 5F32EY014495 and T32 EY007145 (to J.M.T.), and EY014466 and EY08064 (to C.L.C.); Grant sponsor: American Physi- ological Society; Grant number: Functional Genomics grant (to B.B.S.); Grant sponsor: Macula Vision Research Foundation. *Correspondence to: Constance L. Cepko, Department of Genetics, Harvard Medical School, and Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115. E-mail: cepko@genetics.med.harvard.edu Received 12 October 2007; Revised 8 January 2008; Accepted 20 March 2008 DOI 10.1002/cne.21730 Published online May 8, 2008 in Wiley InterScience (www.interscience. wiley.com).