MicroRNA (miRNA) Transcriptome of Mouse Retina and Identification of a Sensory Organ-specific miRNA Cluster

Abstract

Although microRNAs (miRNAs) provide a newly recognized level of regulation of gene expression, the miRNA transcriptome of the retina and the contributions of miRNAs to retinal development and function are largely unknown. To begin to understand the functions of miRNAs in retina, we compared miRNA expression profiles in adult mouse retina, brain, and heart by microarray analysis. Our results show that at least 78 miRNAs are expressed in adult mouse retina, 21 of which are potentially retina-specific. Among these, we identified a polycistronic, sensory organ-specific paralogous miRNA cluster that includes miR-96, miR-182, and miR-183 on mouse chromosome 6qA3 with conservation of synteny to human chromosome 7q32.2. In situ hybridization showed that members of this cluster are expressed in photoreceptors, retinal bipolar and amacrine cells. Consistent with their genomic organization, these miRNAs have a similar expression pattern during development with abundance increasing postnatally and peaking in adult retina. Target prediction and in vitro functional studies showed that MITF, a transcription factor required for the establishment and maintenance of retinal pigmented epithelium, is a direct target of miR-96 and miR-182. Additionally, to identify miRNAs potentially involved in circadian rhythm regulation of the retina, we performed miRNA expression profiling with retinal RNA harvested at noon (Zeitgeber time 5) and midnight (Zeitgeber time 17) and identified a subgroup of 12 miRNAs, including members of the miR-183/96/182 cluster with diurnal variation in expression pattern. Our results suggest that miR-96 and miR-182 are involved in circadian rhythm regulation, perhaps by modulating the expression of adenylyl cyclase VI (ADCY6). MicroRNAs (miRNAs)3 are small, noncoding, regulatory RNAs of 18 -24 nucleotides in length found in all metazoans. Since their discovery in 1993, at least 100 different miRNA genes have been documented in the genomes of Drosophila and Caenorhabditis elegans and more than 250 in vertebrate genomes (1) with recent estimates as high as 800 (2). By influencing translation and stability of mRNAs, miRNAs contribute a newly recognized level of regulation of gene expression affecting a variety of biological processes. miRNAs are transcribed by RNA polymerase II as transcripts (pri-miRNAs) that are capped, polyadenylated, and spliced (3). pri-miRNAs fold into hairpin structures that are cleaved by an RNase III endonuclease, the Drosha-DGCR8 complex, to form 60 -70-nt stem loop intermediates known as pre-miRNA (1, 4, 5) that are transported from the nucleus by an Exportin 5-dependent mechanism. In the cytoplasm they are cleaved by a second RNase III endonuclease, Dicer, to yield double-stranded

Efficient in vivo microRNA targeting of liver metastasis

“…In accordance with the effectiveness of miR-182 suppression, mRNA levels of its direct targets ADCY6 (Xu et al, 2007) and FOXO3 (Segura et al, 2009) were found to be upregulated in the tumors of anti-miR-182-treated mice in both experimental settings ( Figure 2b). Moreover, we also observed an increase in FOXO3 protein expression in the tumors of anti-miR-182-treated mice by immunohistochemistry ( Figure 2c).…”

Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma

“…These miRNAs also highly correlated with hsa-miR-182 by being transcribed as a single polycistronic primarymiRNA. 37 Hsa-miR-96 was also found upregulated in primary cells from chronic myeloid leukemia 38 and in hepatocellular tumors. 39 Moreover, we found hsa-miR-96 to be associated with Gleason score and biochemical relapse.…”

New meaning in the message: Noncoding RNAs and their role in retinal development

“…Several recent studies have characterized miRNAs expressed in the mammalian retina using microarray-based expression profiling and/or in situ hybridization (Deo et al, 2006;Ryan et al, 2006;Arora et al, 2007;Karali et al, 2007;Loscher et al, 2007;Xu et al, 2007). Studies in zebrafish have also identified several miRNAs with cellspecific expression in retina (Kapsimali et al, 2007).…”

“…In zebrafish, miR-9 and miR-92 are highly expressed in the mitotically active ciliary marginal zone (CMZ), and are likely to be progenitor-enriched in mouse (Kapsimali et al, 2007). The targets of these embryonic and early postnatally-enriched mouse miRNAs have yet to be investigated, and no key developmental regulatory genes have yet (Loscher et al, 2007;Xu et al, 2007), species in which retinal expression is observed (Arora et al, 2007;Kapsimali et al, 2007;Karali et al, 2007;Loscher et al, 2007;Xu et al, 2007), developmental expression pattern , mouse cellular expression pattern (Karali et al, 2007;Loscher et al, 2007;Xu et al, 2007), zebrafish cellular expression pattern (Kapsimali et al, 2007), cellular targets (Arora et al, 2007;Xu et al, 2007), expression change in rd animals (Loscher et al, 2007). AC, amacrine cells; CMZ, ciliary marginal zone; GC, ganglion cells; GCL, ganglion cell layer; HC, horizontal cells; HD, homeodomain; INL, inner nuclear layer; MG, Muller glia; NA, not applicable; ND, not determined; NHR, nuclear hormone receptor; ONL, outer nuclear layer; Prog, retinal progenitors; s(prefix) ϭ subset (cell type).…”