Functional microRNA targetome undergoes degeneration-induced shift in the retina

Abstract

SummaryMicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases, including age-related macular degeneration, acting as post-transcriptional gene suppressors through their association with argonaute (AGO) protein family members. However, to understand their role in disease, investigation into the regulatory nature of miRNA with their targets is required. To identify the active-miRnome-targetome interactions in the degenerating retina, AGO2 HITS-CLIP was performed using a mouse model of retinal degeneration. Analysis revealed a similar miRnome between healthy and damaged retinas, however, a shift in the active targetome was observed. This shift was also demonstrated by a change in the seed binding regions of miR-124-3p, the most abundant retinal miRNA loaded in AGO2. Following damage, AGO2 was localised to the inner retinal layers indicating a locational miRNA response to retinal damage. This study provides important insight into the alteration of miRNA regulatory activity that occurs as a response to retinal degeneration.

A Comparative Analysis of Reactive Müller Glia Gene Expression After Light Damage and microRNA-Depleted Müller Glia—Focus on microRNAs

“…miRNA have been profiled for whole normal retina and after light damage (Karali et al, 2007 , 2011 ; Hackler et al, 2010 ; Chu-Tan et al, 2020 ), but not in MG after light damage. In order to profile the miRNAs of reactive MG, we used the MG reporter mice, FACS-purified the MG from undamaged and damaged retinas (7 days after light damage) and performed Nanostring miRNA profiling.…”

“…This means a miRNA identified in a cell does not necessarily regulate gene expression. We therefore used Ago HITS-CLIP data of total retina from a recently published study from the Natoli lab (Chu-Tan et al, 2020 ), to assess if any of the MG miRNAs are bound to Ago2 ( Supplementary Figure 5A ). Although this dataset is from whole retina and not cell type specific, our previous results comparing MG miRNA expression with retinal neuronal miRNA expression allows us to tentatively assign the HITS-CLIP results for some of the MG-specific miRNAs (mGliomiRs).…”

“…This suggests that specific levels of miRNAs are responsible for particular gene targeting. Since all MG miRNAs were also found to be bound to Ago2, they are indeed regulatory miRNAs in retinal cells (Chi et al, 2009 ; Chu-Tan et al, 2020 ). This suggests that MG miRNAs play a role in reactive gliosis.…”

“…Ago HITS-CLIP [Argonoute2 hi gh- t hroughput s equencing of RNAs isolated by c ross l inking i mmuno p recipitation developed in the Darnell lab (Chi et al, 2009 )] data for whole undamaged and light damaged retinas; generated in the Natoli lab (available at BioRxiv), was used to evaluate whether MG miRNAs and mRNAs are Ago2 bound (Chu-Tan et al, 2020 ).…”