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Genome reprogramming during zebrafish retina regeneration

November 2013

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In previous posts in this blog I have discussed how zebrafish are able to regenerate their retinas from the dedifferentiation of quiescent supportive Müller glia (MG) that re-enter the cell cycle and give rise to a cycling population of multipotent progenitors (MGPC) that differentiate into the different retina cell types. Previous studies have suggested that dynamic changes in the DNA methylation landscape can have a function in the transition from MG to MGPC. How much similar is this cellular reprogramming that occurs during regeneration to the reprogramming required to transform somatic cells into induced pluripotent stem cells (iPS) is an interesting question for the field of regenerative medicine. During iPS generation there is an increased DNA demethylation of the promoter regions of pluripotency genes that correlates with an increase in their expression. Similarly, the expression of pluripotency genes as well as other regeneration-associated genes increases during the transition from MG to MGPC.

In a recent paper from the laboratory of Daniel Goldman the authors wonder up to what extend changes in the DNA methylation landscape are important for the transition from MG to MGPC ( First, they checked how the expression of several regulators of DNA methylation changed in MGPCs  (from injured retinas) compared to MG (from uninjured retinas). They found an increased expression of genes associated with both DNA demethylation and methylation, suggesting that the regulation of DNA methylation may be important for MGPC formation. Next, they showed how the induction of DNA demethylation perturbed the migration and differentiation of MGPC-derived progeny. They took then a genomic approach to compare the DNA methylation landscapes between MG from uninjured animals and MGPCs from injured retinas 4 dpi (between 2 and 7 days post-injury there is an asymmetric division and proliferative amplification of MGPCs). They compared the methylation levels of 611,434 individual cytosines within the CpG context and found 9,554 differentially methylated bases (DMBs) that represented an overall difference of 1,54%. Of those changes, 54% corresponded to increased methylation events and 46% to decreased ones. Most DMBs were localized in intergenic and intronic regions with few of them localized in promoter regions.

From 2 to 4 dpi the DNA methylation landscape shifted from one that was predominantly driven by demethylation to one with increasing levels of methylation, which could correlate to the MGPCs getting ready to enter into differentiation. As expected, a decrease methylation in the promoter regions correlated with an increased gene expression. However, and surprisingly, no DMBs were found in the promoters of pluripotency and retina regeneration-associated genes. Even more remarkably was the fact that when the authors checked the levels of methylation of the promoters of those genes in quiescent MG they found that they were also hypomethylated. So, these data made the authors hypothesize that pluripotency and regeneration-associated genes might be poised for activation in quiescent MG, implying that MG would require only limited reprogramming and would be more stem-like than thought before. Because the regenerative capacity of mouse MG is very limited the authors checked the methylation state of mouse MG. Remarkably, they found that the promoters of pluripotency and regeneration-associated genes showed low levels of methylation, as observed in zebrafish.

In summary, this study shows how the global DNA methylation landscape changes during the transition from MG to MGPCs pointing out an important regulatory function during this reprogramming. However, pluripotency and other genes required for regeneration appeared to be hypomethylated already in MG suggesting that they could be already preprogrammed for a regenerative response. These genes could be then regulated by other events such as histone modifications or transcription factors, indicating that changes in the DNA methylation status would be required but it would not be sufficient for MG reprogramming. The fact that mouse MG share this hypomethylated landscape in pluripotency genes opens the door to search for strategies to facilitate their reprogramming into progenitor cells that could enhance the poor regenerative abilities of the mammalian retina.

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Francesc Cebrià

Francesc Cebrià

Francesc Cebrià

I am a Biologist and Professor at the University of Barcelona. I do my research on a fascinating animal: freshwater planarians. You can cut them in as many pieces as you want and each piece will regenerate a complete new flatworm in very few days. In this blog I will keep you updated on the latest news on the field of animal regeneration. You will be able to follow the latest research on how planarians, axolotls, newts, cnidarians and other animals are able to regenerate parts of their bodies

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