Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 110; no. 49; pp. 19814 - 19819
• Main Authors: Powell, Curtis, Grant, Ana R., Cornblath, Eli, Goldman, Daniel
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 03.12.2013; NATIONAL ACADEMY OF SCIENCES; National Acad Sciences
• Subjects: Animals; APOBEC Deaminases; Base Sequence; Biological Sciences; Cytidine Deaminase - metabolism; DNA; DNA methylation; DNA Methylation - genetics; DNA Primers - genetics; DNA, Complementary - genetics; Ependymoglial Cells - chemistry; Fluorescent Antibody Technique; Gene expression; Genomes; Methylation; Mice; Molecular Sequence Data; Muscle Proteins - metabolism; Neuroglia; Pluripotent stem cells; Polymerase chain reaction; Progenitor cells; Regeneration - physiology; Retina; Retina - physiology; Sequence Analysis, DNA; Somatic cells; Stem cells; Zebrafish; multipotent; repair; bisulfite sequencing; Ascl1; DNA sequencing
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1312009110

Upon retinal injury, zebrafish Müller glia (MG) transition from a quiescent supportive cell to a progenitor cell (MGPC). This event is accompanied by the induction of key transcription and pluripotency factors. Because somatic cell reprogramming during induced pluripotent stem cell generation is accompanied by changes in DNA methylation, especially in pluripotency factor gene promoters, we were interested in determining whether DNA methylation changes also underlie MG reprogramming following retinal injury. Consistent with this idea, we found that genes encoding components of the DNA methylation/demethylation machinery were induced in MGPCs and that manipulating MGPC DNA methylation with 5-aza-2′-deoxycytidine altered their properties. A comprehensive analysis of the DNA methylation landscape as MG reprogram to MGPCs revealed that demethylation predominates at early times, whereas levels of de novo methylation increase at later times. We found that these changes in DNA methylation were largely independent of Apobec2 protein expression. A correlation between promoter DNA demethylation and injury-dependent gene induction was noted. In contrast to induced pluripotent stem cell formation, we found that pluripotency factor gene promoters were already hypomethylated in quiescent MG and remained unchanged in MGPCs. Interestingly, these pluripotency factor promoters were also found to be hypomethylated in mouse MG. Our data identify a dynamic DNA methylation landscape as zebrafish MG transition to an MGPC and suggest that DNA methylation changes will complement other regulatory mechanisms to ensure gene expression programs controlling MG reprogramming are appropriately activated during retina regeneration.