Epigenetics in the Eye of the Beholder: DNA Hydroxymethylation Affects Retinal Development

5-hmC DNA Hydroxymethylation Affects Retinal Development

Something we may take for granted is how effortless it is for us to see, to experience the world around us without a second thought. But vision is an incredibly complex process that comes with a complicated functional network involving the generation, positioning, and synaptic wiring of neurons. Consisting of unique nerve cells constructed during early development, these neuronal circuits are typically created within the first week the eye is directly exposed to light. At this time, differentiation of neuronal precursor cells into several types of nerve cells occurs, creating numerous distinct patterns of functional connections among nerves. The drastic changes that happen while the nerve cells mature go hand-in-hand with specific changes in the pattern of gene expression.

A study examining this critical stage of retina development was conducted by researchers from the Ludwig Maximilian University of Munich, including PD Dr. Stylianos Michalakis and Professor Thomas Carell, who are both associated with CiPSM (Center for integrated Protein Science Munich). Along with their team of scientists, they found that DNA hydroxymethylation, an epigenetic mechanism recently growing in popularity in the field of epigenetics, is closely implicated in postnatal retinal network maturation.

Each cell contains the same collection of genes, but what determines the different cell types that are formed depends on the genes that are actually activated. Epigenetic research is beginning to elucidate the process of differentiation, including how the brain develops a certain ‘gender’ and how stem cells form into blood cells via histone demethylation. Chemical modifications or certain epigenetic marks can impact the expression of genes and therefore the types of cells that are formed. Changes in these epigenetic patterns are found to control the growth and formation of the neuronal network during development soon after birth.

DNA methylation is a common epigenetic mechanism, defined as the addition of a methyl group to the DNA. This chemical tag impacts genes by either turning them on or off. In general, DNA methylation often leads to gene suppression or inactivation by preventing transcription of a certain part of genomic DNA into molecules that control the synthesis of proteins.

In 2009, the methylated form of cytosine, known as 5-methylcytosine, was discovered to be further modified by a group of enzymes known as ten-eleven translocation (TET) enzymes. As a result, 5-mC forms into 5-hmC, or 5-hydroxymethylcytosine. 5-hmC was already known to exist, but was thought to be just an intermediate in the process of active demethylation.

“Ever since 5hmC was shown to be the product of a targeted modification reaction, people have suspected that it might play a role in switching genes on and off,” Michalakis said. “At all events, mature nerve cells in the retina contain high levels of 5hmC in their nuclear DNA, and we hypothesized that the production of 5hmC by Tet enzymes plays a significant part in the development of the neuronal network. But it was unclear how the modification is carried out and what its effects are.”

The team at Ludwig Maximilian University demonstrated that DNA hydroxymethylation is involved in the development of retinal neuronal connections. They found that 5-hmC levels were high during the period of early retinal maturation, approximately 2 weeks after birth, and one week after eye opening, they found that levels of 5-hydroxymethylcytosine spiked dramatically in the nuclear layers of the retina. Rod and cone photoreceptors which are responsible for visual signals at varying levels of light were found to be positive for 5-hmC during this time.

They discovered that TET3 specifically interacts with a DNA-bound transcriptional repressor and master regulator known as REST, leading to the conversion of the methylated 5-mC mark, which represses gene expression, to 5-hmC via oxidization. This was found to activate neuronal genes during retinal maturation. TET3 binds to enzymes that attach methyl groups to the histone proteins around which DNA is wrapped and makes previously inactive genes available to the transcriptional apparatus.

Overall, the researchers found that this master regulator of genes linked to neuronal maturation binds and recruits TET3 to the DNA for precise gene activation involved in retinal development. They reported that: “(1) REST regulates TET3 hydroxylase activity, (2) REST target genes accumulate 5hmC during retinal maturation, and (3) overexpression of TET3 activates REST target genes.”

Future directions for this research involve figuring out how and what in particular activates this TET3-driven mechanism.

Michalakis also noted: “We would also like to know whether defects in this mechanism might be responsible for certain diseases. If so, then our findings could also be of therapeutic use.”


Source: Perera, A. et al. (2015). TET3 Is Recruited by REST for Context-Specific Hydroxymethylation and Induction of Gene Expression. Cell Reports, 11(2): 283-294.

Reference: Epigenetic mechanism may influence the pattern of nerve connections during retinal development. Medical Xpress. 3 Apr 2015. Web.

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About Bailey Kirkpatrick 164 Articles
Bailey Kirkpatrick is a science writer with a background in epigenetics and psychology with a passion for conveying scientific concepts to the wider community. She enjoys speculating about the implications of epigenetics and how it might impact our perception of wellbeing and the development of novel preventative strategies. When she’s not combing through research articles, she also enjoys discovering new foods, taking nighttime strolls, and discussing current events over a barrel-aged sour beer or cold-brewed coffee.


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