Position Effect Variegation as a Way to Visualize Age-Related Structural Change of Nuclear DNA
Nuclear DNA is surrounded by transcriptional machinery, protein structures that will attempt to transcribe any gene sequence they encounter. Where DNA is compacted into regions of heterochromatin by being spooled onto histones, genes are silenced because their sequences are hidden from transcriptional machinery. Whether a given stretch of DNA is compacted or not is determined by epigenetic mechanisms, largely decorations (such as methyl groups) attached to DNA and histones that alter their structural behavior. A general feature of aging is a loss of heterochromatin and increasing expression of genes and other sequences that are usually silenced in youth. This leads to, for example, the expression of transposons that can drive DNA damage and inflammation, but also disruption and change in normal cell function.
Some time ago, researchers established a way to visualize whether or not a given region of DNA is compacted into heterochromatin. Flies can be genetically engineered with suitably placed genes that change the color of some of their features, such as eye segments, depending on whether or not they are expressed. Thus just by looking at the fly, researchers will know whether or not the region of DNA containing the inserted gene is compacted. A number of different fly lineages have been constructed over the years, as researchers needed a solution for one region or another. This approach is called position effect variegation.
Today's open acccess paper is a discussion of position effect variegation as a tool to inspect changes in DNA compaction into heterochromatin that occur with age and their correlation with high level outcomes such as mortality risk and longevity. Since increased loss of heretochromatin appears to correlate with longevity in flies, position effect variegation could be used to build aging clocks (in flies at least) that primarily reflect alterations to DNA structure rather than other mechanisms.
The heterochromatin loss model of aging suggests there is an age-dependent reduction in epigenetic factors that form and maintain the heterochromatin state of chromosomes. Position Effect Variegation (PEV) can visually report phenotypes of heterochromatin mediated silencing in Drosophila Melanogaster eyes and we use PEV to examine the association between heterochromatin state changes and aging.
Pericentric inserts causing PEV showed suppressed variegation phenotypes in old age compared to young age and were confirmed to be associated with progressively increasing transcription, indicating loss of heterochromatin mediated silencing. Within a single population, animals with enhanced PEV phenotypes live longer than those with more suppressed PEV phenotypes, suggesting that small differences in environmental or genetic factors within this population could be responsible for differences in heterochromatin and lifespan.
Environmental factors could enhance heterochromatin, reduced nutrient diet and lower temperature coincided with enhanced heterochromatin and longer life. Furthermore, genetic variants associated with long life, including chico mutants, lead to increased heterochromatin and enhanced PEV phenotypes. Therefore, aging can be linked to heterochromatin loss and developmental increases in heterochromatin are associated with longevity. Thus, PEV reporters act as aging clocks demonstrating loss of heterochromatin that progresses with age and epigenetic alterations that can promote longevity.