Establishing the contribution of active histone methylation marks to the aging transcriptional landscape of Drosophila photoreceptors

Abstract

Studies in multiple organisms have shown that aging is accompanied by several molecular phenotypes that include dysregulation of chromatin. Since chromatin regulates DNA-based processes such as transcription, alterations in chromatin modifications could impact the transcriptome and function of aging cells. In flies, as in mammals, the aging eye undergoes changes in gene expression that correlate with declining visual function and increased risk of retinal degeneration. However, the causes of these transcriptome changes are poorly understood. Here, we profiled chromatin marks associated with active transcription in the aging Drosophila eye to understand how chromatin modulates transcriptional outputs. We found that both H3K4me3 and H3K36me3 globally decrease across all actively expressed genes with age. However, we found no correlation with changes in differential gene expression. Downregulation of the H3K36me3 methyltransferase Set2 in young photoreceptors revealed significant changes in splicing events that overlapped significantly with those observed in aging photoreceptors. These overlapping splicing events impacted multiple genes involved in phototransduction and neuronal function. Since proper splicing is essential for visual behavior, and because aging Drosophila undergo a decrease in visual function, our data suggest that H3K36me3 could play a role in maintaining visual function in the aging eye through regulating alternative splicing.

Targeted RNAi screen identifies transcriptional mechanisms that prevent premature degeneration of adult photoreceptors

“…These data also demonstrate that our RNAi screen was capable of detecting repressors, and support our conclusion that old photoreceptors might be most sensitive to decreased activity of the transcriptional mechanisms that promote, rather than repress, gene expression. Supporting this idea, there is a global decrease in chromatin accessibility in aging Drosophila photoreceptors (Jauregui-Lozano et al, 2023), and histone marks associated with active transcription show global genome-wide decreases in aging fly heads (Wood et al, 2010;Wood and Helfand, 2013). While our screen has broadly identified activators of transcription, previous studies in mouse iPSCs (Liu et al, 2011;Miller et al, 2013) and models of rapid aging disorders (Zhang et al, 2015) show that the de-repression of heterochromatin may be a driving force of aging.…”

“…Thus, loss of Spt5 function in Saccharomyces cerevisiae is accompanied by bulk decreases in levels of the active H3K4me3 and H3K36me3 marks deposited by Set1/COMPASS and Set2, respectively (Zhou et al, 2009). We observed decreased genome-wide levels of H3K4me3 and H3K36me3 in aging photoreceptors (Jauregui-Lozano et al, 2023), potentially suggesting that Spt5-dependent transcription activation becomes less efficient with age. However, it is unclear whether aging affects Spt5 activity itself, or an upstream or downstream component of this interconnected transcriptional mechanism.…”

“…We refer to these Rh1-ffluc, Rh1-Gal4>UAS-Dcr2 flies hereafter as Rh1-Gal4 for simplicity. Previous characterization by our lab has shown that the photoreceptor-specific Rh1-Gal4 driver becomes effective in adult flies by 2 days post-eclosion so it does not impact eye development and remains effective throughout aging (Jauregui-Lozano et al, 2023).…”

“…In addition to changes in gene expression, there are agedependent alterations to chromatin accessibility, histone marks, and DNA methylation in the eye. For example, changes in chromatin accessibility have been detected at the onset of the disease state for AMD (Wang et al, 2018) and in aging Drosophila photoreceptors (Jauregui-Lozano et al, 2023). Further, changes in DNA methylation are observed in aging mouse rods, particularly near genes involved in energy metabolism (Corso-Díaz et al, 2020).…”