Fluorescence lifetime clocks quantify senescence and aging

Epigenetic and omics-based clocks have provided invaluable tools to quantify aging, yet these clocks do not provide direct readouts of aging in real-time, in living systems. As methylation changes in nucleolar ribosomal DNA are reliably associated with aging and cellular senescence, we hypothesized that shifts rRNA species could be leveraged to generate image-based clocks using selective dyes. Here, we engineer sensitive and photostable hybrid polymethine dyes selective for rRNA. We present a fluorescence lifetime imaging strategy to visually quantify age- and cellular senescence-dependent nucleolar RNA changes which bypasses requirements for extensive sample preparation such as DNA isolation and enables in vivo, real-time age quantification. We demonstrate resolution through cellular to organismal scales, and demonstrate translatability by generating clocks from cells and tissues, as well as C. elegans, mice, and human samples.