Histone modification clocks for robust cross-species biological age prediction and elucidating senescence regulation

By analyzing ChIP-seq data across six tissues and six histone marks, we developed 36 tissue-specific histone modification-based epigenetic clocks that detect age acceleration in leukemia and reversal following treatment. Many age-associated loci showed nonlinear trajectories peaking at midlife, and super-enhancer fragmentation was observed with age. Functional validation of an H3K27ac peak near IGF2BP3 confirmed its role in senescence via TRA2A regulation. These clocks also generalized to Drosophila melanogaster, highlighting the evolutionary conservation and utility of histone modifications as aging biomarkers. Overall design: RNA-seq: Wild-type HL-60 cells were transfected with a CRISPR-dCas9-HDAC plasmid along with a piRNA plasmid targeting the region near the IGF2BP3 promoter. Two days post-transfection, both wild-type and transfected cells were harvested for total RNA isolation and poly(A)-selected mRNA sequencing. ChIP-seq: Adult flies at 1, 3, 5, 13, 20, 33, 45, 55, 60, and 63 days post-eclosion were collected for ChIP-seq.