Locus-specific LINE-1 mRNA expression reflects cell-type- and stimulus-specific senescence states

Long Interspersed Element-1 (L1) causes DNA damage and inflammation, which are hallmarks of cellular senescence. To understand the role of endogenous L1 in senescence, accurate detection and measurement of L1 messenger RNA (mRNA) expression changes during this process is crucial, as L1 transcription is the prerequisite step of L1-related downstream effects. We developed an automated bioinformatics pipeline to quantify locus-level L1 mRNA expression in ex vivo and in vitro models of normal and cancer human cells under various senescence-inducing stimuli. Contrary to previous studies, our analyses show that L1 expression does not always increase in senescent cells, and when it does, the changes are moderate and independent of overlapping gene expression. We find that each cell type expresses subsets of L1 loci that are either expressed constitutively (core L1s) or only in proliferating or senescent cells. These subsets can be used to identify cellular state and inform the origin of senescent cells and senescence stimuli. Additionally, we present a comprehensive atlas of L1 splice sites used in proliferating and senescent cells, expanding our knowledge of L1 splicing events beyond the few previously validated sites. These findings establish L1 as an additional indicator for identifying and characterizing senescent cell populations.