Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence.

Abstract

Long noncoding RNAs (lncRNAs) regulate transcriptional and epigenetic programs during aging and senescence. However, no comprehensive studies have systematically integrated multilayered analyses to reveal their diverse regulatory roles. Moreover, lncRNAs with therapeutic potential in age-related diseases remain unexplored. Here we systematically perturbed 32 high-abundance aging- and senescence-associated lncRNAs (PtbAlncs) using a Perturb-seq-based CRISPR-dCas9-KRAB knockdown system coupled with single-nucleus multiomics profiling, enabling simultaneous transcriptomic and chromatin accessibility analysis. This analysis uncovered essential roles for previously uncharacterized lncRNAs in senescence regulation, validated computationally and experimentally. These lncRNAs modulate distinct single-cell RNA-sequencing modules through diverse yet overlapping epigenetic motifs in single-cell ATAC-sequencing modules. Among them, HOTAIRM1, a DNA repair-associated PtbAlnc, stabilizes DNA repair by cooperating with BANF1 and p53 at double-strand break loci within condensates. Its deficiency impairs DNA repair and triggers p53-mediated senescence. In aged mouse lungs, adeno-associated virus-mediated HOTAIRM1 overexpression reduced fibrosis, alleviated tissue damage, and promoted cellular proliferation, underscoring its therapeutic potential.