Extended Data Fig. 9: Dispersed nuclear and cytoplasmic DNA fragments activate DNA damage signalling and inflammatory responses, respectively.
From: Mitotic clustering of pulverized chromosomes from micronuclei
a) 53BP1 immunostaining reveals engagement of clustered (top) and dispersed (bottom) nuclear fragments by the DNA damage response. b) Frequency of cells with 53BP1-positive Y chromosomes, as determined by IF-FISH. Data represent mean ± SEM of n = 3 independent experiments; WT: 770, sg3: 735, sg4: 502 cells. c) Examples of cytoplasmic DNA foci that are positive (yellow box, see magnified inset) or negative (white box) for the nuclear membrane marker lamin B1. Scale bar, 5 μm. d) Fluorescent intensity line scan analysis between the indicated arrows depicted in (c) showing examples of cytoplasmic DNA foci with and without lamin B1. e) Proportion of cytoplasmic DNA foci with and without lamin B1 staining from (c). Pie charts represent mean; n = number of foci pooled from 2 independent experiments. f) Gene set enrichment analysis of bulk RNA sequencing of two HeLa cell populations individually transduced with two CIP2A sgRNAs (sgCIP2A) versus a non-targeting control sgRNA (sgNTC) with and without the induction of micronuclei using CENP-E/Mps1 inhibitors. Hallmark pathways with false-discovery rate (FDR) q-values < 0.25 are shown in ranked order. RNA sequencing was performed on three independent replicates per condition. g) Single-cell clonogenic growth assays showing that CIP2A KO cells, but not WT cells, are sensitive to the induction of micronuclei. Data represent mean ± SEM of n = 3 biological replicates.
