Spliceosome–ATM Reciprocal Regulation Modulates Alternative Splicing

The DNA damage response is a complex signaling network that uses post-translational modifications, protein–protein interactions, and altered gene expression to orchestrate cellular responses to DNA lesions. DNA damage has also been shown to drive alternative splicing, which has been attributed in part to changes in RNA polymerase II (RNAPII) activity; however, it remains unclear whether the core spliceosome machinery is regulated by DNA damage. Using quantitative proteomics, Tresini and colleagues found that UV irradiation, which causes RNAPII arrest, in quiescent human dermal fibroblasts led to chromatin depletion of the late-stage small nuclear ribonucleoprotein (snRNP) splicing factors U2 and U5, but not the early factors U1 and U4. Depletion of U2 and U5 spliceosome factors was time- and UV dose–dependent, but independent of proteasomal activity, suggesting that snRNP factors are displaced from damaged chromatin. Indeed, U2 and U5 mobilization increased specifically in response to transcription-blocking DNA lesions, but not DNA double-strand breaks or interstrand crosslinks, and occurred independently of nucleotide excision repair activity. Of note, inhibition of transcription alone was unable to promote a similar extensive spliceosome mobilization, as was observed in response to UV irradiation. Mechanistically, inhibition of the DNA damage response kinase ATM inhibited UV-induced spliceosome relocalization, and resulted in a genome-wide decrease in UV-driven alternative splicing. Activation of ATM signaling following spliceosome displacement was mediated by the formation of R-loops, hybridized RNA/DNA structures generated near transcription-blocking lesions. Silencing of the R-loop resolution factor RNaseH1 led to ATM activation, spliceosome displacement, and intron retention. Furthermore, ATM activation alone was not sufficient to initiate spliceosome mobilization, but amplified spliceosome displacement induced by transcription inhibition. Together, these results highlight reciprocal regulation between the core spliceosome and ATM signaling and identify noncanonical ATM activation in the DNA damage response regulating pre-mRNA splicing.

Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JA, et al. The core spliceosome as target and effector of non-canonical ATM signaling. Nature 2015;523:53–8.