Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA

Abstract

The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.

Alternative polyadenylation of mRNA precursors

“…Telescripting has also been implicated in the global transcript shortening that occurs during transient transcription upregulation upon activation of neurons 86 . A similar phenomenon was recently observed in the human colon carcinoma cell line RKO after exposure to UV damage 89 , such that 5′ intronic PASs were substantially activated, probably owing to reduced levels of U1 snRNA. Notably, 3′ UTR shortening was not obvious in these RKO cells.…”

Selective roles of vertebrate PCF11 in premature and full-length transcript termination

“…The phenomenon of negative gene regulation by premature termination is well described in S. cerevisiae, where it plays a physiological role in response to changing growth conditions (Bresson et al, 2017). In the mammalian system, genome-wide premature termination of protein coding gene transcription has been previously reported in cells depleted for U1 snRNP (Kaida et al, 2010) and upon DNA damage (Devany et al, 2016;Williamson et al, 2017). Interestingly, two studies using different methodology provided evidence that Pol II accumulation at human and Drosophila promoters is not solely due to Pol II pausing, but also associated with premature termination (Nojima et al, 2015;Krebs et al, 2017).…”

“…after UV damage) it is beneficial to down-regulate PCF11 and so reduce CPA and termination efficiency. This may act to counteract the global shortening of transcripts that occurs under such conditions (Devany et al, 2016;Williamson et al, 2017).…”

Connections between 3′ end processing and DNA damage response: Ten years later

“…The CpA machinery operates unhindered as a multitude of core and auxiliary factors function to process the precursor mRNA, including PAP and CstF‐50 (Y. Shi et al, ). Bottom: Upon occurrence and recognition of genotoxic stress, the ribonucleoprotein components of CpA function are altered, as U1 snRNA levels are decreased, allowing for recognition of specific promoter‐proximal poly(A) signals (Devany et al, ). Recruitment of BRCA1/BARD1/p53 complex(es) takes place, inhibiting CpA via CstF‐50 (Kleiman & Manley, ), and activating deadenylation through factors such as PARN (Devany, Zhang, Park, Tian, & Kleiman, ).…”

“…As the spliceosomal U1 snRNP binds the nascent RNA to inhibit the usage of intronic poly(A) sites within first introns (Almada, Wu, Kriz, Burge, & Sharp, 2013;Berg et al, 2012;Kaida et al, 2010), U1 snRNP might also participate in genome integrity maintenance, possibly through currently undescribed complex(es) with genome integrity and DDR factors. In fact, under DNA damaging conditions, the levels of U1 snRNA decrease inducing intronic APA at the promoter-proximal side of the genes (Devany et al, 2016), potentially allowing greater access to DNA repair factors and dissociation of nascent transcripts.…”