The Bidirectional Link Between RNA Cleavage and Polyadenylation and Genome Stability: Recent Insights From a Systematic Screen

Abstract

The integrity of the genome is governed by multiple processes to ensure optimal survival and to prevent the inheritance of deleterious traits. While significant progress has been made to characterize components involved in the DNA Damage Response (DDR), little is known about the interplay between RNA processing and the maintenance of genome stability. Here, we describe the emerging picture of an intricate bidirectional coupling between RNA processing and genome integrity in an integrative manner. By employing insights from a recent large-scale RNAi screening involving the depletion of more than 170 components that direct (alternative) polyadenylation, we provide evidence of bidirectional crosstalk between co-transcriptional RNA 3′end processing and the DDR in a manner that optimizes genomic integrity. We provide instructive examples illustrating the wiring between the two processes and show how perturbations at one end are either compensated by buffering mechanisms at the other end, or even propel the initial insult and thereby become disease-eliciting as evidenced by various disorders.

Pathophysiological Role and Diagnostic Potential of R-Loops in Cancer and Beyond

“…Hence, the depletion of the FACT complex causes excessive R-loop accumulation and impairment in replication and transcription, illustrating a critical function in the resolution of R-loop-mediated TRCs [ 17 ]. In addition, after transcription initiation and elongation, mRNA cleavage and polyadenylation (CPA) factors contribute to maintaining genome integrity by suppressing R-loop formation and modulating efficient mRNA cleavage [ 15 , 29 ]. CPA constitute an essential step in preventing replication-stress-associated DNA damage as transcription hinders replication fork progression and stability, and vice versa, compensatory pausing of co-transcriptional CPA emerges as a conserved mechanism of the DNA damage response (DDR) to allow for DNA repair and to avoid the propagation of genomic mutations [ 29 ].…”

“…In addition, after transcription initiation and elongation, mRNA cleavage and polyadenylation (CPA) factors contribute to maintaining genome integrity by suppressing R-loop formation and modulating efficient mRNA cleavage [ 15 , 29 ]. CPA constitute an essential step in preventing replication-stress-associated DNA damage as transcription hinders replication fork progression and stability, and vice versa, compensatory pausing of co-transcriptional CPA emerges as a conserved mechanism of the DNA damage response (DDR) to allow for DNA repair and to avoid the propagation of genomic mutations [ 29 ]. Hence, perturbations of CPA-mediated co-transcriptional RNA processing are detrimental and can result in the formation of unscheduled R loops and genome instability [ 29 ].…”

“…CPA constitute an essential step in preventing replication-stress-associated DNA damage as transcription hinders replication fork progression and stability, and vice versa, compensatory pausing of co-transcriptional CPA emerges as a conserved mechanism of the DNA damage response (DDR) to allow for DNA repair and to avoid the propagation of genomic mutations [ 29 ]. Hence, perturbations of CPA-mediated co-transcriptional RNA processing are detrimental and can result in the formation of unscheduled R loops and genome instability [ 29 ]. For example, a loss of function of the 3′ end cleavage and polyadenylation factors (including PCF11, CLP1, FIP1L1, CFT2, and WDR33) results in DNA damage [ 15 ].…”

“…However, there are also R-loop-binding proteins that have functions beyond these biological processes [ 6 , 28 ]. As one would conclude from the information above, interference with DNA, RNA, and R-loop processing, for example, by altering the abundance of various facets of transcriptional, co-, and post-transcriptional gene regulation; epigenetic modifications; and further processes (such as RNA splicing, trafficking, and transcription, see Table 2 ), controls and sometimes disrupts the abundance of transcript isoforms encoding R-loop-binding proteins [ 29 , 85 , 86 ]. For example, key components pervasively regulating CPA and alternative polyadenylation (APA) [ 87 ] (including RNA-processing factors involved in the coupling of transcription termination and CPA such as PCF11 [ 85 ]) control the processing of various components involved in the formation and resolution of R-loops [ 87 ].…”

“…Conversely, the loss of function of components involved in R-loop resolution (such as the R-loop-associated helicase, SETX) also affects APA [ 86 ]. This suggests that CPA and R-loops bi-directionally affect each other [ 29 ]. This corresponds to the two-sided nature of R-loops, wherein physiological (‘scheduled’) R-loops tune gene expression (including transcription termination and 3′ end processing), while pathological (‘unscheduled’) R-loops impair genome integrity, which is typically followed by an inhibition of CPA to limit the ‘release’ of emerging faulty transcripts and to allow for the repair of the genomic lesion [ 29 ].…”