Keep calm and reboot - how cells restart transcription after DNA damage and DNA repair

Abstract

The effects of genotoxic agents on DNA and the processes involved in their removal have been thoroughly studied; however, very little is known about the mechanisms governing the reinstatement of cellular activities after DNA repair, despite restoration of the damage-induced block of transcription being essential for cell survival. In addition to impeding transcription, DNA lesions have the potential to disrupt the precise positioning of chromatin domains within the nucleus and alter the meticulously organized architecture of the nucleolus. Alongside the necessity of resuming transcription mediated by RNA polymerase 1 and 2 transcription, it is crucial to restore the structure of the nucleolus to facilitate optimal ribosome biogenesis and ensure efficient and error-free translation. Here, we examine the current understanding of how transcriptional activity from RNA polymerase 2 is reinstated following DNA repair completion and explore the mechanisms involved in reassembling the nucleolus to safeguard the correct progression of cellular functions. Given the lack of information on this vital function, this Review seeks to inspire researchers to explore deeper into this specific subject and offers essential suggestions on how to investigate this complex and nearly unexplored process further.

Keywords: DNA repair; RNA polymerase 1; RNA polymerase 2; UV lesions; chromatin; homeostasis; nucleolus.

Fig. 1

Cellular activity is altered by DNA damage. After genotoxic stress, the DNA damage response (DDR) is activated to safeguard genomic stability. This involves a series of processes, such as setting up a specific signaling network and halting key cellular processes such as transcription, DNA replication and the cell cycle. Depending on the nature of the DNA damage, cells deploy distinct DNA repair mechanisms, each requiring a distinct set of proteins. Following the completion of all the reactions that allow cells to eliminate DNA lesions and restore DNA integrity, resuming essential cellular activities is essential for cell survival. The restart of RNAP2‐ and RNAP1‐mediated transcription, as well as the restoration of nucleolar structure, is far from passive and involves the coordinated action of various proteins.

Fig. 2

Restart of RNAP2 transcriptionafter DNA repair. (A) RNAP2 molecules stalled at sites of DNA damage induce DNA repair through CSB, while concurrently, the upregulation of ATF3 expression leads to its recruitment to promoters, where it exerts a negative regulatory influence on transcription initiation. (B) During DNA repair, RNAP2 undergoes phosphorylation at serine 2 residues within the carboxyl‐terminal domain (CTD) repeat. Concurrently, EXD2 transiently associates with stalled RNAP2 to degrade mRNA under synthesis, while CDK9 and ELL potentially serve as docking sites to recruit additional factors necessary for transcription resumption. In the later stages of DNA repair, the expression of ATF3 is diminished by the histone chaperone HIRA, whereas CSB promotes the ubiquitin‐mediated proteasomal degradation of ATF3 from promoter regions. Additionally, CSB recruits PAF1C to RNAP2 paused around transcription start site (TSS) regions, thereby stimulating productive elongation throughout genes. Chromatin modifications play a critical role in facilitating the efficient restart of RNAP2 transcription post‐DNA repair. The histone methyltransferase DOT1L fosters an open chromatin structure around promoters by methylating histone H3 at lysine 79, while the SPT16 subunit of FACT stimulates H2A‐H2B turnover at sites of damage.

Fig. 3

RNAP1 transcriptional restart and restoration of nucleolar organization. After genotoxic stress, the transcription of ribosomal genes (rDNA) is halted, leading to the export of RNA polymerase 1 (RNAP1; depicted in green) and nucleolar DNA (depicted in blue) to the periphery of the nucleolus. In wild‐type cells (WT), once the repair of nucleolar DNA is fully completed, the nucleolar organization is restored, and rDNA transcription resumes. Conversely, in cells lacking the TCR proteins CSA, CSB and UVSSA, rDNA transcription is permanently inhibited, and RNAP1 remains localized at the nucleolar periphery. In XPC‐mutant cells, lesions on the inactive genome are left unrepaired, causing RNAP1 to remain at the nucleolar periphery where RNAP1‐mediated transcription restarts nonetheless. The depletion of XAB2, a protein involved in recognizing damaged DNA on RNAP2 transcript genes, does not affect the restart of RNAP1 transcription. The restoration of proper nucleolar structure following DNA repair is an active process dependent on the proteins SMN, coilin (COIL) and fibrillarin (FBL).