Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks

Abstract

Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.

Keywords: cohesin; double strand break; helicase; transcription; transcription factors.

FIGURE 1

Sources of DNA damage and DNA damage response (DDR) network. (A) DNA damage repair choices. Small base alterations could be recognized and corrected through base excision repair (BER) pathway; longer base damages that disturb DNA-helix structure, such as bulky DNA adducts, are repaired through the nucleotide excision repair (NER) pathway; for double –strand breaks (DSBs) repair, homologous recombination (HR) and non-homologous end-joining (NHEJ) are two main repair mechanisms. (B) DNA tolerance pathway. Following persistent genotoxic stress, cells allow temporary DNA replication in the presence of unrepaired templates. Monoubiquitinated proliferating cell nuclear antigen (PCNA) facilitates translesion synthesis (TLS) while polyubiquitinated PCNA associates template switching (TS). Apart from Polζ-mediated TLS is an error-prone process, Polη-mediated TLS and TS are error-free processes (modified from reference Ghosal and Chen, 2013). Image created with BioRender.

FIGURE 2

Transcription regulation near the DSBs. (A) dilncRNA-mediated transcriptional induction. When damage occurs, Mre-Rad50-Nbs1 (MRN) directs S2P/S5P to DSB, which conducts bidirectional generation of dilncRNAs. These dilncRNAs are further processed into damage response RNAs (DDRNAs) by Drosha and Dicer. DDRNAs complementary with pre-mature single-strand dilncRNAs, function as a recruiting signal for DDR factors. (B) DARTs-mediated transcriptional induction. DSBs produced by AsiSI enzyme stimulate phosphatidylinositol 3-kinase-related kinase (PIKK) signaling to inhibit the regular RNA polymerase II (RNAPII) transcription but activate c-Abl to facilitate Y1P CTD of RNAPII activity. Y1P generates pri-DARTs which hybrid with template DNA and correspondingly stimulates the production of se-DARTs. The free se-DARTs produced by p-Dicer cleavage of dsRNAs facilitate the recruitment of DDR factors such as MDC1 and 53BP1 to the DSB. (C) RNAPII inhibition after DNA damage. During the transcription initiation stage, REQL5 directly interacts with RNAPII at the DSB, acting as the recruiting signal for TLP which is a negative regulator of TFIIA. Once transcription progresses to the elongation stage, RNAPII PARylation is conducted by PARP1, which subsequently leads to NELF recruitment and shutdown of active transcription. (D) ATM-dependent transcription arrest. ATM triggers the accumulation of RNF8/RNF168/Ube2S/C, enforcing the pausing of actively transcribing RNAPII and consequently repressing the transcription activity nearby the breaks. (E) PARP1-dependent transcription arrest. CDYL1, recruited by PARP1, mediates transcription repression by deposition of H3K9me3. Also, CDYL1 promotes the accumulation of EZH2, further reinforced the transcription silencing with repressive H3K27me3. FRRUC advances the monoubiquitylation and facilitates the H2A.Z incorporation. (F) DNA–PK-dependent transcription arrest. DNA–PK could directly inhibit RNAPII bypass at I-PpoI-induced DSB and impair RNA manufacture. WWP2, associated with DNA–PK, ubiquitylates RNAPII RPB1 at K48 to facilitate proteasome-dependent RNAPII eviction. Image created with BioRender.

FIGURE 3

Localized cohesin recruitment at the DSBs. (A) NIBL-MAU2-mediated cohesin loading to DSBs. Cohesin loader NIBPL-MAU2 is reported to be recruited to DSBs through the MDC1-RNF168/RNF8-HP1γ complex. Another possibility is that RSC ortholog BAF/PBAF co-occupies the genomic locations of NIBPL-MAU2 and acts as the prerequisite for its loading. Whether ESCO2 and sororin also have functions in cohesin recruitment still requires further investigation. (B) Kinase/Complex-mediated cohesin loading. MRN complex activates ATM first, then recruits cohesin to DSB by phosphorylating SMC1 subunit. SMC5/6 complex (Mms21 subunit) regulates cohesin loading through SUMOylating cohesin subunit RAD21. CTCF is a rationale for cohesin recruitment toward chromosomal sites in non-damage conditions; however, its role in cohesin recruitment toward DSBs remains unknown. Image created with BioRender.