Traffic light at DSB-transit regulation between gene transcription and DNA repair

Abstract

Transcription of actively expressed genes is dampened for kilobases around DNA lesions via chromatin modifications. This is believed to favour repair and prevent genome instability. Nonetheless, mounting evidence suggests that transcription may be induced by DNA breakage, resulting in the local de novo synthesis of non-coding RNAs (ncRNAs). Such transcripts have been proposed to play important functions in both DNA damage signalling and repair. Here, we review the recently identified mechanistic details of transcriptional silencing at damaged chromatin, highlighting how post-translational histone modifications can also be modulated by the local synthesis of DNA damage-induced ncRNAs. Finally, we envision that these entangled transcriptional events at DNA breakages can be targeted to modulate DNA repair, with potential implications for locus-specific therapeutic strategies.

Keywords: DNA damage response; DNA double strand break; DNA repair; non‐coding RNAs; transcription.

Fig. 1

DNA damage response (DDR) activation and Damage Induced Transcriptional Silencing in Cis (DISC) is induced at DNA double strand breaks by multiple redundant signalling pathways and coexist with de novo synthesis of damaged induced ncRNAs. Top panel: (1) Upon the generation of a double strand break (lightning), the sensor complex MRN recruits ATM to the break site [3]. ATM phosphorylates the histone H2AX on Ser139 (known as γH2AX), promoting he recruitment of the mediator factor MDC1 [10], and the E3 ubiquitin ligase RNF8, which ubiquitinates the Polycomb factor L3MBTL2 [11], anchoring the E3 ubiquitin ligase RNF168. This second Ubiquitin ligase deposits H2AK13/15Ub histone marks required for DNA repair factors [12]. (2) Furthermore, ATM and Poly [ADP‐ribose] polymerase 1 (PARP1 – another apical DDR factor) recruits DYRK1B to DSB. This kinase in turn recruits PBAF and STAG2 cohesin complexes to break sites, leading to chromatin compaction and gene silencing [28, 32]. (3) ATM also promotes the recruitment of the Bromodomain containing protein BRD7 to DSBs which in turn controls the activity of the chromatin‐modifying complexes Polycomb group 1 and 2 (PcG) and Nucleosome Remodelling and De‐Acetylase (NuRD) complexes, depositing in proximity to DNA damage repressive histone marks on chromatin [31]. (4) PARP1‐dependent recruitment of CDYL1 allow the association of the PRC2 subunit EZH2 to DSBs, mediating the deposition of the repressive H3K27me3 histone mark at the damaged chromatin [33]. (5) PARP1 also contributes to DISC by recruiting remodelling and splicing factor RSF1 and HDAC1, which deacetylate histones, leading to chromatin compaction and silencing [37]. (6) Following the generation of a double strand break, RNAPII synthesizes dilncRNAs that can be then processed by DROSHA and DICER into shorter DDRNAs, necessary to foster DDR signalling [43, 46]. Polycomb repressive complex 1 (PRC1) composed by the E3 catalytic subunit RING1A/B and the Ring finger factor BMI1, instead is known to monoubiquitinate H2A on K119, a repressive modification leading to chromatin compaction and transcriptional repression of DNA break flanking genes [22]. In our preprint, we present data suggesting that the generation of dilncRNAs and DDRNAs might be required for the recruitment of BMI1 and transcriptional silencing at DSB. (7) Hypothetical working model showing how the different factors showed in panels 2–6 contribute to DISC at the same damaged locus. Small numbers refer to panels 2–6 described above. We propose that a dual modulation of transcription exists at DSBs. On the one hand, in the vicinity of the break, non‐coding RNAs are de novo synthesized by RNAPII and further processed by DROSHA and DICER, especially at repetitive loci. On the other hand, the chromatin regions surrounding the break are compacted by histone post‐translational modifications. We propose that these two apparently opposite events might be functionally linked and that histone modifiers might be also recruited at damaged chromatin by sequence specific non‐coding RNAs generated upon DNA damage. Bottom panel: table indicating each factor involved in DDR, DISC and de novo synthesis. ? indicates a postulated interaction between BMI1 and dilncRNAs reported in our pre‐print discussed in the text but still unpublished on peer‐reviewed journal. The figure was created with BioRender.com.

Fig. 2

Site‐specific DDR modulation via antisense oligonucleotides (ASOs). Upon generation of a DNA double strand break (DSB) (lightning), damage‐induced long non‐coding RNAs (dilncRNAs) are transcribed from the break, stimulating the recruitment or the activation of DNA damage response (DDR) factors and the formation of a DDR focus at the site of damage. Inhibitors targeting the activity of DDR factors, such as ATM inhibitors (ATMi, bottom left panel), simultaneously switches off the DDR signalling of all DSBs present in the genome. In contrast, the treatment with site‐specific antisense oligonucleotides (ASOs, bottom right panel) targeting dilncRNAs, might inhibit DDR in a sequence‐specific manner. The figure was created with BioRender.com.