Non-Coding RNA: Sequence-Specific Guide for Chromatin Modification and DNA Damage Signaling

Abstract

Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR) and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi) machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs) and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports show their involvement in DDR. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.

Keywords: DNA-damage response; RNA interference; chromatin modulation; non-coding RNA; transcription.

FIGURE 1

Models of ncRNA-mediated site-specific chromatin modification and DDR modulation. (A) Schematic representation of long ncRNA (lncRNA) in transcriptional repression. (1) RNAPII dependent transcripts fold in protein-binding domains and (2) recruit histone-modifying complexes such as PRC2 to chromatin in cis. (B) Schematic model of small ncRNAs (sncRNAs) generation and chromatin modulation at RNAPII pausing sites. (1) Pausing of RNAPII is induced in physiological condition at promoter and enhancer sequences and at transcription-termination sites prone to form R-loops, but could also occur in the presence of DNA lesions. (2) RNAPII pausing stimulates the loading of another RNAPII in opposite orientation on the complementary DNA template and generates antisense transcripts. DsRNA precursors are then processed by the RNAi-machinery into sncRNA. (3) ARGONAUTE 2 (AGO2) forms a complex with such sequence-specific sncRNA and guide chromatin-modifying enzymes to the pausing site via nascent RNA:sncRNA interaction. (C) Schematic model for sncRNAs generation and function at site of DNA damage. (1) Double-strand break (DSB) generation induces stalling of RNAPII and synthesis of partially complementary transcripts. (2) Stem-loop like secondary structures of the transcripts or long dsRNAs precursors are processed by DROSHA and DICER into sncRNA, DDRNA. (3) DDRNA stimulates DDR activation via an unknown mechanism. Initially, DDR activation leads to chromatin de-compaction, which may increase transcription and favors ATM activation. In turn, ATM induces mono- and poly-ubiquitination of H2A/H2AX by RNF8/RNF168 ubiquitin ligases, consequent chromatin compaction and transcriptional silencing (4). Chromatin compaction might promote reciprocal interactions between DDR proteins through their increased density, further boosting DDR activation in the absence of additional transcription.