DNA double-strand breaks (DSBs) that occur in transcriptionally active regions of the genome pose a challenging problem for cells. Ongoing transcription on damaged templates may limit access of DNA repair factors to DSBs and prevent chromatin changes that facilitate repair. In order to avoid conflict with the transcriptional machinery, the DNA damage response transiently suppresses RNA polymerase I and II-dependent transcription near DSBs (Shanbhag et al, Cell, 2010; Kruhlak et al, Nature, 2007).


RNA polymerase I transcribes the ribosomal genes 5.8S, 18S and 28S, which are organized in more than 300 repeat units around which nucleoli form during interphase. RNA polymerase I-dependent transcription is suppressed in response to DSB formation in a manner dependent on the ATM kinase and the DNA repair factor NBS1 (Figure 6). We have previously shown that TCOF1, a transcriptional regulator of RNA polymerase I, recruits NBS1 to nucleoli after ionizing radiation in an ATM-dependent manner (Figure 7), suggesting that TCOF1 is a novel component of the ATM and NBS1 pathway that suppresses RNA polymerase I-dependent transcription after DNA damage (Ciccia et al, PNAS, 2014).

Figure 6. RNA polymerase I transcriptional machinery 

Figure 7. NBS1 is recruited to nucleoli in response to DNA damage in a TCOF1- and ATM-dependent manner


Regulation of ribosomal DNA transcription is critical for human disease, as indicated by the observation that autosomal dominant mutations in TCOF1 predispose to Treacher Collins syndrome, a childhood disorder characterized by craniofacial abnormalities, growth retardation and hearing loss (Table 2) (Dixon, Hum Mol Genet, 1996). Furthermore, ribosomal synthesis is often elevated in cancer cells. Increased ribosomal synthesis in cancer can result from the expansion of ribosomal repeats generated by the instability of ribosomal DNA (rDNA) loci or from the stimulation of rDNA transcription by alterations of oncogenes or tumor suppressors (Stults et al, Cancer Res, 2009; Arabi et al, Nat Cell Biol, 2005).


Characterization of the molecular mechanisms that suppress ribosomal DNA transcription in reponse to DNA damage

In preliminary studies we have identified an ATM phospho-site in TCOF1 (S1199) required for the recruitment of NBS1 to the nucleolus (Ciccia et al, PNAS, 2014). We are currently determining whether ATM-dependent phosphorylation of TCOF1 and/or other nucleolar factors is necessary for suppressing ribosomal DNA transcription in response to DNA damage. These experiments will define the components of the ATM-dependent pathway that regulate ribosomal RNA (rRNA) synthesis after DNA damage.

Definition of the mechanisms by which suppression of ribosomal DNA transcription in response to DNA damage prevents genomic instability

Maintenance of rDNA copy number is critical for cellular viability. Instability at rDNA loci can potentially lead to growth advantages or impaired proliferation and aging in cells depending on whether rDNA copy numbers are increased or decreased, respectively. We are currently investigating whether the suppression of rRNA synthesis by ATM, NBS1 and TCOF1 could maintain rDNA stability by avoiding interference between the transcriptional and repair machineries. These studies will define how suppression of rRNA synthesis helps preserve genomic stability.