Crosstalk between the nucleolus and the DNA damage response

Abstract

Nucleolar function and the cellular response to DNA damage have long been studied as distinct disciplines. New research and a new appreciation for proteins holding multiple functional roles, however, is beginning to change the way we think about the crosstalk among distinct cellular processes. Here, we focus on the crosstalk between the DNA damage response and the nucleolus, including a comprehensive review of the literature that reveals a role for conventional DNA repair proteins in ribosome biogenesis, and conversely, ribosome biogenesis proteins in DNA repair. Furthermore, with recent advances in nucleolar proteomics and a growing list of proteins that localize to the nucleolus, it is likely that we will continue to identify new DNA repair proteins with a nucleolar-specific role. Given the importance of ribosome biogenesis and DNA repair in essential cellular processes and the role that they play in diverse pathologies, continued elucidation of the overlap between these two disciplines will be essential to the advancement of both fields and to the development of novel therapeutics.

Figure 1. Ribosome biogenesis at a glance

The making of a mature ribosome begins with the transcription of the pre-rRNA from an rDNA locus. The pre-rRNA is then processed to remove internal- and external- transcribed spacer sequences (5’ETS; ITS1; ITS2; 3’ETS) and modified by snoRNPs. In addition, the pre-ribosomal subunits are assembled with ribosomal proteins and the RNAPIII transcribed 5S rRNA, and then exported to the cytoplasm where they can join to form a translationally competent ribosome. The black sticks with a ball on top () indicate rRNA modifications, and the blue () and orange () circles represent ribosomal proteins.

Figure 2. Classification of nucleolar proteins by functional category

Pie chart from an early study by Andersen and colleagues that depicts the functional categories of proteins that localize to the human HeLa cell nucleolus. The number of proteins that fall into each category is indicated in parentheses. Notably, a proportion of nucleolar proteins were classified as DNA repair proteins. Now, as many as 4,500 proteins may localize to the human nucleolus, and in our analysis of NOPdb, the human T-cell nucleolar proteome, and the Human Protein Atlas, 166 unique nucleolar proteins can be classified as DNA repair proteins (Supplemental Table 1). Reprinted by permission from Macmillan Publishers Ltd: Nature Publishing Group. http://www.nature.com/nature/journal/v433/n7021/full/nature03207.html

Figure 3. Nucleolar response to DNA damage

There are currently two mechanisms proposed for the transient RNAPI transcriptional silencing caused by DSBs in nuclear chromatin. A. RNAPI inhibition requires ATM, NBS1 and MDC1. Kruhlak and colleagues identified the ATM-dependent inhibition of RNAPI in nucleoli proximal to DSBs. Inhibition required ATM, NBS1 and MDC1. B. RNAPI inhibition requires ATM, PARP, NBS1, and TCOF1 (not MDC1). Larsen and colleagues on the other hand identified ATM-dependent RNAPI transcriptional silencing in all nucleoli. This silencing was not only dependent on (1) PARP recruitment of TCOF1 to sites of DSBs, but also on (2) the interaction between TCOF1 and NBS1 and their recruitment to nucleoli.

Figure 4. DNA repair in the nucleolus

DSBs in the 28S rRNA result in the ATM-dependent silencing of RNAPI transcription, which results in nucleolar cap formation and recruitment of proteins involved in the DNA damage response. Repair may be primarily through the HDR response supported by unscheduled DNA synthesis in G1 cells and recruitment of HDR proteins to nucleolar caps^, , or by NHEJ supported by prolonged RNAPI silencing upon DNA-PK inhibition and greater DNA damage in cells depleted of NHEJ proteins (DNA-PK; XRCC4). The DNA damage response may be mediated by SMC5, or NBS1 and MDC1, as well as chromatin modifications by HDAC1 and CARM1 interactions with TCOF1.

Figure 5. Crosstalk between the nucleolus and the DNA damage response

Diagram of the role of DNA repair proteins in ribosome biogenesis, and conversely the role of ribosome biogenesis proteins in the DNA damage response. A. Roles for DNA repair proteins in ribosome biogenesis. A number of DNA repair proteins have been localized to the nucleolus. Based on studies of APEX1, WRN, and BLM, these proteins may play important roles in pre-rRNA transcription and pre-rRNA quality control. B. Roles for ribosome biogenesis factors in the DNA damage response. Evidence also supports a role for proteins involved in ribosome biogenesis to have a dual role in DNA repair. Based on studies of TCOF1, NPM1, NCL, and uS3, these proteins may play important roles in both the recognition of DNA damage and chromatin remodeling at sites of DNA damage, as well as both the functional and transcriptional regulation of DNA repair proteins.