The Mechanism by which Irradiation Causes Genomic Instability

　Cells have sophisticated mechanisms to respond to DNA damage caused by external stress, such as radiation. Genomic abnormalities in transcriptionally active regions can lead to diseases, including many types of cancer. Our laboratory focuses on elucidating how chromosome translocations occur in transcriptionally active regions. For example, it is well known that fusion genes generated by chromosome translocations at specific gene regions, such as BCR-ABL, produce oncogenic proteins. However, the mechanisms of how chromosome translocations occur in cells remain unclear.

　Chromosome translocations can be generated by three steps: 1) DNA double-strand breaks (DSBs) on two different chromosomes, 2) Proximity of those chromosomes, and 3) abnormal DSB repair. Our approaches to understanding these steps of chromosome translocation vary from molecular/cell biological methods to biochemical techniques. Moreover, we have been developing unique systems to analyze cancer genome databases.

　In our previous studies, we identified two novel transcription-associated DSB repair pathways taking care of transcriptionally active regions (Yasuhara et al. Cell 2018, Cell Reports 2022). Furthermore, relating to the proximity of chromosomes, we discovered nucleolar condensates formed by RNA-binding proteins upon cellular stresses involve transcriptionally active regions of the genome into nucleoli and promote the proximity among these regions. (Yasuhara et al. Molecular Cell 2022).

DSB Repair Mechanism Initiated by R-loop

　R-loop is a special nucleic acid structure consisting of DNA-RNA hybrid and single-stranded DNA. It is obvious that R-loops accumulate at genomic regions where transcription is active because of the abundance of RNA. Interestingly, recent studies have revealed that R-loops have many important roles in the process of DSB repair.

　In general, DSBs at transcriptionally active regions must precisely be repaired given the importance of these parts of the genome. We assume that the presence of R-loops around DSBs serves as a mark for cells to initiate precise repair mechanisms. Indeed, we revealed that R-loops around a DSB initiate two accurate repair mechanisms: transcription-associated homologous recombination repair (TA-HRR) or transcription-associated end-joining (TA-EJ) (Figure 1). Without these repair systems, irradiated cells had genomic abnormalities at a higher frequency, suggesting that these repair mechanisms guard our genome against mutations. We are currently working to elucidate the detailed molecular mechanisms of these repair pathways to understand how our DSB repair systems suppress chromosome translocations..

Figure 1. Two transcription-associated DNA double-strand break repair pathways initiated by R-loops.

Liquid-liquid phase separation and chromosome translocation

　Chromosome translocations that lead to disease always occur in specific regions of the genome. For years, the question of whether this is due to survival selection pressure or whether there is any bias that these regions are fragile to cause genomic aberrations has been unsolved. Our work has provided evidence for the latter possibility, i.e., there is a plausible reason for transcriptionally active regions to have a higher chance of chromosome translocations.

　Recently, a set of proteins that have unstructured domains self-assembling via liquid-liquid phase separation has been rigorously studied. We hypothesized that liquid-liquid phase separation could cause the proximity of chromosomes by involving the genome together with unstructured proteins. We found that certain RNA-binding proteins form condensates (Condensate Induced by Transcription Inhibition; CITI) in nucleoli upon transcription inhibition (Figure 2) and that CITIs bring chromosomes, especially the transcriptionally active regions, into nucleoli to increase the chance of chromosome translocations. We are now working on the questions of 1) what kind of stresses cause CITIs, and 2) what the physiological functions of CITIs are.

Figure 2. CITI formed via liquid-liquid phase separation upon transcriptional stresses.

Diseases caused by chromosome translocation

　Chromosome translocations are a major cause of cancer. They are also a risk factor for some neuropsychiatric disorders, infertility, and fetal chromosome aberrations. We believe that understanding how genomic instability occurs and causes the diseases will give us a clue to develop new preventive and therapeutic strategies against these diseases. In an age of long-life expectancy, we hope to contribute to solving various problems, such as cancer and infertility in reproductive medicine, through our research which sheds light on the underlying fundamental mechanisms behind diseases.