Stabilization and targeting of INO80 to replication forks by BAP1 during normal DNA synthesis

Abstract

The INO80 chromatin-remodelling complex has been implicated in DNA replication during stress in yeast. However, its role in normal DNA replication and its underlying mechanisms remain unclear. Here, we show that INO80 binds to replication forks and promotes fork progression in human cells under unperturbed, normal conditions. We find that Ino80, which encodes the catalytic ATPase of INO80, is essential for mouse embryonic DNA replication and development. Ino80 is recruited to replication forks through interaction with ubiquitinated H2A-aided by BRCA1-associated protein-1 (BAP1), a tumour suppressor and nuclear de-ubiquitinating enzyme that also functions to stabilize Ino80. Importantly, Ino80 is downregulated in BAP1-defective cancer cells due to the lack of an Ino80 stabilization mechanism via BAP1. Our results establish a role for INO80 in normal DNA replication and uncover a mechanism by which this remodeler is targeted to replication forks, suggesting a molecular basis for the tumour-suppressing function of BAP1.

The BAP1/ASXL2 Histone H2A Deubiquitinase Complex Regulates Cell Proliferation and Is Disrupted in Cancer

“…Interestingly, INO80 chromatin remodeling factor also possesses a DEUBAD, and through molecular mimicry, this domain associates with and inhibits UCH37 (55,56). Of note, BAP1 also interacts with INO80 ATPase, a component of the INO80 chromatin remodeling complex, and promotes its deubiquitination (29). As INO80G (NFRKB) subunit of the complex inhibits UCHL5 through its DEUBAD, it will be interesting to determine whether, in specific contexts, this factor could also negatively regulate the DUB activity of BAP1.…”

“…Nonetheless, as the catalytic dead BAP1 binds ubiquitin, it is possible that these effects are associated mostly with BAP1/ ASXL1/2 binding to H2Aub rather than catalysis. Deregulation of H2Aub levels or its recognition might cause defects in transcriptional events (26), DNA double strand break repair (24), or replication fork progression (29), all of which could promote the induction of DNA damage and the p53 response and lead to genomic instability and cancer development. Although further studies are needed to address these possibilities, our findings nonetheless suggest that the proper balance of BAP1-ASXL1/2 complexes and their coordinated binding to ubiquitinated substrates and/or DUB activity are essential for normal control of cell proliferation.…”

“…BAP1 is recruited at gene promoter regions to activate transcription, and has been shown to regulate the expression of genes involved in cell proliferation (15,26,27). BAP1 is also recruited to sites of DNA double strand breaks to promote repair by homologous recombination (24,28), and it is implicated in DNA replication-associated processes (29,30). Moreover, BAP1 functions appear to be regulated by posttranslational modifications, including phosphorylation and ubiquitination (24,30,31).…”

Role of Deubiquitinating Enzymes in DNA Repair

“…While BAP1 was shown to be involved in HR repair as discussed above, a more recent study showed that BAP1 is also required for DNA replication fork progression by deubiquitinating and stabilizing the INO80 ATPase subunit of the large INO80 complex, a chromatin remodeler that is involved in DNA replication and transcription (197). BAP1 is visible at the PCNA-containing replication fork foci, and by associating with H2A-Ub, it recruits INO80 to the replication foci (197). Similar to the effect of INO80 depletion, BAP1 depletion leads to impairment of replication fork progression, aneuploidy, chromosomal aberration, and developmental defects of mice (197).…”

“…BAP1 is visible at the PCNA-containing replication fork foci, and by associating with H2A-Ub, it recruits INO80 to the replication foci (197). Similar to the effect of INO80 depletion, BAP1 depletion leads to impairment of replication fork progression, aneuploidy, chromosomal aberration, and developmental defects of mice (197). The role of BAP1 in DNA replication progression is partly attributed to stabilizing INO80 at replication forks, but there may be another unknown function of BAP1 in supporting DNA replication and alleviating replication stress (197).…”