Table 1.
CDC48/p97 substrates in the chromatin environment.
| Cdc48/p97-dependent process | Substrate(s) | Cofactor/Accessory factors | Experimental system | Reference |
|---|---|---|---|---|
| DNA replication | ||||
| Replication fork progression, G2/M checkpoint | n.d. | DVC1 | Mammalian cells, patient cells | Lessel et al., 2014 |
| Replication licensing | CDT-1, CDC-45-GINS | UFD-1, NPL-4, UBXN-3/FAF1 | C. elegans, X. laevis, mammalian cells | Mouysset et al., 2008; Franz et al., 2011, 2016 |
| Replication stress | FANCI, FANCD2 | DVC1 | Mammalian cells | Gibbs-Seymour et al., 2015 |
| Replication stress, DNA damage tolerance (DDT) | Polη, a.o. | DVC1 | Mammalian cells, C. elegans | Davis et al., 2012; Mosbech et al., 2012 |
| Replication termination | MCM7 | Dia2 | S. cerevisiae, X. laevis | Maric et al., 2014; Moreno et al., 2014; Maculins et al., 2015 |
| DNA repair | ||||
| Diverse genotoxic insults | SUMO/Ubiquitin-conjugates | Ufd1, Npl4 | S. cerevisiae | Nie et al., 2012 |
| Diverse genotoxic insults | SUMO/Ubiquitin-conjugates | Ufd1, Npl4, Rfp1, Pli1 | S. pombe | Køhler et al., 2013 |
| DNA damage response (DDR) | Top1, SUMO-conjugates | Wss1, Doa1 | S. cerevisiae | Balakirev et al., 2015 |
| DNA-double strand break repair | L3MBTL1 | UFD1, NPL4 | Mammalian cells, C. elegans | Acs et al., 2011 |
| DNA-double strand break repair | SUMO-Rad52 | Ufd1 | S. cerevisiae, mammalian cells | Bergink et al., 2013 |
| DNA-double strand break repair | Ubiquitin-(K48)-conjugates | UFD1, NPL4 | Mammalian cells | Meerang et al., 2011 |
| DNA-double strand break repair | DNA-PKcs | n.d. | Mammalian cells | Jiang et al., 2013 |
| DNA-protein crosslink (DPC) | Top1, a.o. | Wss1 | S. cerevisiae | Stingele et al., 2014 |
| PCNA-dependent response to UV-light | n.d. | DVC1, mono-ubiquitylated PCNA | Mammalian cells | Centore et al., 2012 |
| UV-light induced protein turnover | CSB | UFD1, UBXN7, CUL4 | Mammalian cells | He et al., 2016 |
| UV-light induced protein turnover | CDT1, SET8 | UFD1, NPL4, a.o. | Mammalian cells, X. leavis | Raman et al., 2011 |
| UV-light induced protein turnover | DDB2, XPC | UFD1, NPL4, UBXN7, CUL4 | Mammalian cells | Puumalainen et al., 2014 |
| UV-light induced protein turnover | Rbp1 | Ufd1, Npl4, Ubx4, Ubx5, Cul3 | S. cerevisiae | Verma et al., 2011 |
| Transcription | ||||
| Histone ubiquitylation | Histone 2B | Ubx3 | S. cerevisiae, mammalian cells | Bonizec et al., 2014 |
| Mating-type switch | α2 | Ufd1, Npl4, Doa10, a.o. | S. cerevisiae | Wilcox and Laney, 2009 |
| Transcriptional inactivation | HIF1α | UBXN7, CUL2, VHL | Mammalian cells | Alexandru et al., 2008 |
| Transcriptional regulation | LexA-VP16, Met4, R-Smads | Ufd1, Npl4 | S. cerevisiae | Ndoja et al., 2014 |
| Heterochromatin decondensation | CenH3 | Ufd1, Npl4 | A. thaliana | Merai et al., 2014 |
| Telomere maintenance | ||||
| Telomerase efficiency | Cdc13 | Vms1 | S. cerevisiae | Baek et al., 2012 |
| Telomerase efficiency | Est1 | Ufd1, Npl4, Ufd4 | S. cerevisiae | Lin et al., 2015 |
| Sister-chromatid segregation | ||||
| Anaphase degradation | n.d. | Ubx4 | S. cerevisiae | Chien and Chen, 2013 |
| Chromatin decondensation/congression | Aurora-B | Ufd1, Npl4 | X. leavis, mammalian cells | Ramadan et al., 2007; Dobrynin et al., 2011 |
| Meiosis | AIR-2 | n.d. | C. elegans | Sasagawa et al., 2012 |
| Others | ||||
| Global analysis | SUMO-conjugates | Ufd1, STUbL | S. pombe | Køhler et al., 2015 |
The table lists the identified chromatin-associated substrates of CDC48/p97, sorted by their functional relevance in indicated cellular processes. In addition, the involvement of cofactors and/or accessory factors is displayed along with the experimental system that was used in the respective publication (a.o. and others, n.d. not determined).