# DNA–protein crosslink proteases in genome stability

**Authors:** Annamaria Ruggiano, Kristijan Ramadan

PMC · DOI: 10.1038/s42003-020-01539-3 · 2021-01-04

## TL;DR

This paper explores enzymes that break DNA-protein crosslinks, which are harmful DNA lesions, and their role in maintaining genome stability and preventing disease.

## Contribution

The paper highlights new insights into DPC proteases beyond DPC repair, such as their role in DNA replication and checkpoint control.

## Key findings

- DPC proteases degrade protein components of DNA–protein crosslinks to prevent genomic instability.
- These proteases also regulate DNA replication by degrading excess histones and controlling checkpoints.
- Dysfunction in DPC proteases is directly linked to human diseases and cancer therapy.

## Abstract

Proteins covalently attached to DNA, also known as DNA–protein crosslinks (DPCs), are common and bulky DNA lesions that interfere with DNA replication, repair, transcription and recombination. Research in the past several years indicates that cells possess dedicated enzymes, known as DPC proteases, which digest the protein component of a DPC. Interestingly, DPC proteases also play a role in proteolysis beside DPC repair, such as in degrading excess histones during DNA replication or controlling DNA replication checkpoints. Here, we discuss the importance of DPC proteases in DNA replication, genome stability and their direct link to human diseases and cancer therapy.

DNA–protein crosslink (DPC) proteases digest the protein component of crosslinks that otherwise can cause genomic instability and disease. Ruggiano and Ramadan discuss recent insights into the roles of DPC proteases in the repair of DPCs and beyond.

## Linked entities

- **Diseases:** cancer (MONDO:0004992)

## Full-text entities

- **Genes:** DDI1 (DDI proteasomal shuttling factor 1) [NCBI Gene 414301], FAM111A (FAM111 trypsin like peptidase A) [NCBI Gene 63901] {aka GCLEB, KCS2}, CDH1 (cadherin 1) [NCBI Gene 999] {aka Arc-1, BCDS1, CD324, CDHE, ECAD, LCAM}, Parp1 (poly (ADP-ribose) polymerase family, member 1) [NCBI Gene 11545] {aka 5830444G22Rik, ARTD1, Adprp, Adprt1, PARP, PPOL}, GCNA [NCBI Gene 107425], RFC1 (replication factor C subunit 1) [NCBI Gene 5981] {aka A1, CANVAS, MHCBFB, PO-GA, RECC1, RFC}, RPA1 (replication protein A1) [NCBI Gene 6117] {aka HSSB, MST075, PFBMFT6, REPA1, RF-A, RP-A}, SPRTN (SprT-like N-terminal domain) [NCBI Gene 83932] {aka C1orf124, DVC1, PRO4323, spartan}, BRCA1 (BRCA1 DNA repair associated) [NCBI Gene 672] {aka BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4}, TEX264 (testis expressed 264, ER-phagy receptor) [NCBI Gene 51368] {aka ZSIG11}, Sprtn (SprT-like N-terminal domain) [NCBI Gene 244666] {aka Gm505}, Tdp1 (tyrosyl-DNA phosphodiesterase 1) [NCBI Gene 104884] {aka 2810481F14Rik, 4921509N21Rik, E430034L06Rik, Gm40556, MLZ-501, SCAN1}, GCNA (germ cell nuclear acidic peptidase) [NCBI Gene 93953] {aka ACRC, NAAR1, SPGFX4}, Ddi1 (DNA-damage inducible 1) [NCBI Gene 71829] {aka 1700011N24Rik}, Hmces (5-hydroxymethylcytosine (hmC) binding, ES cell specific) [NCBI Gene 232210] {aka 8430410A17Rik, Srap1}, DDI1 (Ddi1p) [NCBI Gene 856886] {aka VSM1}, SPRTN (SprT-like N-terminal domain) [NCBI Gene 421530] {aka C1orf124, C3H1ORF124, DDDL1880, DVC1, PRO4323, Spartan}, USP11 (ubiquitin specific peptidase 11) [NCBI Gene 8237] {aka UHX1}, PCNA (proliferating cell nuclear antigen) [NCBI Gene 5111] {aka ATLD2}, DDI2 (DDI proteasomal shuttling factor 2) [NCBI Gene 84301] {aka RSC1A1}, FUS (FUS RNA binding protein) [NCBI Gene 2521] {aka ALS6, ETM4, FUS1, HNRNPP2, POMP75, TLS}, POLR2A (RNA polymerase II subunit A) [NCBI Gene 5430] {aka NEDHIB, POLR2, POLRA, RPB1, RPBh1, RPO2}, DNAH8 (dynein axonemal heavy chain 8) [NCBI Gene 1769] {aka ATPase, SPGF46, hdhc9}, PIP (prolactin induced protein) [NCBI Gene 5304] {aka BRST-2, GCDFP-15, GCDFP15, GPIP4}, sprtn.S (SprT-like N-terminal domain S homeolog) [NCBI Gene 100036995] {aka Spartan, c1orf124, sprtn}, SPI1 (Spi-1 proto-oncogene) [NCBI Gene 6688] {aka AGM10, OF, PU.1, SFPI1, SPI-1, SPI-A}, VCP (valosin containing protein) [NCBI Gene 7415] {aka CDC48, FTDALS6, TERA, p97}, FAM111B (FAM111 trypsin like peptidase B) [NCBI Gene 374393] {aka CANP, POIKTMP}, NPY4R (neuropeptide Y receptor Y4) [NCBI Gene 5540] {aka NPY4-R, PP1, PPYR1, Y4}, PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) [NCBI Gene 5290] {aka CCM4, CLAPO, CLOVE, CWS5, HMH, MCAP}, UBI4 (ubiquitin) [NCBI Gene 850620] {aka SCD2, UB14}, DDI3 (cyanamide hydratase) [NCBI Gene 850483] {aka DDI2}, PARP1 (poly(ADP-ribose) polymerase 1) [NCBI Gene 142] {aka ADPRT, ADPRT 1, ADPRT1, ARTD1, PARP, PARP-1}, CDC45 (cell division cycle 45) [NCBI Gene 8318] {aka CDC45L, CDC45L2, MGORS7, PORC-PI-1}, RAD18 (RAD18 E3 ubiquitin protein ligase) [NCBI Gene 56852] {aka RNF73}, SUMO1 (small ubiquitin like modifier 1) [NCBI Gene 7341] {aka DAP1, GMP1, OFC10, PIC1, SMT3, SMT3C}, DNMT1 (DNA methyltransferase 1) [NCBI Gene 1786] {aka ADCADN, AIM, CXXC9, DNMT, HSN1E, MCMT}, atr (ATR checkpoint kinase) [NCBI Gene 567770] {aka si:dkey-231j24.1}, sprtn (SprT-like N-terminal domain) [NCBI Gene 101886162], RPN1 (ribophorin I) [NCBI Gene 6184] {aka OST1, RBPH1}, MUL1 (mitochondrial E3 ubiquitin protein ligase 1) [NCBI Gene 79594] {aka C1orf166, GIDE, MAPL, MULAN, RNF218}
- **Diseases:** RJALS (OMIM:616200), HCC (MESH:D006528), toxicity (MESH:D064420), poikiloderma (MESH:D011038), cell cycle abnormalities (MESH:D000091622), liver damage (MESH:D056486), pulmonary fibrosis (MESH:D011658), ND (MESH:C537849), hypoparathyroidism (MESH:D007011), GCTs (MESH:D009373), autosomal recessive progeroid disease (MESH:C536423), cancer (MESH:D009369), autosomal dominant disease (MESH:D030342), skeletal abnormalities (MESH:D009139), KCS2 (MESH:C537020), DPC (MESH:D011488), chromosomal instability (MESH:D043171), abnormal bone development (MESH:D002658), carcinogenesis (MESH:D063646), GCLEB (MESH:C537291), cataracts (MESH:D002386), short stature (MESH:D006130), fertility defects (MESH:D007246), Embryonic lethality (MESH:D020964), hypocalcemia (MESH:D006996),  (MESH:D042822)
- **Chemicals:** EU (MESH:D005063), etoposide (MESH:D005047), 5-aza-2'-deoxycytidine (MESH:D000077209), tyrosine (MESH:D014443), PAR (MESH:D011064), HU (MESH:D006918), DPC (-), FA (MESH:D005557), Niraparib (MESH:C545685), talazoparib (MESH:C586365), CPT (MESH:D002166), EdU (MESH:C022811), lipid (MESH:D008055), aldehydes (MESH:D000447), 5-Hydroxymethylcytosine (MESH:C011865)
- **Species:** Diptera (flies, order) [taxon 7147], Drosophila melanogaster (fruit fly, species) [taxon 7227], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Homo sapiens (human, species) [taxon 9606], Danio rerio (leopard danio, species) [taxon 7955], Xenopus laevis (African clawed frog, species) [taxon 8355], Mus musculus (house mouse, species) [taxon 10090], Gallus gallus (bantam, species) [taxon 9031], C.elegans [taxon 328850]
- **Mutations:** Y117C, R569H
- **Cell lines:** U2 — Homo sapiens (Human), Fibrosarcoma, Cancer cell line (CVCL_M019), U1 — Homo sapiens (Human), Adult acute monocytic leukemia, Cancer cell line (CVCL_M769)

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC7782752/full.md

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Source: https://tomesphere.com/paper/PMC7782752