This is a repository copy of Rad5, HLTF, and SHPRH: A fresh view of an old story. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/159493/ Version: Published Version Article: Elserafy, M., Abugable, A.A. orcid.org/0000-0003-1275-3328, Atteya, R. et al. (1 more author) (2018) Rad5, HLTF, and SHPRH: A fresh view of an old story. Trends in Genetics, 34 (8). pp. 574-577. ISSN 0168-9525 https://doi.org/10.1016/j.tig.2018.04.006 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ impact of mismatches on the recombina- The presence of dispersed Alu elements chromosomal double strand breaks. Methods Mol. Biol. 920, 379–391 fi tion ef ciency. Their reporter was inte- throughout the genome [3], and other 9. Sugawara, N. et al. (2004) Heteroduplex rejection during grated in the genome in such a way that repetitive DNA sequences, provides end- single-strand annealing requires Sgs1 helicase and mis- match repair proteins Msh2 and Msh6 but not Pms1. Proc. they could use one Crispr/Cas9 guide RNA less opportunities for RMDs that disrupt Natl. Acad. Sci. U. S. A. 101, 9315–9320 to cut near the upstream homology region genome function. The relatively efficient and a second guide RNA to cut varying excision of tens of kilobases of DNA at distances (16 bp to 28.4 kb) from the DSBs means that many copies of Alu downstream homology region. may be exposed in single-strand regions, Forum leading to many possible rearrangements. Using their assay [7], the Stark lab showed The human genome could not survive the Rad5, HLTF, and that the frequency of repeat-mediated resulting instability if it did not have strong SHPRH: A Fresh View deletions (RMDs) increased when the regulators inhibiting these RMDs. DSB is close to the repetitive elements of an Old Story and declines rapidly with distance, fol- There are a number of situations in which Menattallah Elserafy,1,2,3 lowed by a very gradual decline up to at someoftheDSBrepairpathways are either Arwa A. Abugable,2,3 least 28.4 kb. At the longer distances, the suppressed or defective in humans. Can- Reham Atteya,2 and RMD was much more dependent on cer is the most obvious situation in which 1,2, ,@ Rad52 then at shorter distances. The role some of these genes, such as msh2, Sherif F. El-Khamisy * of Rad52 in SSA is to help anneal homolo- brca1,andbrca2 are commonly defective. gous or homologous sequences to form Thus, in various cancers one might expect Not only have helicase-like tran- heteroduplexes [1], whereas NHEJ and alt- tosee increases intheabundanceofRMDs scription factor (HLTF) and SNF2 NHEJ pathways are Rad52-independent. and possibly other changes in the nature of histone-linker PHD-finger RING-fin- They also showed that even a modest level repeat-mediated genomic rearrange- ger helicase (SHPRH) proved to be of mismatch between the repetitive ments that might lead to more genetic important players in post-replication sequences (1–3%) significantly inhibited instability, which in turn helps the cancer repair like their yeast counterpart, RMD at all distances. This inhibition by evolve to a more malignant form. Rad5, but they are also involved in mismatches between repetitive elements 1 multiple biological functions and are was largely dependent on Msh2, which Tulane Cancer Center, Tulane University, New Orleans, LA 70122, USA associated with several human dis- would be expected for a process mediated orders. We provide here an updated by heteroduplex rejection [9]. *Correspondence: [email protected] (P. Deininger). view of their functions, associated https://doi.org/10.1016/j.tig.2018.05.003 diseases, and potential therapeutic This new study tested the dependence of References approaches. RMD on various proteins involved in DSB 1. Ceccaldi, R. et al. (2016) Repair pathway choices and conse- repair. For example, loss of KU70 and quences at the double-strand break. Trends Cell Biol. 26, 52–64 XRCC4 (proteins involved in c-NHEJ) 2. Symington, L.S. and Gautier, J. (2011) Double-strand break RAD5, a Gene All[134_TD$DIFF] Budding Yeast end resection and repair pathway choice. Annu. Rev. Genet. increased RMD, while loss of CtIP and 45, 247–271 Laboratories Should Know about BRCA1 (which are involved in the resec- 3. Lander, E.S. et al. (2018) Initial sequencing and analysis of Yeast has served as a prominent model the human genome. Nature 409, 860–921 tion pathway) was found to decrease organism in DNA repair research for dec- 4. Carvalho, C.M. and Lupski, J.R. (2016) Mechanisms under- RMD. This indicates that there may be lying structural variant formation in genomic disorders. Nat. ades [1]. Rad5 is a RING-finger-containing competition between the nonresection Rev. Genet. 17, 224–238 ubiquitin ligase and helicase that[135_TD$DIFF] was 5. Belancio, V.P. et al. (2008) Mammalian non-LTR retrotrans- and resection pathways (Figure 1). How- posons: for better or worse, in sickness and in health. discovered in budding yeast and was ever, the authors found that direct regu- Genome Res. 18, 343–358 found to play a role in template switching lation by heteroduplex rejection (Msh2- 6. Morales, M.E. et al. (2015) The contribution of alu elements (TS) and translesion synthesis (TLS) post- to mutagenic DNA double-strand break repair. PLoS Genet. mediated) is a stronger inhibitor of RMD 11, e1005016 replication repair (PRR) mechanisms. TS than competition with c-NHEJ. These 7. Mendez-Dorantes, C. et al. (2018) Repeat- utilizes a clever mechanismusing thenewly mediated deletions can be induced by a data indicate that there could be multiple chromosomal break far from a repeat, but multiple synthesized sister DNA strand as a tem- pathways that suppress RMD between pathways suppress such rearrangements. Genes Dev. plate to bypass lesions, while TLSswitches 32, 524–536 the high concentration of repetitive replicative polymerases to low-fidelity pol- 8. Gunn, A. and Stark, J.M. (2012) I-SceI-based assays to sequences throughout the genome. examine distinct repair outcomes of mammalian ymerases to overcome lesions [2]. 574 Trends in Genetics, August 2018, Vol. 34, No. 8 The wild-type W303 yeast strain used by to predict prognosis and survival. More- Vpr and DCAF1 [9]. Mutations in this motif numerous laboratories harbors a RAD5 over, in cervical, thyroid, and head and or the addition of a zinc-chelating agent, mutation (rad5-535). Some researchers neck cancers, alternative splicing of HLTF TPEN N,N,N,N[136_TD$DIFF] -tetrakis-(2-pyridylmethyl) have started to use a strain in which the mRNA increases the expression of trun- ethylenediamine, was found to disrupt mutation has been corrected. Conse- cated versions lacking functional DNA the Vpr–CRL4 (DCAF1) interaction and quently, conflicting results have been repair domains [8]. Heterozygosity in the therefore their function. Nevertheless, reported in the literature by laboratories long arm of chromosome 6, where the TPEN did not affect the assembly of the using the W303 rad5-535 versus W303 SHPRH gene resides, has been reported cellular CRL4 E3 complex. This opens the RAD5 strains [3]. While it is important to in malignant melanoma, ovarian, and cer- door to developing novel antiviral thera- raise the awareness of yeast researchers vical cancers. Furthermore, SHPRH was pies against[137_TD$DIFF] HIV-1 in which the interaction to the importance of RAD5 genotype in found to be truncated or to contain mis- between Vpr and CRL4/DCAF1 is selec- yeast, it is equally important to highlight sense mutations in tumor cell lines, which tively disrupted [9] (Figure 1B). how the mammalian Rad5 orthologs, is consistent with a tumor-suppressor such as HLTF and SHPRH, play multiple function [2]. HLTF and Inflammatory Bowel Disease important roles in mammalian cells. (IBD) Interestingly, HLTF was found to be one of Gene expression analysis of regenerating HLTF and SHPRH; Rad5 Human the genetic determinants conferring sensi- gene (REG) family members has shown that Orthologs tivity or resistance to lysosomal autophagy the genes encoding REG-Ia (REG1A), REG- HLTF is considered to be the closest inhibitors such as hydroxychloroquine Ib (REG1B), and REG-IV (REG4)areover- ortholog to yeast Rad5; it shows higher (HCQ) in several cancer cell lines [8]. HLTF expressed in IBD. Upregulation of REG sequence conservation to Rad5 than to expression was found to be low in HCQ- genesisbeneficial on the one hand because SHPRH. HLTF contains the conserved sensitive cell lines and high in resistant cell it induces the proliferation of intestinal epi- HIRAN domain that is responsible for lines. HLTF protected against HCQ- thelial cells, protecting them from damage 30-single-stranded (ss)DNA binding [4], induced cell death because it is essential caused by the immune system, but on the and is able to complement UV sensitivity for repairing the resulting reactive oxygen other hand upregulation increases therisk of in the Drad5 yeast strain. It also pos- species (ROS)-induced DNA damage [8]. developing colon cancer [10]. sesses double-stranded (ds)DNA translo- Because lysosome inhibitors are currently case activity which is utilized to reverse in clinical trials for efficacy as single or com- A recent study investigating the link stalled replication forks [5].