ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells

Liu, Xiaojing; Liu, Tingting; Shang, Yanfeng; Dai, Peng; Zhang, Wubing; Lee, Brian J.; Huang, Min; Yang, Dingpeng; Wu, Qiu Liang; Liu, Liu Daisy; Zheng, Xiaoqi; Zhou, Bo; Dong, Jing; Yeap, Leng-Siew; Hu, Jiazhi; Xiao, Tengfei; Zha, Shan; Casellas, Rafael; Liu, X Shirley; Meng, Fei-Long

doi:10.1038/s41422-020-0328-3

Cited by 52 publications

(50 citation statements)

References 68 publications

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“…Unexpectedly, given that ALC1 is recruited to sites of DNA damage in a PAR-dependent manner, Alc1 −/− MEFs also showed exquisite PARPi sensitivity as measured by cell survival or proliferative capacity ( Figures 1 I and 1J). Depletion of ALC1 has also scored as sensitizing human cells to PARPi in unbiased CRISPR screens, but the basis of this was unclear ( Liu et al., 2020 ; Zimmermann et al., 2018 ).…”

Section: Resultsmentioning

confidence: 99%

Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD

et al. 2021

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Summary Chromatin is a barrier to efficient DNA repair, as it hinders access and processing of certain DNA lesions. ALC1/CHD1L is a nucleosome-remodeling enzyme that responds to DNA damage, but its precise function in DNA repair remains unknown. Here we report that loss of ALC1 confers sensitivity to PARP inhibitors, methyl-methanesulfonate, and uracil misincorporation, which reflects the need to remodel nucleosomes following base excision by DNA glycosylases but prior to handover to APEX1. Using CRISPR screens, we establish that ALC1 loss is synthetic lethal with homologous recombination deficiency (HRD), which we attribute to chromosome instability caused by unrepaired DNA gaps at replication forks. In the absence of ALC1 or APEX1, incomplete processing of BER intermediates results in post-replicative DNA gaps and a critical dependence on HR for repair. Hence, targeting ALC1 alone or as a PARP inhibitor sensitizer could be employed to augment existing therapeutic strategies for HRD cancers.

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Section: Resultsmentioning

confidence: 99%

Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD

et al. 2021

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“…In combination with our findings, these observations suggest that increased accumulation of base damage and the resultant genesis of replication-coupled gaps may provide a new avenue for enhancing PARPi cytotoxicity. ALC1 loss has also been reported to produce PARPi sensitivity in genome wide screens in BRCA-proficient cell lines passaged for over several weeks at olaparib concentrations of 0.5-2 μM (50-200 fold higher doses than used in our studies) or 5 µM veliparib, albeit investigation of underlying mechanisms was not described in these studies 29,77,78 . These findings, together with our data from isogenic cell lines (Extended data Fig.…”

Section: Discussionmentioning

confidence: 79%

ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination deficient cells

Verma

Zhou

Cao

et al. 2020

Preprint

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The response to Poly (ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair mechanisms and the abundance of lesions that trap PARP enzymes on chromatin. It remains unclear, however, if the established role of PARP in promoting chromatin accessibility impacts viability in these settings. Using a CRISPR based screen, we identify the PAR-binding Snf2-like ATPase, ALC1/CHD1L, as a key determinant of PARPi toxicity in HR-deficient cells. ALC1 loss reduced viability of BRCA mutant cells and enhanced their sensitivity to PARPi by up to 250-fold, while overcoming several known resistance mechanisms. ALC1 loss was not epistatic to other repair pathways that execute the PARPi response. Instead, ALC1 deficiency reduced chromatin accessibility concomitant with a decrease in the association of repair factors. This resulted in an accumulation of replication associated DNA damage and a reliance on HR. These findings establish PAR-dependent chromatin remodeling as a mechanistically distinct aspect of PARPi responses, implicating ALC1 inhibition as a new approach to overcome therapeutic resistance in HR-deficient cancers.

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“…4A). CH12F3 cells can undergo class switch recombination stimulated by anti-CD40/Interleukin 4/ TGF-β and activation-induced deaminase (AID) initiates substantial DSBs in the switch (S) regions (Liu et al 2020). We examined the hotspot region in Chr12 and all the DSBs enriched at S regions as anticipated (Supplemental Fig.…”

Section: Resultsmentioning

confidence: 99%

Global detection of DNA repair outcomes induced by CRISPR-Cas9

Liu

Zhang

Xin

et al. 2021

Preprint

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CRISPR-Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing. The repair of DSBs leads to small insertions or deletions (indels) and other complex byproducts, including large deletions and chromosomal translocations. Indels are well understood to disrupt target genes, while the other deleterious byproducts remain elusive. We developed a new in silico analysis pipeline for the previously described primer-extension-mediated sequencing assay to comprehensively characterize CRISPR-Cas9-induced DSB repair outcomes in human or mouse cells. We identified tremendous deleterious DSB repair byproducts of CRISPR-Cas9 editing, including large deletions, plasmid integrations, and chromosomal translocations. We further elucidated the important roles of microhomology, chromosomal interaction, recurrent DSBs, and DSB repair pathways in the generation of these byproducts. Our findings provide an extra dimension for genome editing safety besides off-targets. And caution should be exercised to avoid not only off-target damages but also deleterious DSB repair byproducts during genome editing.

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ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells

Cited by 52 publications

References 68 publications

Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD

Defective ALC1 nucleosome remodeling confers PARPi sensitization and synthetic lethality with HRD

ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination deficient cells

Global detection of DNA repair outcomes induced by CRISPR-Cas9

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