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Thomas A, Cox J, Wolfe KB, Mingalone CH, Yaspan HR, McVey M. Division of Labor by the HELQ, BLM, and FANCM Helicases during Homologous Recombination Repair in Drosophila melanogaster. Genes (Basel) 2022; 13. [PMID: 35328029 DOI: 10.3390/genes13030474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Repair of DNA double-strand breaks by homologous recombination (HR) requires a carefully orchestrated sequence of events involving many proteins. One type of HR, synthesis-dependent strand annealing (SDSA), proceeds via the formation of a displacement loop (D-loop) when RAD51-coated single-stranded DNA invades a homologous template. The 3' end of the single-stranded DNA is extended by DNA synthesis. In SDSA, the D-loop is then disassembled prior to strand annealing. While many helicases can unwind D-loops in vitro, how their action is choreographed in vivo remains to be determined. To clarify the roles of various DNA helicases during SDSA, we used a double-strand gap repair assay to study the outcomes of homologous recombination repair in Drosophila melanogaster lacking the BLM, HELQ, and FANCM helicases. We found that the absence of any of these three helicases impairs gap repair. In addition, flies lacking both BLM and HELQ or HELQ and FANCM had more severe SDSA defects than the corresponding single mutants. In the absence of BLM, a large percentage of repair events were accompanied by flanking deletions. Strikingly, these deletions were mostly abolished in the blm helq and blm fancm double mutants. Our results suggest that the BLM, HELQ, and FANCM helicases play distinct roles during SDSA, with HELQ and FANCM acting early to promote the formation of recombination intermediates that are then processed by BLM to prevent repair by deletion-prone mechanisms.
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Benjamin R, Banerjee A, Wu X, Geurink C, Buczek L, Eames D, Trimidal SG, Pluth JM, Schiller MR. XRCC4 and MRE11 Roles and Transcriptional Response to Repair of TALEN-Induced Double-Strand DNA Breaks. Int J Mol Sci 2022; 23:ijms23020593. [PMID: 35054780 PMCID: PMC8776116 DOI: 10.3390/ijms23020593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 02/04/2023] Open
Abstract
Double-strand breaks (DSB) are one of the most lethal forms of DNA damage that, if left unrepaired, can lead to genomic instability, cellular transformation, and cell death. In this work, we examined how repair of transcription activator-like effector nuclease (TALEN)-induced DNA damage was altered when knocking out, or inhibiting a function of, two DNA repair proteins, XRCC4 and MRE11, respectively. We developed a fluorescent reporter assay that uses TALENs to introduce DSB and detected repair by the presence of GFP fluorescence. We observed repair of TALEN-induced breaks in the XRCC4 knockout cells treated with mirin (a pharmacological inhibitor of MRE11 exonuclease activity), albeit with ~40% reduced efficiency compared to normal cells. Editing in the absence of XRCC4 or MRE11 exonuclease was robust, with little difference between the indel profiles amongst any of the groups. Reviewing the transcriptional profiles of the mirin-treated XRCC4 knockout cells showed 307 uniquely differentially expressed genes, a number far greater than for either of the other cell lines (the HeLa XRCC4 knockout sample had 83 genes, and the mirin-treated HeLa cells had 30 genes uniquely differentially expressed). Pathways unique to the XRCC4 knockout+mirin group included differential expression of p53 downstream pathways, and metabolic pathways indicating cell adaptation for energy regulation and stress response. In conclusion, our study showed that TALEN-induced DSBs are repaired, even when a key DSB repair protein or protein function is not operational, without a change in indel profiles. However, transcriptional profiles indicate the induction of unique cellular responses dependent upon the DNA repair protein(s) hampered.
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Affiliation(s)
- Ronald Benjamin
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
- Correspondence: (R.B.); (M.R.S.); Tel.: +1-(702)927-9325 (R.B.); +1-(702)895-5546 (M.R.S.)
| | - Atoshi Banerjee
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Xiaogang Wu
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
| | - Corey Geurink
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Lindsay Buczek
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Danielle Eames
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Sara G. Trimidal
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Janice M. Pluth
- Health Physics and Diagnostic Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA;
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA; (A.B.); (X.W.); (C.G.); (L.B.); (D.E.); (S.G.T.)
- School of Life Science, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
- Correspondence: (R.B.); (M.R.S.); Tel.: +1-(702)927-9325 (R.B.); +1-(702)895-5546 (M.R.S.)
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Abstract
Humans have evolved a series of DNA double-strand break (DSB) repair pathways to efficiently and accurately rejoin nascently formed pairs of double-stranded DNA ends (DSEs). In G0/G1-phase cells, non-homologous end joining (NHEJ) and alternative end joining (A-EJ) operate to support covalent rejoining of DSEs. While NHEJ is predominantly utilized and collaborates extensively with the DNA damage response (DDR) to support pairing of DSEs, much less is known about A-EJ collaboration with DDR factors when NHEJ is absent. Non-cycling lymphocyte progenitor cells use NHEJ to complete V(D)J recombination of antigen receptor genes, initiated by the RAG1/2 endonuclease which holds its pair of targeted DSBs in a synapse until each specified pair of DSEs is handed off to the NHEJ DSB sensor complex, Ku. Similar to designer endonuclease DSBs, the absence of Ku allows for A-EJ to access RAG1/2 DSEs but with random pairing to complete their repair. Here, we describe recent insights into the major phases of DSB end joining, with an emphasis on synapsis and tethering mechanisms, and bring together new and old concepts of NHEJ vs. A-EJ and on RAG2-mediated repair pathway choice.
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Gopalakrishnan V, Sharma S, Ray U, Manjunath M, Lakshmanan D, Vartak SV, Gopinatha VK, Srivastava M, Kempegowda M, Choudhary B, Raghavan SC. SCR7, an inhibitor of NHEJ can sensitize tumor cells to ionization radiation. Mol Carcinog 2021; 60:627-643. [PMID: 34192388 DOI: 10.1002/mc.23329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022]
Abstract
Nonhomologous end joining (NHEJ), one of the major DNA double-strand break repair pathways, plays a significant role in cancer cell proliferation and resistance to radio and chemotherapeutic agents. Previously, we had described a small molecule inhibitor, SCR7, which inhibited NHEJ in a DNA Ligase IV dependent manner. Here, we report that SCR7 potentiates the effect of γ-radiation (IR) that induces DNA breaks as intermediates to eradicate cancer cells. Dose fractionation studies revealed that coadministration of SCR7 and IR (0.5 Gy) in mice Dalton's lymphoma (DLA) model led to a significant reduction in mice tumor cell proliferation, which was equivalent to that observed for 2 Gy dose when both solid and liquid tumor models were used. Besides, co-treatment with SCR7 and 1 Gy of IR further improved the efficacy. Notably, there was no significant change in blood parameters, kidney and liver functions upon combinatorial treatment of SCR7 and IR. Further, the co-treatment of SCR7 and IR resulted in a significant increase in unrepaired DSBs within cancer cells compared to either of the agent alone. Anatomy, histology, and other studies in tumor models confirmed the cumulative effects of both agents in activating apoptotic pathways to induce cytotoxicity by modulating DNA damage response and repair pathways. Thus, we report that SCR7 has the potential to reduce the side effects of radiotherapy by lowering its effective dose ex vivo and in mice tumor models, with implications in cancer therapy.
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Affiliation(s)
- Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India.,Department of Zoology, St. Joseph's College (Autonomous), Irinjalakuda, Kerala, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India
| | - Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Lakshmanan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mrinal Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
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Abstract
Bacteria and bacteriophages (phages) have evolved potent defense and counterdefense mechanisms that allowed their survival and greatest abundance on Earth. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated) is a bacterial defense system that inactivates the invading phage genome by introducing double-strand breaks at targeted sequences. While the mechanisms of CRISPR defense have been extensively investigated, the counterdefense mechanisms employed by phages are poorly understood. Here, we report a novel counterdefense mechanism by which phage T4 restores the genomes broken by CRISPR cleavages. Catalyzed by the phage-encoded recombinase UvsX, this mechanism pairs very short stretches of sequence identity (minihomology sites), as few as 3 or 4 nucleotides in the flanking regions of the cleaved site, allowing replication, repair, and stitching of genomic fragments. Consequently, a series of deletions are created at the targeted site, making the progeny genomes completely resistant to CRISPR attack. Our results demonstrate that this is a general mechanism operating against both type II (Cas9) and type V (Cas12a) CRISPR-Cas systems. These studies uncovered a new type of counterdefense mechanism evolved by T4 phage where subtle functional tuning of preexisting DNA metabolism leads to profound impact on phage survival. IMPORTANCE Bacteriophages (phages) are viruses that infect bacteria and use them as replication factories to assemble progeny phages. Bacteria have evolved powerful defense mechanisms to destroy the invading phages by severing their genomes soon after entry into cells. We discovered a counterdefense mechanism evolved by phage T4 to stitch back the broken genomes and restore viral infection. In this process, a small amount of genetic material is deleted or another mutation is introduced, making the phage resistant to future bacterial attack. The mutant virus might also gain survival advantages against other restriction conditions or DNA damaging events. Thus, bacterial attack not only triggers counterdefenses but also provides opportunities to generate more fit phages. Such defense and counterdefense mechanisms over the millennia led to the extraordinary diversity and the greatest abundance of bacteriophages on Earth. Understanding these mechanisms will open new avenues for engineering recombinant phages for biomedical applications.
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Affiliation(s)
- Xiaorong Wu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Jingen Zhu
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Pan Tao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Venigalla B. Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC, USA
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6
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Zhou Q, Howard ME, Tu X, Zhu Q, Denbeigh JM, Remmes NB, Herman MG, Beltran CJ, Yuan J, Greipp PT, Boughey JC, Wang L, Johnson N, Goetz MP, Sarkaria JN, Lou Z, Mutter RW. Inhibition of ATM Induces Hypersensitivity to Proton Irradiation by Upregulating Toxic End Joining. Cancer Res 2021; 81:3333-3346. [PMID: 33597272 PMCID: PMC8260463 DOI: 10.1158/0008-5472.can-20-2960] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/30/2020] [Accepted: 02/11/2021] [Indexed: 12/15/2022]
Abstract
Proton Bragg peak irradiation has a higher ionizing density than conventional photon irradiation or the entrance of the proton beam profile. Whether targeting the DNA damage response (DDR) could enhance vulnerability to the distinct pattern of damage induced by proton Bragg peak irradiation is currently unknown. Here, we performed genetic or pharmacologic manipulation of key DDR elements and evaluated DNA damage signaling, DNA repair, and tumor control in cell lines and xenografts treated with the same physical dose across a radiotherapy linear energy transfer spectrum. Radiotherapy consisted of 6 MV photons and the entrance beam or Bragg peak of a 76.8 MeV spot scanning proton beam. More complex DNA double-strand breaks (DSB) induced by Bragg peak proton irradiation preferentially underwent resection and engaged homologous recombination (HR) machinery. Unexpectedly, the ataxia-telangiectasia mutated (ATM) inhibitor, AZD0156, but not an inhibitor of ATM and Rad3-related, rendered cells hypersensitive to more densely ionizing proton Bragg peak irradiation. ATM inhibition blocked resection and shunted more DSBs to processing by toxic ligation through nonhomologous end-joining, whereas loss of DNA ligation via XRCC4 or Lig4 knockdown rescued resection and abolished the enhanced Bragg peak cell killing. Proton Bragg peak monotherapy selectively sensitized cell lines and tumor xenografts with inherent HR defects, and the repair defect induced by ATM inhibitor coadministration showed enhanced efficacy in HR-proficient models. In summary, inherent defects in HR or administration of an ATM inhibitor in HR-proficient tumors selectively enhances the relative biological effectiveness of proton Bragg peak irradiation. SIGNIFICANCE: Coadministration of an ATM inhibitor rewires DNA repair machinery to render cancer cells uniquely hypersensitive to DNA damage induced by the proton Bragg peak, which is characterized by higher density ionization.See related commentary by Nickoloff, p. 3156.
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Affiliation(s)
- Qin Zhou
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Xinyi Tu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Janet M Denbeigh
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Michael G Herman
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Chris J Beltran
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jian Yuan
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, Minnesota
| | - Judy C Boughey
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Matthew P Goetz
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, Minnesota.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota.
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7
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Luessing J, Sakhteh M, Sarai N, Frizzell L, Tsanov N, Ramberg KO, Maretto S, Crowley PB, Lowndes NF. The nuclear kinesin KIF18B promotes 53BP1-mediated DNA double-strand break repair. Cell Rep 2021; 35:109306. [PMID: 34192545 DOI: 10.1016/j.celrep.2021.109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
53BP1 is recruited to chromatin in the vicinity of DNA double-strand breaks (DSBs). We identify the nuclear kinesin, KIF18B, as a 53BP1-interacting protein and define its role in 53BP1-mediated DSB repair. KIF18B is a molecular motor protein involved in destabilizing astral microtubules during mitosis. It is primarily nuclear throughout the interphase and is constitutively chromatin bound. Our observations indicate a nuclear function during the interphase for a kinesin previously implicated in mitosis. We identify a central motif in KIF18B, which we term the Tudor-interacting motif (TIM), because of its interaction with the Tudor domain of 53BP1. TIM enhances the interaction between the 53BP1 Tudor domain and dimethylated lysine 20 of histone H4. TIM and the motor function of KIF18B are both required for efficient 53BP1 focal recruitment in response to damage and for fusion of dysfunctional telomeres. Our data suggest a role for KIF18B in efficient 53BP1-mediated end-joining of DSBs.
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8
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Liang Z, Kumar V, Le Bouteiller M, Zurita J, Kenrick J, Lin SG, Lou J, Hu J, Ye AY, Boboila C, Alt FW, Frock RL. Ku70 suppresses alternative end joining in G1-arrested progenitor B cells. Proc Natl Acad Sci U S A 2021; 118:e2103630118. [PMID: 34006647 DOI: 10.1073/pnas.2103630118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Classical nonhomologous end joining (C-NHEJ) repairs DNA double-strand breaks (DSBs) throughout interphase but predominates in G1 phase when homologous recombination is unavailable. Complexes containing the Ku70/80 ("Ku") and XRCC4/ligase IV (Lig4) core C-NHEJ factors are required, respectively, for sensing and joining DSBs. While XRCC4/Lig4 are absolutely required for joining RAG1/2 endonuclease ("RAG")-initiated DSBs during V(D)J recombination in G1-phase progenitor lymphocytes, cycling cells deficient for XRCC4/Lig4 also can join chromosomal DSBs by alternative end-joining (A-EJ) pathways. Restriction of V(D)J recombination by XRCC4/Lig4-mediated joining has been attributed to RAG shepherding V(D)J DSBs exclusively into the C-NHEJ pathway. Here, we report that A-EJ of DSB ends generated by RAG1/2, Cas9:gRNA, and Zinc finger endonucleases in Lig4-deficient G1-arrested progenitor B cell lines is suppressed by Ku. Thus, while diverse DSBs remain largely as free broken ends in Lig4-deficient G1-arrested progenitor B cells, deletion of Ku70 increases DSB rejoining and translocation levels to those observed in Ku70-deficient counterparts. Correspondingly, while RAG-initiated V(D)J DSB joining is abrogated in Lig4-deficient G1-arrested progenitor B cell lines, joining of RAG-generated DSBs in Ku70-deficient and Ku70/Lig4 double-deficient lines occurs through a translocation-like A-EJ mechanism. Thus, in G1-arrested, Lig4-deficient progenitor B cells are functionally end-joining suppressed due to Ku-dependent blockage of A-EJ, potentially in association with G1-phase down-regulation of Lig1. Finally, we suggest that differential impacts of Ku deficiency versus Lig4 deficiency on V(D)J recombination, neuronal apoptosis, and embryonic development results from Ku-mediated inhibition of A-EJ in the G1 cell cycle phase in Lig4-deficient developing lymphocyte and neuronal cells.
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9
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Ghosh D, Raghavan SC. Nonhomologous end joining: new accessory factors fine tune the machinery. Trends Genet 2021; 37:582-599. [PMID: 33785198 DOI: 10.1016/j.tig.2021.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023]
Abstract
Nonhomologous DNA end joining (NHEJ) is one of the major DNA double-strand break (DSB) repair pathways in eukaryotes. The well-known critical proteins involved in NHEJ include Ku70/80, DNA-PKcs, Artemis, DNA pol λ/μ, DNA ligase IV-XRCC4, and XLF. Recent studies have added a number of new proteins to the NHEJ repertoire namely paralog of XRCC4 and XLF (PAXX), modulator of retroviral infection (MRI)/ cell cycle regulator of NHEJ (CYREN), transactivation response DNA-binding protein (TARDBP) of 43 kDa (TDP-43), intermediate filament family orphan (IFFO1), ERCC excision repair 6 like 2 (ERCC6L2), and RNase H2. PAXX acts as a stabilizing factor for the main NHEJ components. MRI/CYREN seems to play a dual role stimulating NHEJ in the G1 phase of the cell cycle, while inhibiting the pathway in the S and G2 phases. TDP-43 can recruit the ligase IV-XRCC4 complex to the DSB sites and stimulate ligation in neuronal cells. RNase H2 excises out the ribonucleotides inserted during repair by DNA polymerase μ/TdT. This review provides a brief glimpse into how these new partners were discovered and their contribution to the mechanism and regulation of NHEJ.
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Affiliation(s)
- Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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10
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Wierson WA, Welker JM, Almeida MP, Mann CM, Webster DA, Torrie ME, Weiss TJ, Kambakam S, Vollbrecht MK, Lan M, McKeighan KC, Levey J, Ming Z, Wehmeier A, Mikelson CS, Haltom JA, Kwan KM, Chien CB, Balciunas D, Ekker SC, Clark KJ, Webber BR, Moriarity BS, Solin SL, Carlson DF, Dobbs DL, McGrail M, Essner J. Efficient targeted integration directed by short homology in zebrafish and mammalian cells. eLife 2020; 9:e53968. [PMID: 32412410 PMCID: PMC7228771 DOI: 10.7554/elife.53968] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Here, we describe a set of resources to streamline reporter gene knock-ins in zebrafish and demonstrate the broader utility of the method in mammalian cells. Our approach uses short homology of 24-48 bp to drive targeted integration of DNA reporter cassettes by homology-mediated end joining (HMEJ) at high frequency at a double strand break in the targeted gene. Our vector series, pGTag (plasmids for Gene Tagging), contains reporters flanked by a universal CRISPR sgRNA sequence which enables in vivo liberation of the homology arms. We observed high rates of germline transmission (22-100%) for targeted knock-ins at eight zebrafish loci and efficient integration at safe harbor loci in porcine and human cells. Our system provides a straightforward and cost-effective approach for high efficiency gene targeting applications in CRISPR and TALEN compatible systems.
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MESH Headings
- Animals
- Animals, Genetically Modified
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Fibroblasts/metabolism
- Gene Expression Regulation
- Gene Knock-In Techniques
- Genes, Reporter
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Humans
- K562 Cells
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Recombinational DNA Repair
- Sequence Homology, Nucleic Acid
- Sus scrofa
- Transcription Activator-Like Effector Nucleases/genetics
- Transcription Activator-Like Effector Nucleases/metabolism
- Zebrafish/genetics
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Affiliation(s)
- Wesley A Wierson
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Jordan M Welker
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Maira P Almeida
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Carla M Mann
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | | | - Melanie E Torrie
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Trevor J Weiss
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Sekhar Kambakam
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | | | - Merrina Lan
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Kenna C McKeighan
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Jacklyn Levey
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Zhitao Ming
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Alec Wehmeier
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Christopher S Mikelson
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Jeffrey A Haltom
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Kristen M Kwan
- Department of Human Genetics, University of Utah School of MedicineSalt Lake CityUnited States
| | - Chi-Bin Chien
- Department of Neurobiology and Anatomy, University of Utah Medical CenterSalt Lake CityUnited States
| | - Darius Balciunas
- Department of Biology, Temple UniversityPhiladelphiaUnited States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo ClinicRochesterUnited States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo ClinicRochesterUnited States
| | - Beau R Webber
- Department of Pediatrics, Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
| | - Branden S Moriarity
- Department of Pediatrics, Masonic Cancer Center, University of MinnesotaMinneapolisUnited States
| | | | | | - Drena L Dobbs
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
| | - Jeffrey Essner
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmesUnited States
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11
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Abstract
The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is initiated by nucleolytic degradation of the 5'-terminated strands in a process termed end resection. End resection generates 3'-single-stranded DNA tails, substrates for Rad51 to catalyze homologous pairing and DNA strand exchange, and for activation of the DNA damage checkpoint. The commonly accepted view is that end resection occurs by a two-step mechanism. In the first step, Sae2/CtIP activates the Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex to endonucleolytically cleave the 5'-terminated DNA strands close to break ends, and in the second step Exo1 and/or Dna2 nucleases extend the resected tracts to produce long 3'-ssDNA-tailed intermediates. Initiation of resection commits a cell to repair a DSB by HR because long ssDNA overhangs are poor substrates for non-homologous end joining (NHEJ). Thus, the initiation of end resection has emerged as a critical control point for repair pathway choice. Here, I review recent studies on the mechanism of end resection and how this process is regulated to ensure the most appropriate repair outcome.
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Affiliation(s)
- Lorraine S Symington
- a Department of Microbiology & Immunology , Columbia University Medical Center , New York , USA
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12
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Sfeir A, Symington LS. Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway? Trends Biochem Sci 2015; 40:701-14. [PMID: 26439531 DOI: 10.1016/j.tibs.2015.08.006] [Citation(s) in RCA: 382] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/13/2015] [Accepted: 08/18/2015] [Indexed: 12/12/2022]
Abstract
DNA double-strand breaks (DSBs) disrupt the continuity of chromosomes and their repair by error-free mechanisms is essential to preserve genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism that involves alignment of microhomologous sequences internal to the broken ends before joining, and is associated with deletions and insertions that mark the original break site, as well as chromosome translocations. Whether MMEJ has a physiological role or is simply a back-up repair mechanism is a matter of debate. Here we review recent findings pertaining to the mechanism of MMEJ and discuss its role in normal and cancer cells.
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13
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Deng SK, Chen H, Symington LS. Replication protein A prevents promiscuous annealing between short sequence homologies: Implications for genome integrity. Bioessays 2014; 37:305-13. [PMID: 25400143 DOI: 10.1002/bies.201400161] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Replication protein A (RPA) is the main eukaryotic single-stranded DNA (ssDNA) binding protein, having essential roles in all DNA metabolic reactions involving ssDNA. RPA binds ssDNA with high affinity, thereby preventing the formation of secondary structures and protecting ssDNA from the action of nucleases, and directly interacts with other DNA processing proteins. Here, we discuss recent results supporting the idea that one function of RPA is to prevent annealing between short repeats that can lead to chromosome rearrangements by microhomology-mediated end joining or the formation of hairpin structures that are substrates for structure-selective nucleases. We suggest that replication fork catastrophe caused by depletion of RPA could result from cleavage of secondary structures by nucleases, and that failure to cleave hairpin structures formed at DNA ends could lead to gene amplification. These studies highlight the important role RPA plays in maintaining genome integrity.
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Affiliation(s)
- Sarah K Deng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, USA
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14
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Abstract
Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid, and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.
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Affiliation(s)
- Adam B Fisher
- Integrative Life Sciences Program, Virginia Commonwealth University , Richmond, VA , USA
| | - Zachary B Canfield
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
| | - Laura C Hayward
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
| | - Stephen S Fong
- Integrative Life Sciences Program, Virginia Commonwealth University , Richmond, VA , USA ; Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
| | - George H McArthur
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
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15
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Grundy GJ, Rulten SL, Zeng Z, Arribas-Bosacoma R, Iles N, Manley K, Oliver A, Caldecott KW. APLF promotes the assembly and activity of non-homologous end joining protein complexes. EMBO J 2013; 32:112-25. [PMID: 23178593 PMCID: PMC3545299 DOI: 10.1038/emboj.2012.304] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 10/29/2012] [Indexed: 11/08/2022] Open
Abstract
Non-homologous end joining (NHEJ) is critical for the maintenance of genetic integrity and DNA double-strand break (DSB) repair. NHEJ is regulated by a series of interactions between core components of the pathway, including Ku heterodimer, XLF/Cernunnos, and XRCC4/DNA Ligase 4 (Lig4). However, the mechanisms by which these proteins assemble into functional protein-DNA complexes are not fully understood. Here, we show that the von Willebrand (vWA) domain of Ku80 fulfills a critical role in this process by recruiting Aprataxin-and-PNK-Like Factor (APLF) into Ku-DNA complexes. APLF, in turn, functions as a scaffold protein and promotes the recruitment and/or retention of XRCC4-Lig4 and XLF, thereby assembling multi-protein Ku complexes capable of efficient DNA ligation in vitro and in cells. Disruption of the interactions between APLF and either Ku80 or XRCC4-Lig4 disrupts the assembly and activity of Ku complexes, and confers cellular hypersensitivity and reduced rates of chromosomal DSB repair in avian and human cells, respectively. Collectively, these data identify a role for the vWA domain of Ku80 and a molecular mechanism by which DNA ligase proficient complexes are assembled during NHEJ in mammalian cells, and reveal APLF to be a structural component of this critical DSB repair pathway.
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Affiliation(s)
| | - Stuart L Rulten
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Zhihong Zeng
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | | | - Natasha Iles
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Katie Manley
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Antony Oliver
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
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16
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Falck J, Forment JV, Coates J, Mistrik M, Lukas J, Bartek J, Jackson SP. CDK targeting of NBS1 promotes DNA-end resection, replication restart and homologous recombination. EMBO Rep 2012; 13:561-8. [PMID: 22565321 PMCID: PMC3367243 DOI: 10.1038/embor.2012.58] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/28/2012] [Accepted: 04/13/2012] [Indexed: 12/14/2022] Open
Abstract
The conserved MRE11–RAD50–NBS1 (MRN) complex is an important sensor of DNA double-strand breaks (DSBs) and facilitates DNA repair by homologous recombination (HR) and end joining. Here, we identify NBS1 as a target of cyclin-dependent kinase (CDK) phosphorylation. We show that NBS1 serine 432 phosphorylation occurs in the S, G2 and M phases of the cell cycle and requires CDK activity. This modification stimulates MRN-dependent conversion of DSBs into structures that are substrates for repair by HR. Impairment of NBS1 phosphorylation not only negatively affects DSB repair by HR, but also prevents resumption of DNA replication after replication-fork stalling. Thus, CDK-mediated NBS1 phosphorylation defines a molecular switch that controls the choice of repair mode for DSBs.
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Affiliation(s)
- Jacob Falck
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
| | - Josep V Forment
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Julia Coates
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Martin Mistrik
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
- Institute of Molecular and Translational Medicine, Palacky University, Olomouc CZ-77515, Czech Republic
| | - Jiri Lukas
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
| | - Jiri Bartek
- Centre for Genotoxic Stress Research, Danish Cancer Society, Strandboulevarden 49, Copenhagen DK-2100, Denmark
- Institute of Molecular and Translational Medicine, Palacky University, Olomouc CZ-77515, Czech Republic
| | - Stephen P Jackson
- Department of Biochemistry, Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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17
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Gunn A, Bennardo N, Cheng A, Stark JM. Correct end use during end joining of multiple chromosomal double strand breaks is influenced by repair protein RAD50, DNA-dependent protein kinase DNA-PKcs, and transcription context. J Biol Chem 2011; 286:42470-42482. [PMID: 22027841 PMCID: PMC3234933 DOI: 10.1074/jbc.m111.309252] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 10/19/2011] [Indexed: 12/27/2022] Open
Abstract
During repair of multiple chromosomal double strand breaks (DSBs), matching the correct DSB ends is essential to limit rearrangements. To investigate the maintenance of correct end use, we examined repair of two tandem noncohesive DSBs generated by endonuclease I-SceI and the 3' nonprocessive exonuclease Trex2, which can be expressed as an I-SceI-Trex2 fusion. We examined end joining (EJ) repair that maintains correct ends (proximal-EJ) versus using incorrect ends (distal-EJ), which provides a relative measure of incorrect end use (distal end use). Previous studies showed that ATM is important to limit distal end use. Here we show that DNA-PKcs kinase activity and RAD50 are also important to limit distal end use, but that H2AX is dispensable. In contrast, we find that ATM, DNA-PKcs, and RAD50 have distinct effects on repair events requiring end processing. Furthermore, we developed reporters to examine the effects of the transcription context on DSB repair, using an inducible promoter. We find that a DSB downstream from an active promoter shows a higher frequency of distal end use, and a greater reliance on ATM for limiting incorrect end use. Conversely, DSB transcription context does not affect end processing during EJ, the frequency of homology-directed repair, or the role of RAD50 and DNA-PKcs in limiting distal end use. We suggest that RAD50, DNA-PKcs kinase activity, and transcription context are each important to limit incorrect end use during EJ repair of multiple DSBs, but that these factors and conditions have distinct roles during repair events requiring end processing.
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Affiliation(s)
- Amanda Gunn
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Nicole Bennardo
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Anita Cheng
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Jeremy M Stark
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010.
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18
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Abstract
Terminal deoxynucleotidyl transferase (TdT; EC 2.7.7.31) adds nucleotides to DNA ends generated during V(D)J recombination that are subsequently processed by proteins involved in general double-strand break (DSB) repair pathways. We report an association between TdT and a 55-kDa protein in lymphoid cells. This protein, identified as hPso4, is a homolog of the protein encoded by the PS04/PRP19 gene in Saccharomyces cerevisiae that has pleiotropic functions in DNA recombination and error-prone repair. Purified hPso4 binds double-stranded DNA in a sequence-nonspecific manner but does not bind single-stranded DNA. hPso4 protein is induced 15- to 30-fold in cells by gamma radiation and chemical mutagens but not by UV treatment. Loss of hPso4 expression induced by siRNA results in accumulation of DSBs, apoptosis, and decreased cell survival after DNA damage. We conclude that hPso4 plays a major and previously undefined role in mammalian DNA DSB repair.
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Affiliation(s)
- Kiran N Mahajan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7295, USA.
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