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Moor NA, Vasil'eva IA, Lavrik OI. Human DNA ligases I and IIIα as determinants of accuracy and efficiency of base excision DNA repair. Biochimie 2024; 219:84-95. [PMID: 37573020 DOI: 10.1016/j.biochi.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/17/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Mammalian Base Excision Repair (BER) DNA ligases I and IIIα (LigI, LigIIIα) are major determinants of DNA repair fidelity, alongside with DNA polymerases. Here we compared activities of human LigI and LigIIIα on specific and nonspecific substrates representing intermediates of distinct BER sub-pathways. The enzymes differently discriminate mismatches in the nicked DNA, depending on their identity and position, but are both more selective against the 3'-end non-complementarity. LigIIIα is less active than LigI in premature ligation of one-nucleotide gapped DNA and more efficiently discriminates misinsertion products of DNA polymerase β-catalyzed gap filling, that reinforces a leading role of LigIIIα in the accuracy of short-patch BER. LigI and LigIIIα reseal the intermediate of long-patch BER containing an incised synthetic AP site (F) with different efficiencies, depending on the DNA sequence context, 3'-end mismatch presence and coupling of the ligation reaction with DNA repair synthesis. Processing of this intermediate in the absence of flap endonuclease 1 generates non-canonical DNAs with bulged F site, which are very inefficiently repaired by AP endonuclease 1 and represent potential mutagenic repair products. The extent of conversion of the 5'-adenylated intermediates of specific and nonspecific substrates is revealed to depend on the DNA sequence context; a higher sensitivity of LigI to the sequence is in line with the enzyme structural feature of DNA binding. LigIIIα exceeds LigI in generation of potential abortive ligation products, justifying importance of XRCC1-mediated coordination of LigIIIα and aprataxin activities for the efficient DNA repair.
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Affiliation(s)
- Nina A Moor
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Inna A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia.
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Laverde EE, Polyzos AA, Tsegay PP, Shaver M, Hutcheson JD, Balakrishnan L, McMurray CT, Liu Y. Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair. Genes (Basel) 2022; 14:genes14010098. [PMID: 36672839 PMCID: PMC9859040 DOI: 10.3390/genes14010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.
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Affiliation(s)
- Eduardo E. Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Aris A. Polyzos
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pawlos P. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana-Purdue University, Indianapolis, IN 46202, USA
| | - Cynthia T. McMurray
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
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Jiang Z, Lai Y, Beaver JM, Tsegay PS, Zhao ML, Horton JK, Zamora M, Rein HL, Miralles F, Shaver M, Hutcheson JD, Agoulnik I, Wilson SH, Liu Y. Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase. Cells 2020; 9:E225. [PMID: 31963223 PMCID: PMC7016758 DOI: 10.3390/cells9010225] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
DNA damage and base excision repair (BER) are actively involved in the modulation of DNA methylation and demethylation. However, the underlying molecular mechanisms remain unclear. In this study, we seek to understand the mechanisms by exploring the effects of oxidative DNA damage on the DNA methylation pattern of the tumor suppressor breast cancer 1 (BRCA1) gene in the human embryonic kidney (HEK) HEK293H cells. We found that oxidative DNA damage simultaneously induced DNA demethylation and generation of new methylation sites at the CpGs located at the promoter and transcribed regions of the gene ranging from -189 to +27 in human cells. We demonstrated that DNA damage-induced demethylation was mediated by nucleotide misincorporation by DNA polymerase β (pol β). Surprisingly, we found that the generation of new DNA methylation sites was mediated by coordination between pol β and the de novo DNA methyltransferase, DNA methyltransferase 3b (DNMT3b), through the interaction between the two enzymes in the promoter and encoding regions of the BRCA1 gene. Our study provides the first evidence that oxidative DNA damage can cause dynamic changes in DNA methylation in the BRCA1 gene through the crosstalk between BER and de novo DNA methylation.
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Affiliation(s)
- Zhongliang Jiang
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Jill M. Beaver
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Julie K. Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Marco Zamora
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Hayley L. Rein
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Frank Miralles
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA; (M.S.); (J.D.H.)
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA; (M.S.); (J.D.H.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
| | - Irina Agoulnik
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
- Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; (M.-L.Z.); (J.K.H.); (S.H.W.)
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA; (Z.J.); (J.M.B.); (P.S.T.)
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (Y.L.); (M.Z.); (H.L.R.); (F.M.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA;
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Hossain MA, Lin Y, Yan S. Single-Strand Break End Resection in Genome Integrity: Mechanism and Regulation by APE2. Int J Mol Sci 2018; 19:ijms19082389. [PMID: 30110897 PMCID: PMC6122073 DOI: 10.3390/ijms19082389] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/07/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
DNA single-strand breaks (SSBs) occur more than 10,000 times per mammalian cell each day, representing the most common type of DNA damage. Unrepaired SSBs compromise DNA replication and transcription programs, leading to genome instability. Unrepaired SSBs are associated with diseases such as cancer and neurodegenerative disorders. Although canonical SSB repair pathway is activated to repair most SSBs, it remains unclear whether and how unrepaired SSBs are sensed and signaled. In this review, we propose a new concept of SSB end resection for genome integrity. We propose a four-step mechanism of SSB end resection: SSB end sensing and processing, as well as initiation, continuation, and termination of SSB end resection. We also compare different mechanisms of SSB end resection and DSB end resection in DNA repair and DNA damage response (DDR) pathways. We further discuss how SSB end resection contributes to SSB signaling and repair. We focus on the mechanism and regulation by APE2 in SSB end resection in genome integrity. Finally, we identify areas of future study that may help us gain further mechanistic insight into the process of SSB end resection. Overall, this review provides the first comprehensive perspective on SSB end resection in genome integrity.
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Affiliation(s)
- Md Akram Hossain
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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Guo J, Zhang CD, An JX, Xiao YY, Shao S, Zhou NM, Dai DQ. Expression of miR-634 in gastric carcinoma and its effects on proliferation, migration, and invasion of gastric cancer cells. Cancer Med 2018; 7:776-787. [PMID: 29464926 PMCID: PMC5852365 DOI: 10.1002/cam4.1204] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/24/2017] [Accepted: 08/25/2017] [Indexed: 12/18/2022] Open
Abstract
This study aims to observe the expression of microRNA (miR)‐634 in different gastric cancer cell lines and tissues, and to study the effects of miR‐634 on the proliferation, migration, and invasion of the gastric cancer cells. The miR‐634 mimics and miR‐634 inhibitors were transfected by lentivirus into human gastric cancer SGC‐7901 and MGC‐803 cells, and the miR‐634 cells without transfection were used as the control group (NC group). The expression of miR‐634 in the transfected cells was detected by qRT‐PCR. Cell viability was measured by the CCK8 assay. The migration and invasion ability of the cells were detected by scratch assays and Transwell® chamber assays, respectively, and the luciferase assay verified the binding of miR‐634 to the target gene JAG1. The expression level of miR‐634 in gastric cancer tissues and cell lines was significantly lower than that in normal adjacent tissues and control cells. The survival of cells was significantly decreased, and number of cells migrating and invading was decreased in the miR‐634 mimics group. However, in the miR‐634 inhibitor group, the opposite results were observed. Over‐expression of miR‐634 inhibited the proliferation, migration, and invasion of gastric cancer cell lines, and the miR‐634 target gene was JAG1.
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Affiliation(s)
- Jiao Guo
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Chun-Dong Zhang
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Jia-Xiang An
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Yun-Yun Xiao
- Department of Obstetrics and Gynecology, the Shengjing Affiliated Hospital of China Medical University, Shenyang, 110004, China
| | - Shuai Shao
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Nuo-Ming Zhou
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China.,Cancer Center, the Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
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