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Kumari A, Yadav A, Lahiri I. Transient State Kinetics of Plasmodium falciparum Apicoplast DNA Polymerase Suggests the Involvement of Accessory Factors for Efficient and Accurate DNA Synthesis. Biochemistry 2022; 61:2319-2333. [PMID: 36251801 DOI: 10.1021/acs.biochem.2c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plasmodium, the causative agent of malaria, belongs to the phylum Apicomplexa. Most apicomplexans, including Plasmodium, contain an essential nonphotosynthetic plastid called the apicoplast that harbors its own genome that is replicated by a dedicated organellar replisome. This replisome employs a single DNA polymerase (apPol), which is expected to perform both replicative and translesion synthesis. Unlike other replicative polymerases, no processivity factor for apPol has been identified. While preliminary structural and biochemical studies have provided an overall characterization of apPol, the kinetic mechanism of apPol's activity remains unknown. We have used transient state methods to determine the kinetics of replicative and translesion synthesis by apPol and show that apPol has low processivity and efficiency while copying undamaged DNA. Moreover, while apPol can bypass oxidatively damaged lesions, the bypass is error-prone. Taken together, our results raise the following question─how does a polymerase with low processivity, efficiency, and fidelity (for translesion synthesis) faithfully replicate the apicoplast organellar DNA within the hostile environment of the human host? We hypothesize that interactions with putative components of the apicoplast replisome and/or an as-yet-undiscovered processivity factor transform apPol into an efficient and accurate enzyme.
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Affiliation(s)
- Anamika Kumari
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Anjali Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India
| | - Indrajit Lahiri
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Punjab 140306, India.,Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, U.K
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2
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Zhang S, Xiao X, Kong J, Lu K, Dou SX, Wang PY, Ma L, Liu Y, Li G, Li W, Zhang H. DNA polymerase Gp90 activities and regulations on strand displacement DNA synthesis revealed at single-molecule level. FASEB J 2021; 35:e21607. [PMID: 33908664 DOI: 10.1096/fj.202100033rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/18/2021] [Accepted: 04/05/2021] [Indexed: 11/11/2022]
Abstract
Strand displacement DNA synthesis (SDDS) is an essential step in DNA replication. With magnetic tweezers, we investigated SDDS kinetics of wild-type gp90 and its exonuclease-deficient polymerase gp90 exo- at single-molecule level. A novel binding state of gp90 to the fork flap was confirmed prior to SDDS, suggesting an intermediate in the initiation of SDDS. The rate and processivity of SDDS by gp90 exo- or wt-gp90 are increased with force and dNTP concentration. The rate and processivity of exonuclease by wt-gp90 are decreased with force. High GC content decreases SDDS and exonuclease processivity but increases exonuclease rate for wt-gp90. The high force and dNTP concentration and low GC content facilitate the successive SDDS but retard the successive exonuclease for wt-gp90. Furthermore, increasing GC content accelerates the transition from SDDS or exonuclease to exonuclease. This work reveals the kinetics of SDDS in detail and offers a broader cognition on the regulation of various factors on SDDS at single-polymerase level.
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Affiliation(s)
- Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Xue Xiao
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingwei Kong
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ke Lu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuo-Xing Dou
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Ye Wang
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Songshan Lake Materials Laboratory, Dongguan, China
| | - Lu Ma
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yuru Liu
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,Songshan Lake Materials Laboratory, Dongguan, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, China.,Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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3
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Zhang H. Mechanisms of mutagenesis induced by DNA lesions: multiple factors affect mutations in translesion DNA synthesis. Crit Rev Biochem Mol Biol 2020; 55:219-251. [PMID: 32448001 DOI: 10.1080/10409238.2020.1768205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental mutagens lead to mutagenesis. However, the mechanisms are very complicated and not fully understood. Environmental mutagens produce various DNA lesions, including base-damaged or sugar-modified DNA lesions, as well as epigenetically modified DNA. DNA polymerases produce mutation spectra in translesion DNA synthesis (TLS) through misincorporation of incorrect nucleotides, frameshift deletions, blockage of DNA replication, imbalance of leading- and lagging-strand DNA synthesis, and genome instability. Motif or subunit in DNA polymerases further affects the mutations in TLS. Moreover, protein interactions and accessory proteins in DNA replisome also alter mutations in TLS, demonstrated by several representative DNA replisomes. Finally, in cells, multiple DNA polymerases or cellular proteins collaborate in TLS and reduce in vivo mutagenesis. Summaries and perspectives were listed. This review shows mechanisms of mutagenesis induced by DNA lesions and the effects of multiple factors on mutations in TLS in vitro and in vivo.
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Affiliation(s)
- Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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4
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Mi C, Zhang S, Huang W, Dai M, Chai Z, Yang W, Deng S, Ao L, Zhang H. Strand displacement DNA synthesis by DNA polymerase gp90 exo - of Pseudomonas aeruginosa phage 1. Biochimie 2020; 170:73-87. [PMID: 31911177 DOI: 10.1016/j.biochi.2019.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/31/2019] [Indexed: 12/27/2022]
Abstract
Strand displacement DNA synthesis is essential for DNA replication. Gp90, the sole DNA polymerase of Pseudomonas aeruginosa phage 1, can bypass multiply DNA lesions. However, whether it can perform strand displacement synthesis is still unknown. In this work, we found that gp90 exo- could perform strand displacement synthesis, albeit its activity and processivity were lower than those of primer extension. Gp90 exo- itself could not unwind Y-shaped or fork DNA. Tail and gap at DNA fork were necessary for efficient synthesis. High GC content obviously inhibited strand displacement synthesis. Consecutive GC sequence at the entrance of fork showed more inhibition effect on DNA synthesis than that in the downstream DNA fork. The fraction of productive polymerase and DNA complex (A values) was higher for fork than gap; while their average extension rates (kp values) were similar. However, both A and kp values were lower than those for the primer/template (P/T) substrate. The binding of gp90 exo- to fork was tighter than P/T or gap in the absence of dATP. In the presence of dATP to form ternary complex, the binding affinity of gp90 exo- to P/T or gap was increased compared with that in the binary complex. Abasic site, 8-oxoG, and O6-MeG inhibited and even blocked strand displacement synthesis. This work shows that gp90 exo- could perform strand displacement DNA synthesis at DNA fork, discovering the presence of new functions of PaP1 DNA polymerase in DNA replication and propagation of PaP1.
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Affiliation(s)
- Chenyang Mi
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenxin Huang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengyuan Dai
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Zili Chai
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Wang Yang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Shanshan Deng
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500, China
| | - Lin Ao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing, PR China.
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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Zhang S, Li B, Du K, Liang T, Dai M, Huang W, Zhang H, Ling Y, Zhang H. Epigenetically modified N6-methyladenine inhibits DNA replication by human DNA polymerase iota. Biochimie 2020; 168:134-143. [DOI: 10.1016/j.biochi.2019.10.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
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Zou Z, Liang T, Xu Z, Xie J, Zhang S, Chen W, Wan S, Ling Y, Zhang H. Protein interactions in T7 DNA replisome inhibit the bypass of abasic site by DNA polymerase. Mutagenesis 2019; 34:355-361. [PMID: 31318416 DOI: 10.1093/mutage/gez013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/14/2019] [Indexed: 11/13/2022] Open
Abstract
Abasic site as a common DNA lesion blocks DNA replication and is highly mutagenic. Protein interactions in T7 DNA replisome facilitate DNA replication and translesion DNA synthesis. However, bypass of an abasic site by T7 DNA replisome has never been investigated. In this work, we used T7 DNA replisome and T7 DNA polymerase alone as two models to study DNA replication on encountering an abasic site. Relative to unmodified DNA, abasic site strongly inhibited primer extension and completely blocked strand-displacement DNA synthesis, due to the decreased fraction of enzyme-DNA productive complex and the reduced average extension rates. Moreover, abasic site at DNA fork inhibited the binding of DNA polymerase or helicase onto fork and the binding between polymerase and helicase at fork. Notably and unexpectedly, we found DNA polymerase alone bypassed an abasic site on primer/template (P/T) substrate more efficiently than did polymerase and helicase complex bypass it at fork. The presence of gp2.5 further inhibited the abasic site bypass at DNA fork. Kinetic analysis showed that this inhibition at fork relative to that on P/T was due to the decreased fraction of productive complex instead of the average extension rates. Therefore, we found that protein interactions in T7 DNA replisome inhibited the bypass of DNA lesion, different from all the traditional concept that protein interactions or accessory proteins always promote DNA replication and DNA damage bypass, providing new insights in translesion DNA synthesis performed by DNA replisome.
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Affiliation(s)
- Zhenyu Zou
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Tingting Liang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhongyan Xu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayu Xie
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Weina Chen
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Siqi Wan
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.,The Key Laboratory of Environment and Health Among Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
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7
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Epigenetic DNA modification N6-methyladenine inhibits DNA replication by Sulfolobus solfataricus Y-family DNA polymerase Dpo4. Arch Biochem Biophys 2019; 675:108120. [DOI: 10.1016/j.abb.2019.108120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 12/18/2022]
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8
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Li B, Du K, Gu S, Xie J, Liang T, Xu Z, Gao H, Ling Y, Lu S, Sun Z, Zhang H. Epigenetic DNA Modification N 6-Methyladenine Inhibits DNA Replication by DNA Polymerase of Pseudomonas aeruginosa Phage PaP1. Chem Res Toxicol 2019; 32:840-849. [PMID: 30938985 DOI: 10.1021/acs.chemrestox.8b00348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
N6-methyladenine (6mA), a newly identified epigenetic modification, plays important roles in regulation of various biological processes. However, the effect of 6mA on DNA replication has been little addressed. In this work, we investigated how 6mA affected DNA replication by DNA polymerase of Pseudomonas aeruginosa Phage PaP1 (gp90 exo-). The presence of 6mA, as well as its intermediate hypoxanthine (Hyp), inhibited DNA replication by gp90 exo-. The 6mA reduced dTTP incorporation efficiency by 10-fold and inhibited next-base extension efficiency by 100-fold. Differently, dCTP was preferentially incorporated opposite Hyp among four dNTPs. Gp90 exo- reduced the extension priority beyond the 6mA:T pair rather than the 6mA:C mispair and preferred to extend beyond Hyp:C rather than the Hyp:T pair. Incorporation of dTTP opposite 6mA and dCTP opposite Hyp showed fast burst phases. The burst rate and burst amplitude were both reduced for 6mA compared with unmodified A. Moreover, the total incorporation efficiency ( kpol/ Kd,dNTP) was decreased for dTTP incorporation opposite 6mA and dCTP incorporation opposite Hyp compared with dTTP incorporation opposite A. 6mA reduced the incorporation rate ( kpol), and Hyp increased the dissociation constant ( Kd,dNTP). However, 6mA or Hyp on template did not affect the binding of DNA polymerase to DNA in binary or ternary complexes. This work provides new insight into the inhibited effects of epigenetic modification of 6mA on DNA replication in PaP1.
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Affiliation(s)
- Bianbian Li
- School of Biological Engineering , Dalian Polytechnic University , Dalian , 116034 , China.,Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Ke Du
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Shiling Gu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Jiayu Xie
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Tingting Liang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Zhongyan Xu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
| | - Hui Gao
- School of Biological Engineering , Dalian Polytechnic University , Dalian , 116034 , China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis , Guangzhou Medical University , Xinzao, Panyu District, Guangzhou , China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Science , Third Military Medical University , Chongqing , China
| | - Zhen Sun
- School of Biological Engineering , Dalian Polytechnic University , Dalian , 116034 , China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital , Sichuan University , Chengdu , China
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Du K, Zhang X, Zou Z, Li B, Gu S, Zhang S, Qu X, Ling Y, Zhang H. Epigenetically modified N 6-methyladenine inhibits DNA replication by human DNA polymerase η. DNA Repair (Amst) 2019; 78:81-90. [PMID: 30991231 DOI: 10.1016/j.dnarep.2019.03.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 01/06/2023]
Abstract
N6-methyladenine (6mA), as a newly reported epigenetic marker, plays significant roles in regulation of various biological processes in eukaryotes. However, the effect of 6mA on human DNA replication remain elusive. In this work, we used Y-family human DNA polymerase η as a model to investigate the kinetics of bypass of 6mA by hPol η. We found 6mA and its intermediate hypoxanthine (I) on template partially inhibited DNA replication by hPol η. dTMP incorporation opposite 6mA and dCMP incorporation opposite I can be considered as correct incorporation. However, both 6mA and I reduced correct incorporation efficiency, next-base extension efficiency, and the priority in extension beyond correct base pair. Both dTMP incorporation opposite 6mA and dCTP opposite I showed fast burst phases. However, 6mA and I reduced the burst incorporation rates (kpol) and increased the dissociation constant (Kd,dNTP), compared with that of dTMP incorporation opposite unmodified A. Biophysical binding assays revealed that both 6mA and I on template reduced the binding affinity of hPol η to DNA in binary or ternary complex compared with unmodified A. All the results explain the inhibition effects of 6mA and I on DNA replication by hPol η, providing new insight in the effects of epigenetically modified 6mA on human DNA replication.
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Affiliation(s)
- Ke Du
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China; Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiangqian Zhang
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China
| | - Zhenyu Zou
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Bianbian Li
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shiling Gu
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shuming Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoyi Qu
- College of Life Science, Yan´an University, Yan'an, Shaanxi, China
| | - Yihui Ling
- Institute for Chemical Carcinogenesis, Guangzhou Medical University, Xinzao Panyu District, Guangzhou, China
| | - Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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