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An L, Li Y, Fan Y, He N, Ran F, Qu H, Wang Y, Zhao X, Ye C, Jiang Y, Fang X, Hang H. The Trends in Global Gene Expression in Mouse Embryonic Stem Cells During Spaceflight. Front Genet 2019; 10:768. [PMID: 31552089 PMCID: PMC6743352 DOI: 10.3389/fgene.2019.00768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/19/2019] [Indexed: 02/06/2023] Open
Abstract
The environment in space differs greatly from the environment on the ground. Spaceflight causes a number of physiological changes in astronauts, such as bone loss and immune system dysregulation. These effects threaten astronauts’ space missions, and understanding the underlying cellular and molecular mechanisms is important to manage the risks of space missions. The biological effects of spaceflight on mammalian cells, especially with regards to DNA damage, have attracted much attention. Rad9−/− mouse embryonic stem cells (mESCs) are known to be extremely sensitive to DNA damage agents. In this study, a project of the SJ-10 satellite programme, we investigated the gene expression profiles of both Rad9−/− mESCs and Rad9+/+ (wild-type) mESCs in space with a focus on genes critical for inducing, preventing, or repairing genomic DNA lesions. We found that spaceflight downregulated more genes than it upregulated in both wild-type and Rad9−/− mESCs, indicating a suppressive effect of spaceflight on global gene expression. In contrast, Rad9 deletion upregulated more genes than it downregulated. Of note, spaceflight mainly affected organ development and influenced a wide range of cellular functions in mESCs, while Rad9 deletion mainly affected the development and function of the hematological system, especially the development, differentiation and function of immune cells. The patterns of gene expression in mouse embryonic stem cells in space is distinct from those in other types of cells. In addition, both spaceflight and Rad9 deletion downregulated DNA repair genes, suggesting a possibility that spaceflight has negative effects on genome for embryonic stem cells and the effects are likely worsen when the genome maintenance mechanism is defective.
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Affiliation(s)
- Lili An
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanming Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Yingjun Fan
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ning He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Fanlei Ran
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hongzhu Qu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yanqiu Wang
- Center for Space Science and Applied Research, Chinese Academy of Sciences, Beijing, China
| | - Xuetong Zhao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Ye
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanda Jiang
- Center for Space Science and Applied Research, Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haiying Hang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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2
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Shultz AJ, Sackton TB. Immune genes are hotspots of shared positive selection across birds and mammals. eLife 2019; 8:e41815. [PMID: 30620335 PMCID: PMC6338464 DOI: 10.7554/elife.41815] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/08/2019] [Indexed: 12/16/2022] Open
Abstract
Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across a group of species. We use alignments of orthologous protein-coding genes from 39 species of birds to estimate parameters related to positive selection for 11,000 genes conserved across birds. We show that functional pathways related to the immune system, recombination, lipid metabolism, and phototransduction are enriched for positively selected genes. By comparing our results with mammalian data, we find a significant enrichment for positively selected genes shared between taxa, and that these shared selected genes are enriched for viral immune pathways. Using pathogen-challenge transcriptome data, we show that genes up-regulated in response to pathogens are also enriched for positively selected genes. Together, our results suggest that pathogens, particularly viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time.
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Affiliation(s)
- Allison J Shultz
- Informatics GroupHarvard UniversityCambridgeUnited States
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeUnited States
- Museum of Comparative ZoologyHarvard UniversityCambridgeUnited States
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3
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Li R, Wang W, Li F, Wang Q, Wang S, Xu Y, Chen F. Response of alternative splice isoforms of OsRad9 gene from Oryza sativa to environmental stress. ACTA ACUST UNITED AC 2017; 72:325-334. [DOI: 10.1515/znc-2016-0257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/11/2017] [Indexed: 12/16/2022]
Abstract
Abstract
Rad9 protein plays an important role in cell-cycle checkpoint signal transduction in human and yeast cells, but knowledge about Rad9 in plants is limited. This study reports that the Rad9 gene of rice can generate the transcript products OsRad9.1 and OsRad9.2 through alternative splicing. OsRad9.1, with all nine exons, is the main cell-cycle checkpoint protein involved in the response of rice to genotoxic stresses (ultraviolet radiation and antibiotic stress), environmental stresses (drought, salt, and heavy metal stress), and auxin stimuli (2,4-D, IAA, and IBA). Meanwhile, transcript isoform OsRad9.2, which lost exon7 and exon8, showed different preferential stimulation effects on these stresses and pollen development duration. These results might indicat that besides the monitoring and repair of DNA damage, Rad9 might involve in the development of pollen.
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Affiliation(s)
- Rui Li
- College of Pharmacy and Biological Engineering , Chengdu University , 1 Shiling , Chengdu 610106 , China
| | - Wenguo Wang
- Biogas Institute of Ministry of Agriculture , Chengdu 610041 , China
| | - Fosheng Li
- Key Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu 610064 , China
| | - Qingwei Wang
- Key Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu 610064 , China
| | - Shenghua Wang
- Key Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu 610064 , China
| | - Ying Xu
- Key Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu 610064 , China , Tel.: +86 28 85417281, Fax: 86 028 85417281
| | - Fang Chen
- Key Lab of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science , Sichuan University , Chengdu 610064 , China
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4
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Huang L, Wang ZB, Qi ST, Ma XS, Liang QX, Lei G, Meng TG, Liang LF, Xian YX, Hou Y, Sun XF, Zhao Y, Wang WH, Sun QY. Rad9a is required for spermatogonia differentiation in mice. Oncotarget 2016; 7:86350-86358. [PMID: 27861152 PMCID: PMC5349919 DOI: 10.18632/oncotarget.13405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/09/2016] [Indexed: 12/14/2022] Open
Abstract
Spermatogenesis in testes requires precise spermatogonia differentiation. Spermatocytes lacking the Rad9a gene are arrested in pachytene prophase, implying a possible role for RAD9A in spermatogonia differentiation. However, numerous RAD9A-positive pachytene spermatocytes are still observed in mouse testes following Rad9a excision using the Stra8-Cre system, and it is unclear whether Rad9a deletion in spermatogonia interrupts differentiation. Here, we generated a mouse model in which Rad9a was specifically deleted in spermatogonial stem cells (SSCs) using Cre recombinase expression driven by the germ cell-specific Vasa promoter. Adult Rad9a-null male mice were infertile as a result of completely blocked spermatogonia differentiation. No early spermatocytes were detected in mutant testicular cords of 9-day-old mice. Mutant spermatogonia were prone to apoptosis, although proliferation rates were unaffected. Rad9a deletion also resulted in malformation of seminiferous tubules, in which cells assembled irregularly into clusters, and malformation led to testicular cord disruption. Our findings suggest that Rad9a is indispensable for spermatogonia differentiation and testicular development in mice.
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Affiliation(s)
- Lin Huang
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Hospital Affiliated to Guangzhou Medical University, Guangdong, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shu-Tao Qi
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Hospital Affiliated to Guangzhou Medical University, Guangdong, China
| | - Xue-Shan Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qiu-Xia Liang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Guo Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tie-Gang Meng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li-Feng Liang
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Hospital Affiliated to Guangzhou Medical University, Guangdong, China
| | - Ye-Xin Xian
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Hospital Affiliated to Guangzhou Medical University, Guangdong, China
| | - Yi Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Fang Sun
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Hospital Affiliated to Guangzhou Medical University, Guangdong, China
| | - Yong Zhao
- State Key Laboratory of Biomembrane, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei-Hua Wang
- Key Laboratory of Major Obstetrics Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Hospital Affiliated to Guangzhou Medical University, Guangdong, China.,Houston Fertility Institute/Houston Fertility Laboratory, Houston, Texas, USA
| | - Qing-Yuan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
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5
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Ngo GHP, Lydall D. The 9-1-1 checkpoint clamp coordinates resection at DNA double strand breaks. Nucleic Acids Res 2015; 43:5017-32. [PMID: 25925573 PMCID: PMC4446447 DOI: 10.1093/nar/gkv409] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/16/2015] [Indexed: 11/13/2022] Open
Abstract
DNA-end resection, the generation of single-stranded DNA at DNA double strand break (DSB) ends, is critical for controlling the many cellular responses to breaks. Here we show that the conserved DNA damage checkpoint sliding clamp (the 9-1-1 complex) plays two opposing roles coordinating DSB resection in budding yeast. We show that the major effect of 9-1-1 is to inhibit resection by promoting the recruitment of Rad9(53BP1) near DSBs. However, 9-1-1 also stimulates resection by Exo1- and Dna2-Sgs1-dependent nuclease/helicase activities, and this can be observed in the absence of Rad9(53BP1). Our new data resolve the controversy in the literature about the effect of the 9-1-1 complex on DSB resection. Interestingly, the inhibitory role of 9-1-1 on resection is not observed near uncapped telomeres because less Rad9(53BP1) is recruited near uncapped telomeres. Thus, 9-1-1 both stimulates and inhibits resection and the effects of 9-1-1 are modulated by different regions of the genome. Our experiments illustrate the central role of the 9-1-1 checkpoint sliding clamp in the DNA damage response network that coordinates the response to broken DNA ends. Our results have implications in all eukaryotic cells.
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Affiliation(s)
- Greg H P Ngo
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David Lydall
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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6
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Li N, An L, Hang H. Increased sensitivity of DNA damage response-deficient cells to stimulated microgravity-induced DNA lesions. PLoS One 2015; 10:e0125236. [PMID: 25915950 PMCID: PMC4411073 DOI: 10.1371/journal.pone.0125236] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 03/22/2015] [Indexed: 12/02/2022] Open
Abstract
Microgravity is a major stress factor that astronauts have to face in space. In the past, the effects of microgravity on genomic DNA damage were studied, and it seems that the effect on genomic DNA depends on cell types and the length of exposure time to microgravity or simulated microgravity (SMG). In this study we used mouse embryonic stem (MES) and mouse embryonic fibroblast (MEF) cells to assess the effects of SMG on DNA lesions. To acquire the insight into potential mechanisms by which cells resist and/or adapt to SMG, we also included Rad9-deleted MES and Mdc1-deleted MEF cells in addition to wild type cells in this study. We observed significant SMG-induced DNA double strand breaks (DSBs) in Rad9-/- MES and Mdc1-/- MEF cells but not in their corresponding wild type cells. A similar pattern of DNA single strand break or modifications was also observed in Rad9-/- MES. As the exposure to SMG was prolonged, Rad9-/- MES cells adapted to the SMG disturbance by reducing the induced DNA lesions. The induced DNA lesions in Rad9-/- MES were due to SMG-induced reactive oxygen species (ROS). Interestingly, Mdc1-/- MEF cells were only partially adapted to the SMG disturbance. That is, the induced DNA lesions were reduced over time, but did not return to the control level while ROS returned to a control level. In addition, ROS was only partially responsible for the induced DNA lesions in Mdc1-/- MEF cells. Taken together, these data suggest that SMG is a weak genomic DNA stress and can aggravate genomic instability in cells with DNA damage response (DDR) defects.
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Affiliation(s)
- Nan Li
- Key Laboratory for Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lili An
- Key Laboratory for Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (HYH); (LLA)
| | - Haiying Hang
- Key Laboratory for Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (HYH); (LLA)
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7
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Zhang Z, Cai Z, Li K, Fang Y, An L, Hu Z, Wang S, Hang H. The Effect of Ionizing Radiation on mRNA Levels of the DNA Damage Response Genes Rad9, Rad1 and Hus1 in Various Mouse Tissues. Radiat Res 2015; 183:94-104. [DOI: 10.1667/rr13781.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zhenya Zhang
- Department of General Surgery, the Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, 050011 China
| | - Zeyuan Cai
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaiming Li
- Department of General Surgery, the Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, 050011 China
| | - Yu Fang
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili An
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhishang Hu
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haiying Hang
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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8
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Zanotti KJ, Maul RW, Castiblanco DP, Yang W, Choi YJ, Fox JT, Myung K, Saribasak H, Gearhart PJ. ATAD5 deficiency decreases B cell division and Igh recombination. THE JOURNAL OF IMMUNOLOGY 2014; 194:35-42. [PMID: 25404367 DOI: 10.4049/jimmunol.1401158] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mammalian ATPase family AAA domain-containing protein 5 (ATAD5) and its yeast homolog enhanced level of genomic instability 1 are responsible for unloading proliferating cell nuclear antigen from newly synthesized DNA. Prior work in HeLa and yeast cells showed that a decrease in ATAD5 protein levels resulted in accumulation of chromatin-bound proliferating cell nuclear antigen, slowed cell division, and increased genomic instability. In this study, B cells from heterozygous (Atad5(+/m)) mice were used to examine the effects of decreased cell proliferation on Ab diversity. ATAD5 haploinsufficiency did not change the frequency or spectrum of somatic hypermutation in Ab genes, indicating that DNA repair and error-prone DNA polymerase η usage were unaffected. However, immunized Atad5(+/m) mice had decreased serum IgG1 Abs, demonstrating a functional effect on class switch recombination. The mechanism of this altered immune response was then examined following ex vivo stimulation of splenic B cells, where Atad5(+/m) cells accumulated in the S phase of the cell cycle and had reduced proliferation compared with wild-type cells. These haploinsufficient cells underwent a significant decline in activation-induced deaminase expression, resulting in decreased switch region DNA double-strand breaks and interchromosomal translocations in the Igh locus. Class switch recombination to several isotypes was also reduced in Atad5(+/m) cells, although the types of end-joining pathways were not affected. These results describe a defect in DNA replication that affects Igh recombination via reduced cell division.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; and
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; and
| | - Diana P Castiblanco
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; and
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; and
| | - Yong Jun Choi
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jennifer T Fox
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kyungjae Myung
- Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; and
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224; and
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9
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Agustina L, Hahm SH, Han SH, Tran AHV, Chung JH, Park JH, Park JW, Han YS. Visualization of the physical and functional interaction between hMYH and hRad9 by Dronpa bimolecular fluorescence complementation. BMC Mol Biol 2014; 15:17. [PMID: 25127721 PMCID: PMC4151078 DOI: 10.1186/1471-2199-15-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/04/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Human MutY glycosylase homolog (hMYH), a component of the base excision repair pathway, is responsible for the generation of apurinic/apyrimidinic sites. Rad9-Rad1-Hus1 (9-1-1) is a heterotrimeric protein complex that plays a role in cell cycle checkpoint control and DNA repair. In humans, hMYH and 9-1-1 interact through Hus1 and to a lesser degree with Rad1 in the presence of DNA damage. In Saccharomyces pombe, each component of the 9-1-1 complex interacts directly with SpMYH. The glycosylase activity of hMYH is stimulated by Hus1 and the 9-1-1 complex and enhanced by DNA damage treatment. Cells respond to different stress conditions in different manners. Therefore, we investigated whether Rad9 interacted with hMYH under different stresses. Here, we identified and visualized the interaction between hRad9 and hMYH and investigated the functional consequences of this interaction. RESULTS Co-IP and BiFC indicates that hMYH interacts with hRad9. As shown by GST-pull down assay, this interaction is direct. Furthermore, BiFC with deletion mutants of hMYH showed that hRad9 interacts with N-terminal region of hMYH. The interaction was enhanced by hydroxyurea (HU) treatment. mRNA and protein levels of hMYH and hRad9 were increased following HU treatment. A marked increase in p-Chk1 (S345) and p-Cdk2 (T14, Y15) was observed. But this phosphorylation decreased in siMYH- or siRad9-transfected cells, and more pronounced decrease observed in co-transfected cells. CONCLUSIONS Our data reveal that hRad9 interacts directly with N-terminal region of hMYH. This interaction is enhanced by HU treatment. Knockdown of one or both protein result in decreasing Chk1 and Cdk2 phosphorylation. Since both protein functions in the early detection of DNA damage, we suggest that this interaction occurs early in DNA damage pathway.
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Affiliation(s)
- Lia Agustina
- Department of Advanced Technology Fusion, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Soo-Hyun Hahm
- Department of Advanced Technology Fusion, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Se Hee Han
- Department of Advanced Technology Fusion, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - An Hue Vy Tran
- Department of Advanced Technology Fusion, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
| | - Ji Hyung Chung
- Department of Applied Bioscience, College of Life Science, CHA University, Gyeonggi-do 463-836, Korea
| | - Jong-Hwa Park
- Department of Genetic Engineering and Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Jin Woo Park
- BioActs, DKC Corporation, 693-2 Gojan-dong, Namdong-gu, Incheon 405-820, Korea
| | - Ye Sun Han
- Department of Advanced Technology Fusion, Konkuk University, 1 Hwayang-dong, Gwangjin-gu, Seoul 143-701, Korea
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10
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Ngo GHP, Balakrishnan L, Dubarry M, Campbell JL, Lydall D. The 9-1-1 checkpoint clamp stimulates DNA resection by Dna2-Sgs1 and Exo1. Nucleic Acids Res 2014; 42:10516-28. [PMID: 25122752 PMCID: PMC4176354 DOI: 10.1093/nar/gku746] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) at DNA ends is an important regulator of the DNA damage response. Resection, the generation of ssDNA, affects DNA damage checkpoint activation, DNA repair pathway choice, ssDNA-associated mutation and replication fork stability. In eukaryotes, extensive DNA resection requires the nuclease Exo1 and nuclease/helicase pair: Dna2 and Sgs1BLM. How Exo1 and Dna2-Sgs1BLM coordinate during resection remains poorly understood. The DNA damage checkpoint clamp (the 9-1-1 complex) has been reported to play an important role in stimulating resection but the exact mechanism remains unclear. Here we show that the human 9-1-1 complex enhances the cleavage of DNA by both DNA2 and EXO1 in vitro, showing that the resection-stimulatory role of the 9-1-1 complex is direct. We also show that in Saccharomyces cerevisiae, the 9-1-1 complex promotes both Dna2-Sgs1 and Exo1-dependent resection in response to uncapped telomeres. Our results suggest that the 9-1-1 complex facilitates resection by recruiting both Dna2-Sgs1 and Exo1 to sites of resection. This activity of the 9-1-1 complex in supporting resection is strongly inhibited by the checkpoint adaptor Rad953BP1. Our results provide important mechanistic insights into how DNA resection is regulated by checkpoint proteins and have implications for genome stability in eukaryotes.
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Affiliation(s)
- Greg H P Ngo
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Marion Dubarry
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Judith L Campbell
- Divisions of Biology and Chemistry, Caltech, Braun Laboratories, Pasadena, CA 91125, USA
| | - David Lydall
- Institute for Cell and Molecular Biosciences (ICaMB), Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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11
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Lyndaker AM, Vasileva A, Wolgemuth DJ, Weiss RS, Lieberman HB. Clamping down on mammalian meiosis. Cell Cycle 2013; 12:3135-45. [PMID: 24013428 DOI: 10.4161/cc.26061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The RAD9A-RAD1-HUS1 (9-1-1) complex is a PCNA-like heterotrimeric clamp that binds damaged DNA to promote cell cycle checkpoint signaling and DNA repair. While various 9-1-1 functions in mammalian somatic cells have been established, mounting evidence from lower eukaryotes predicts critical roles in meiotic germ cells as well. This was investigated in 2 recent studies in which the 9-1-1 complex was disrupted specifically in the mouse male germline through conditional deletion of Rad9a or Hus1. Loss of these clamp subunits led to severely impaired fertility and meiotic defects, including faulty DNA double-strand break repair. While 9-1-1 is critical for ATR kinase activation in somatic cells, these studies did not reveal major defects in ATR checkpoint pathway signaling in meiotic cells. Intriguingly, this new work identified separable roles for 9-1-1 subunits, namely RAD9A- and HUS1-independent roles for RAD1. Based on these studies and the high-level expression of the paralogous proteins RAD9B and HUS1B in testis, we propose a model in which multiple alternative 9-1-1 clamps function during mammalian meiosis to ensure genome maintenance in the germline.
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Affiliation(s)
- Amy M Lyndaker
- Department of Biomedical Sciences; Cornell University; Ithaca, NY USA
| | - Ana Vasileva
- Center for Radiological Research; College of Physicians and Surgeons; Columbia University Medical Center; New York, NY USA
| | - Debra J Wolgemuth
- Genetics & Development and Obstetrics & Gynecology; The Institute of Human Nutrition; Herbert Irving Comprehensive Cancer Center; Columbia University Medical Center; New York, NY USA
| | - Robert S Weiss
- Department of Biomedical Sciences; Cornell University; Ithaca, NY USA
| | - Howard B Lieberman
- Department of Environmental Health Sciences; Mailman School of Public Health; Columbia University Medical Center; New York, NY USA
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Abstract
Rad9 plays a crucial role in maintaining genomic stability by regulating cell cycle checkpoints, DNA repair, telomere stability, and apoptosis. Rad9 controls these processes mainly as part of the heterotrimeric 9-1-1 (Rad9-Hus1-Rad1) complex. However, in recent years it has been demonstrated that Rad9 can also act independently of the 9-1-1 complex as a transcriptional factor, participate in immunoglobulin class switch recombination, and show 3'-5' exonuclease activity. Aberrant Rad9 expression has been associated with prostate, breast, lung, skin, thyroid, and gastric cancers. High expression of Rad9 is causally related to, at least, human prostate cancer growth. On the other hand, deletion of Mrad9, the mouse homolog, is responsible for increased skin cancer incidence. These results reveal that Rad9 can act as an oncogene or tumor suppressor. Which of the many functions of Rad9 are causally related to initiation and progression of tumorigenesis and the mechanistic details by which Rad9 induces or suppresses tumorigenesis are presently not known, but are crucial for the development of targeted therapeutic interventions.
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Affiliation(s)
- Constantinos G Broustas
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
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Ronald S, Sunavala-Dossabhoy G, Adams L, Williams B, De Benedetti A. The expression of Tousled kinases in CaP cell lines and its relation to radiation response and DSB repair. Prostate 2011; 71:1367-73. [PMID: 21647934 DOI: 10.1002/pros.21358] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 01/14/2011] [Indexed: 12/22/2022]
Abstract
BACKGROUND The Tousled-like kinases (TLKs) function in processes of chromatin assembly, including replication, transcription, repair, and chromosome segregation. TLK1/1B interacts specifically with the chromatin assembly factor Asf1, a histone H3-H4 chaperone, and with Rad9, a protein involved in DNA repair, and these interactions are believed to be responsible for the action of TLKs in double-strand break repair and radioprotection. METHODS Western blotting and RT-PCR were used to analyze the expression of TLK1, TLK1B, and TLK2 in a panel of prostate cancer (CaP) cell lines. The pattern of radiotolerance in the cell lines was analyzed in parallel. DU145 and PC-3 cells were also probed with assays utilizing transfected plasmids that could be cleaved in vivo with adeno-expressed HO nuclease to assess the potential contribution of TLK1/1B in DSB repair. RESULTS This is the first report of TLKs' expression in a panel of CaP cell lines and their relationship to radioresistance. Furthermore, expression of TLK1B in non-expressing PC-3 cells rendered them highly resistant to radiation, and conversely, knockdown to TLK1/1B in expressing DU145 reduced their radiotolerance. CONCLUSIONS TLKs appear to be intimately linked to the pattern of resistance to DNA damage, and specifically DSBs, a finding that was not reported before for any cell lines, and certainly not systematically for human prostate cell lines.
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Affiliation(s)
- Sharon Ronald
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130-3932, USA
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14
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Lieberman HB, Bernstock JD, Broustas CG, Hopkins KM, Leloup C, Zhu A. The role of RAD9 in tumorigenesis. J Mol Cell Biol 2011; 3:39-43. [PMID: 21278450 DOI: 10.1093/jmcb/mjq039] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
RAD9 regulates multiple cellular processes that influence genomic integrity, and for at least some of its functions the protein acts as part of a heterotrimeric complex bound to HUS1 and RAD1 proteins. RAD9 participates in DNA repair, including base excision repair, homologous recombination repair and mismatch repair, multiple cell cycle phase checkpoints and apoptosis. In addition, functions including the transactivation of downstream target genes, immunoglobulin class switch recombination, as well as 3'-5' exonuclease activity have been reported. Aberrant RAD9 expression has been linked to breast, lung, thyroid, skin and prostate tumorigenesis, and a cause-effect relationship has been demonstrated for the latter two. Interestingly, human RAD9 overproduction correlates with prostate cancer whereas deletion of Mrad9, the corresponding mouse gene, in keratinocytes leads to skin cancer. These results reveal that RAD9 protein can function as an oncogene or tumor suppressor, and aberrantly high or low levels can have deleterious health consequences. It is not clear which of the many functions of RAD9 is critical for carcinogenesis, but several alternatives are considered herein and implications for the development of novel cancer therapies based on these findings are examined.
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Affiliation(s)
- Howard B Lieberman
- Center for Radiological Research, Columbia University College of Physicians and Surgeons, 630 W 168th St, New York, NY 10032, USA.
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15
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Targeted deletion of mouse Rad1 leads to deficient cellular DNA damage responses. Protein Cell 2011; 2:410-22. [PMID: 21637962 DOI: 10.1007/s13238-011-1049-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022] Open
Abstract
The Rad1 gene is evolutionarily conserved from yeast to human. The fission yeast Schizosaccharomyces pombe Rad1 ortholog promotes cell survival against DNA damage and is required for G(2)/M checkpoint activation. In this study, mouse embryonic stem (ES) cells with a targeted deletion of Mrad1, the mouse ortholog of this gene, were created to evaluate its function in mammalian cells. Mrad1 (-/-) ES cells were highly sensitive to ultraviolet-light (UV light), hydroxyurea (HU) and gamma rays, and were defective in G(2)/M as well as S/M checkpoints. These data indicate that Mrad1 is required for repairing DNA lesions induced by UV-light, HU and gamma rays, and for mediating G(2)/M and S/M checkpoint controls. We further demonstrated that Mrad1 plays an important role in homologous recombination repair (HRR) in ES cells, but a minor HRR role in differentiated mouse cells.
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Wit N, Krijger PHL, van den Berk PCM, Jacobs H. Lysine residue 185 of Rad1 is a topological but not a functional counterpart of lysine residue 164 of PCNA. PLoS One 2011; 6:e16669. [PMID: 21304913 PMCID: PMC3031632 DOI: 10.1371/journal.pone.0016669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 01/10/2011] [Indexed: 12/11/2022] Open
Abstract
Monoubiquitylation of the homotrimeric DNA sliding clamp PCNA at lysine residue 164 (PCNAK164) is a highly conserved, DNA damage-inducible process that is mediated by the E2/E3 complex Rad6/Rad18. This ubiquitylation event recruits translesion synthesis (TLS) polymerases capable of replicating across damaged DNA templates. Besides PCNA, the Rad6/Rad18 complex was recently shown in yeast to ubiquitylate also 9-1-1, a heterotrimeric DNA sliding clamp composed of Rad9, Rad1, and Hus1 in a DNA damage-inducible manner. Based on the highly similar crystal structures of PCNA and 9-1-1, K185 of Rad1 (Rad1K185) was identified as the only topological equivalent of PCNAK164. To investigate a potential role of posttranslational modifications of Rad1K185 in DNA damage management, we here generated a mouse model with a conditional deletable Rad1K185R allele. The Rad1K185 residue was found to be dispensable for Chk1 activation, DNA damage survival, and class switch recombination of immunoglobulin genes as well as recruitment of TLS polymerases during somatic hypermutation of immunoglobulin genes. Our data indicate that Rad1K185 is not a functional counterpart of PCNAK164.
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Affiliation(s)
- Niek Wit
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Peter H. L. Krijger
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Heinz Jacobs
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- * E-mail:
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