1
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Bomber ML, Wang J, Liu Q, Barnett KR, Layden HM, Hodges E, Stengel KR, Hiebert SW. Human SMARCA5 is continuously required to maintain nucleosome spacing. Mol Cell 2023; 83:507-522.e6. [PMID: 36630954 PMCID: PMC9974918 DOI: 10.1016/j.molcel.2022.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Genetic models suggested that SMARCA5 was required for DNA-templated events including transcription, DNA replication, and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch complexes in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6 h of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
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Affiliation(s)
- Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kelly R Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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2
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Chung HJ, Lee JR, Kim TM, Kim S, Park K, Kim MJ, Jung E, Kim S, Lee EA, Ra JS, Hwang S, Lee JY, Schärer OD, Kim Y, Myung K, Kim H. ZNF212 promotes genomic integrity through direct interaction with TRAIP. Nucleic Acids Res 2023; 51:631-649. [PMID: 36594163 PMCID: PMC9881131 DOI: 10.1093/nar/gkac1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 01/04/2023] Open
Abstract
TRAIP is a key factor involved in the DNA damage response (DDR), homologous recombination (HR) and DNA interstrand crosslink (ICL) repair. However, the exact functions of TRAIP in these processes in mammalian cells are not fully understood. Here we identify the zinc finger protein 212, ZNF212, as a novel binding partner for TRAIP and find that ZNF212 colocalizes with sites of DNA damage. The recruitment of TRAIP or ZNF212 to sites of DNA damage is mutually interdependent. We show that depletion of ZNF212 causes defects in the DDR and HR-mediated repair in a manner epistatic to TRAIP. In addition, an epistatic analysis of Zfp212, the mouse homolog of human ZNF212, in mouse embryonic stem cells (mESCs), shows that it appears to act upstream of both the Neil3 and Fanconi anemia (FA) pathways of ICLs repair. We find that human ZNF212 interacted directly with NEIL3 and promotes its recruitment to ICL lesions. Collectively, our findings identify ZNF212 as a new factor involved in the DDR, HR-mediated repair and ICL repair though direct interaction with TRAIP.
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Affiliation(s)
| | | | | | | | | | - Myung-Jin Kim
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Eunyoung Jung
- Department of Biological Sciences, Research Institute of Women's Health and Digital Humanity Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea,Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Yonghwan Kim
- Correspondence may also be addressed to Yonghwan Kim. Tel: +82 2 710 9552;
| | - Kyungjae Myung
- Correspondence may also be addressed to Kyungjae Myung. Tel: +82 52 217 5323; Fax: +82 52 217 5519;
| | - Hongtae Kim
- To whom correspondence should be addressed. Tel: +82 52 217 5404; Fax: +82 52 217 5519;
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3
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Min S, Ji JH, Heo Y, Cho H. Transcriptional regulation and chromatin dynamics at DNA double-strand breaks. Exp Mol Med 2022; 54:1705-1712. [PMID: 36229590 PMCID: PMC9636152 DOI: 10.1038/s12276-022-00862-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/29/2022] Open
Abstract
In eukaryotic cells, DNA damage can occur at any time and at any chromatin locus, including loci at which active transcription is taking place. DNA double-strand breaks affect chromatin integrity and elicit a DNA damage response to facilitate repair of the DNA lesion. Actively transcribed genes near DNA lesions are transiently suppressed by crosstalk between DNA damage response factors and polycomb repressive complexes. Epigenetic modulation of the chromatin environment also contributes to efficient DNA damage response signaling and transcriptional repression. On the other hand, RNA transcripts produced in the G1 phase, as well as the active chromatin context of the lesion, appear to drive homologous recombination repair. Here, we discuss how the ISWI family of chromatin remodeling factors coordinates the DNA damage response and transcriptional repression, especially in transcriptionally active regions, highlighting the direct modulation of the epigenetic environment.
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Affiliation(s)
- Sunwoo Min
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Jae-Hoon Ji
- grid.267309.90000 0001 0629 5880Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, Texas, 78229-3000 USA
| | - Yungyeong Heo
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
| | - Hyeseong Cho
- grid.251916.80000 0004 0532 3933Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499 Korea ,grid.251916.80000 0004 0532 3933Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499 Korea
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4
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Ju MK, Lee JR, Choi Y, Park SY, Sul HJ, Chung HJ, An S, Lee S, Jung E, Kim B, Choi BY, Kim BJ, Kim HS, Lim H, Kang HS, Soh JS, Myung K, Kim KC, Cho JW, Seo J, Kim TM, Lee JY, Kim Y, Kim H, Zang DY. PWWP2B promotes DNA end resection and homologous recombination. EMBO Rep 2022; 23:e53492. [PMID: 35582821 PMCID: PMC9253748 DOI: 10.15252/embr.202153492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 04/18/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2023] Open
Abstract
Genome instability is one of the leading causes of gastric cancers. However, the mutational landscape of driver genes in gastric cancer is poorly understood. Here, we investigate somatic mutations in 25 Korean gastric adenocarcinoma patients using whole-exome sequencing and show that PWWP2B is one of the most frequently mutated genes. PWWP2B mutation correlates with lower cancer patient survival. We find that PWWP2B has a role in DNA double-strand break repair. As a nuclear protein, PWWP2B moves to sites of DNA damage through its interaction with UHRF1. Depletion of PWWP2B enhances cellular sensitivity to ionizing radiation (IR) and impairs IR-induced foci formation of RAD51. PWWP2B interacts with MRE11 and participates in homologous recombination via promoting DNA end-resection. Taken together, our data show that PWWP2B facilitates the recruitment of DNA repair machinery to sites of DNA damage and promotes HR-mediated DNA double-strand break repair. Impaired PWWP2B function might thus cause genome instability and promote gastric cancer development.
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Affiliation(s)
- Min Kyung Ju
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Joo Rak Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Yeonsong Choi
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Seon Young Park
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hee Jung Sul
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Hee Jin Chung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Soyeong An
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
| | - Semin Lee
- Department of Biomedical EngineeringUlsan National Institute of Science and TechnologyUlsanKorea
| | - Eunyoung Jung
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Bohyun Kim
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bo Youn Choi
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
| | - Bum Jun Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyeong Su Kim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Hyun Lim
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Ho Suk Kang
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Jae Seung Soh
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Kyungjae Myung
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Kab Choong Kim
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Ji Woong Cho
- Department of SurgeryHallym University Medical CenterHallym University College of MedicineAnyang‐siKorea
| | - Jinwon Seo
- Department of PathologyHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
| | - Tae Moon Kim
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Ja Yil Lee
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Yonghwan Kim
- Department of Biological SciencesResearch Institute of Women’s HealthSookmyung Women's UniversitySeoulKorea
| | - Hongtae Kim
- Department of Biological SciencesUlsan National Institute of Science and TechnologyUlsanKorea
- Center for Genomic Integrity Institute for Basic Science (IBS)UlsanKorea
| | - Dae Young Zang
- Hallym Translational Research InstituteHallym University Sacred Heart HospitalAnyang‐siKorea
- Department of Internal MedicineHallym University Sacred Heart HospitalHallym University College of MedicineAnyang‐siKorea
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5
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Kieffer SR, Lowndes NF. Immediate-Early, Early, and Late Responses to DNA Double Stranded Breaks. Front Genet 2022; 13:793884. [PMID: 35173769 PMCID: PMC8841529 DOI: 10.3389/fgene.2022.793884] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 12/18/2022] Open
Abstract
Loss or rearrangement of genetic information can result from incorrect responses to DNA double strand breaks (DSBs). The cellular responses to DSBs encompass a range of highly coordinated events designed to detect and respond appropriately to the damage, thereby preserving genomic integrity. In analogy with events occurring during viral infection, we appropriate the terms Immediate-Early, Early, and Late to describe the pre-repair responses to DSBs. A distinguishing feature of the Immediate-Early response is that the large protein condensates that form during the Early and Late response and are resolved upon repair, termed foci, are not visible. The Immediate-Early response encompasses initial lesion sensing, involving poly (ADP-ribose) polymerases (PARPs), KU70/80, and MRN, as well as rapid repair by so-called ‘fast-kinetic’ canonical non-homologous end joining (cNHEJ). Initial binding of PARPs and the KU70/80 complex to breaks appears to be mutually exclusive at easily ligatable DSBs that are repaired efficiently by fast-kinetic cNHEJ; a process that is PARP-, ATM-, 53BP1-, Artemis-, and resection-independent. However, at more complex breaks requiring processing, the Immediate-Early response involving PARPs and the ensuing highly dynamic PARylation (polyADP ribosylation) of many substrates may aid recruitment of both KU70/80 and MRN to DSBs. Complex DSBs rely upon the Early response, largely defined by ATM-dependent focal recruitment of many signalling molecules into large condensates, and regulated by complex chromatin dynamics. Finally, the Late response integrates information from cell cycle phase, chromatin context, and type of DSB to determine appropriate pathway choice. Critical to pathway choice is the recruitment of p53 binding protein 1 (53BP1) and breast cancer associated 1 (BRCA1). However, additional factors recruited throughout the DSB response also impact upon pathway choice, although these remain to be fully characterised. The Late response somehow channels DSBs into the appropriate high-fidelity repair pathway, typically either ‘slow-kinetic’ cNHEJ or homologous recombination (HR). Loss of specific components of the DSB repair machinery results in cells utilising remaining factors to effect repair, but often at the cost of increased mutagenesis. Here we discuss the complex regulation of the Immediate-Early, Early, and Late responses to DSBs proceeding repair itself.
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6
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Min S, Lee HS, Ji JH, Heo Y, Kim Y, Chae S, Choi YW, Kang HC, Nakanishi M, Cho H. The chromatin remodeler RSF1 coordinates epigenetic marks for transcriptional repression and DSB repair. Nucleic Acids Res 2021; 49:12268-12283. [PMID: 34850117 PMCID: PMC8643642 DOI: 10.1093/nar/gkab1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
DNA lesions impact on local transcription and the damage-induced transcriptional repression facilitates efficient DNA repair. However, how chromatin dynamics cooperates with these two events remained largely unknown. We here show that histone H2A acetylation at K118 is enriched in transcriptionally active regions. Under DNA damage, the RSF1 chromatin remodeling factor recruits HDAC1 to DSB sites. The RSF1-HDAC1 complex induces the deacetylation of H2A(X)-K118 and its deacetylation is indispensable for the ubiquitination of histone H2A at K119. Accordingly, the acetylation mimetic H2A-K118Q suppressed the H2A-K119ub level, perturbing the transcriptional repression at DNA lesions. Intriguingly, deacetylation of H2AX at K118 also licenses the propagation of γH2AX and recruitment of MDC1. Consequently, the H2AX-K118Q limits DNA repair. Together, the RSF1-HDAC1 complex controls the traffic of the DNA damage response and transcription simultaneously in transcriptionally active chromatins. The interplay between chromatin remodelers and histone modifiers highlights the importance of chromatin versatility in the maintenance of genome integrity.
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Affiliation(s)
- Sunwoo Min
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Ho-Soo Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, TX 78229-3000, USA
| | - Yungyeong Heo
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Yonghyeon Kim
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon 16499, Korea
| | - Yong Won Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Ho-Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
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7
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Lee HS, Min S, Jung YE, Chae S, Heo J, Lee JH, Kim T, Kang HC, Nakanish M, Cha SS, Cho H. Spatiotemporal coordination of the RSF1-PLK1-Aurora B cascade establishes mitotic signaling platforms. Nat Commun 2021; 12:5931. [PMID: 34635673 PMCID: PMC8505570 DOI: 10.1038/s41467-021-26220-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
The chromatin remodeler RSF1 enriched at mitotic centromeres is essential for proper chromosome alignment and segregation and underlying mechanisms remain to be disclosed. We here show that PLK1 recruitment by RSF1 at centromeres creates an activating phosphorylation on Thr236 in the activation loop of Aurora B and this is indispensable for the Aurora B activation. In structural modeling the phosphorylated Thr236 enhances the base catalysis by Asp200 nearby, facilitating the Thr232 autophosphorylation. Accordingly, RSF1-PLK1 is central for Aurora B-mediated microtubule destabilization in error correction. However, under full microtubule-kinetochore attachment RSF1-PLK1 positions at kinetochores, halts activating Aurora B and phosphorylates BubR1, regardless of tension. Spatial movement of RSF1-PLK1 to kinetochores is triggered by Aurora B-mediated phosphorylation of centromeric histone H3 on Ser28. We propose a regulatory RSF1-PLK1 axis that spatiotemporally controls on/off switch on Aurora B. This feedback circuit among RSF1-PLK1-Aurora B may coordinate dynamic microtubule-kinetochore attachment in early mitosis when full tension yet to be generated.
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Affiliation(s)
- Ho-Soo Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
| | - Sunwoo Min
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Ye-Eun Jung
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, 16499, Korea
| | - June Heo
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, 16499, Korea
| | - Jae-Ho Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
- Institute of Medical Science, Ajou University School of Medicine, Suwon, 16499, Korea
| | - TaeSoo Kim
- Department of Life Science, Ewha Womans University, Seoul, 03760, Korea
| | - Ho-Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Makoto Nakanish
- Division of Cancer Cell Biology, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyeseong Cho
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
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8
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Cai G, Yang Q, Sun W. RSF1 in cancer: interactions and functions. Cancer Cell Int 2021; 21:315. [PMID: 34147108 PMCID: PMC8214769 DOI: 10.1186/s12935-021-02012-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/10/2021] [Indexed: 12/25/2022] Open
Abstract
RSF1, remodelling and spacing factor 1, is an important interphase centromere protein and is overexpressed in many types of cancers and correlated with poor overall survival. RSF1 has functions mainly in maintaining chromosome stability, facilitating DNA repair, maintaining the protein homeostasis of RSF1 and suppressing the transcription of some oncogenes when RSF1 protein is expressed at an optimal level; however, RSF1 overexpression facilitates drug resistance and cell cycle checkpoint inhibition to prompt cancer proliferation and survival. The RSF1 expression level and gene background are crucial for RSF1 functions, which may explain why RSF1 has different functions in different cancer types. This review summarizes the functional domains of RSF1, the overexpression status of RSF1 and SNF2H in cancer based on the TCGA and GTEX databases, the cancer-related functions of RSF1 in interacting with H2Aub, HDAC1, CENP-A, PLK1, ATM, CENP-S, SNF2H, HBX, BubR1, cyclin E1, CBP and NF-κB and the potential clinical value of RSF1, which will lay a theoretical foundation for the structural biology study of RSF1 and application of RSF1 inhibitors, truncated RSF1 proteins and SNF2H inhibitors in the treatment of RSF1-overexpressing tumours.
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Affiliation(s)
- Guiyang Cai
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Yang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.
| | - Wei Sun
- Department of Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, School of Life Sciences, China Medical University, Shenyang, China.
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9
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Tian J, Kong E, Wang X, Xie Z, Chang CYY, Sheu JJC, Hao Q, Sun L. RSF-1 siRNA Enhances Tumor Radiosensitivity in Cervical Cancer via Enhanced DNA Damage, Cell Cycle Redistribution, and Promotion of Apoptosis. Onco Targets Ther 2020; 13:3061-3071. [PMID: 32308437 PMCID: PMC7154003 DOI: 10.2147/ott.s246632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/23/2020] [Indexed: 01/31/2023] Open
Abstract
Background Remodeling and spacing factor-1 (RSF-1) is an identified tumor biomarker that is overexpressed in a variety of human cancers, but its effect on radiotherapy remains unclear. In this study, we aimed to explore the effect of RSF-1 siRNA on sensitizing cervical cancer cells to radiation and its underlying mechanism. Methods The mRNA and protein expression of RSF-1 in tissue and cells were measured by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting. Cell counting kit-8 (CCK-8) and colony formation assay were used to examine cell proliferation. Flow cytometry was used to analyzed the cell cycle and cell apoptosis. DNA damage was examined by the comet assay. ATM, ATR, CHK1, CHK2, H2AX, γH2AX and phosphorylated ATM, ATR, CHK1 and CHK2 were detected by Western blotting. γH2AX foci were demonstrated by immunofluorescence staining. Results RSF-1 was upregulated in cervical cancer tissue and decreased after effective treatment. RSF-1 siRNA in combination with radiation suppressed cell viability, redistributed cell cycles and also induced cell apoptosis in HeLa and SiHa cell lines. Further, knockdown of RSF-1 induced DNA damage by attenuating DNA repair capability, thereby sensitizing cervical cancer cells to radiation. Conclusions These data demonstrate that RSF-1 siRNA enhanced the sensitivity of radiotherapy, and targeting RSF-1 may be a promising approach for the development of novel radiosensitizing agents for the treatment of cervical cancer.
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Affiliation(s)
- Jing Tian
- Department of Gynecological Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, People's Republic of China
| | - Enqi Kong
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan 250200, People's Republic of China
| | - Xiangyu Wang
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou 510515, People's Republic of China
| | - Zhaoguang Xie
- Department of Maternity, Jinan Maternal and Child Health Hospital Affiliated to Shandong First Medical University, Jinan, 250001, People's Republic of China
| | - Cherry Yin-Yi Chang
- Department of Obstetrics and Gynecology, China Medical University Hospital, Taichung 40447, Taiwan
| | - Jim Jinn-Chyuan Sheu
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.,Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.,School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan.,Department of Health and Nutrition Biotechnology, Asia University, Taichung 41354, Taiwan
| | - Quan Hao
- Department of Gynecological Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, People's Republic of China, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, People's Republic of China
| | - Li Sun
- Department of Gynecological Oncology, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, 266042, People's Republic of China.,Department of Gynecological Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, People's Republic of China
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10
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Ji JH, Min S, Chae S, Ha GH, Kim Y, Park YJ, Lee CW, Cho H. De novo phosphorylation of H2AX by WSTF regulates transcription-coupled homologous recombination repair. Nucleic Acids Res 2020; 47:6299-6314. [PMID: 31045206 PMCID: PMC6614800 DOI: 10.1093/nar/gkz309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/25/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Histone H2AX undergoes a phosphorylation switch from pTyr142 (H2AX-pY142) to pSer139 (γH2AX) in the DNA damage response (DDR); however, the functional role of H2AX-pY142 remains elusive. Here, we report a new layer of regulation involving transcription-coupled H2AX-pY142 in the DDR. We found that constitutive H2AX-pY142 generated by Williams-Beuren syndrome transcription factor (WSTF) interacts with RNA polymerase II (RNAPII) and is associated with RNAPII-mediated active transcription in proliferating cells. Also, removal of pre-existing H2AX-pY142 by ATM-dependent EYA1/3 phosphatases disrupts this association and requires for transcriptional silencing at transcribed active damage sites. The following recovery of H2AX-pY142 via translocation of WSTF to DNA lesions facilitates transcription-coupled homologous recombination (TC-HR) in the G1 phase, whereby RAD51 loading, but not RPA32, utilizes RNAPII-dependent active RNA transcripts as donor templates. We propose that the WSTF-H2AX-RNAPII axis regulates transcription and TC-HR repair to maintain genome integrity.
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Affiliation(s)
- Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, South Korea
| | - Sunwoo Min
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, South Korea
| | - Geun-Hyoung Ha
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Yonghyeon Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Yeon-Ji Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Hyeseong Cho
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, South Korea.,Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, South Korea
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11
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Alvarez-Saavedra M, Yan K, De Repentigny Y, Hashem LE, Chaudary N, Sarwar S, Yang D, Ioshikhes I, Kothary R, Hirayama T, Yagi T, Picketts DJ. Snf2h Drives Chromatin Remodeling to Prime Upper Layer Cortical Neuron Development. Front Mol Neurosci 2019; 12:243. [PMID: 31680852 PMCID: PMC6811508 DOI: 10.3389/fnmol.2019.00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 01/23/2023] Open
Abstract
Alterations in the homeostasis of either cortical progenitor pool, namely the apically located radial glial (RG) cells or the basal intermediate progenitors (IPCs) can severely impair cortical neuron production. Such changes are reflected by microcephaly and are often associated with cognitive defects. Genes encoding epigenetic regulators are a frequent cause of intellectual disability and many have been shown to regulate progenitor cell growth, including our inactivation of the Smarca1 gene encoding Snf2l, which is one of two ISWI mammalian orthologs. Loss of the Snf2l protein resulted in dysregulation of Foxg1 and IPC proliferation leading to macrocephaly. Here we show that inactivation of the closely related Smarca5 gene encoding the Snf2h chromatin remodeler is necessary for embryonic IPC expansion and subsequent specification of callosal projection neurons. Telencephalon-specific Smarca5 cKO embryos have impaired cell cycle kinetics and increased cell death, resulting in fewer Tbr2+ and FoxG1+ IPCs by mid-neurogenesis. These deficits give rise to adult mice with a dramatic reduction in Satb2+ upper layer neurons, and partial agenesis of the corpus callosum. Mice survive into adulthood but molecularly display reduced expression of the clustered protocadherin genes that may further contribute to altered dendritic arborization and a hyperactive behavioral phenotype. Our studies provide novel insight into the developmental function of Snf2h-dependent chromatin remodeling processes during brain development.
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Affiliation(s)
- Matías Alvarez-Saavedra
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Yves De Repentigny
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lukas E. Hashem
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Nidhi Chaudary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Shihab Sarwar
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Doo Yang
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Ilya Ioshikhes
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rashmi Kothary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, Tokushima, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - David J. Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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12
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Densham RM, Morris JR. Moving Mountains-The BRCA1 Promotion of DNA Resection. Front Mol Biosci 2019; 6:79. [PMID: 31552267 PMCID: PMC6733915 DOI: 10.3389/fmolb.2019.00079] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA double-strand breaks (DSBs) occur in our cells in the context of chromatin. This type of lesion is toxic, entirely preventing genome continuity and causing cell death or terminal arrest. Several repair mechanisms can act on DNA surrounding a DSB, only some of which carry a low risk of mutation, so that which repair process is utilized is critical to the stability of genetic material of cells. A key component of repair outcome is the degree of DNA resection directed to either side of the break site. This in turn determines the subsequent forms of repair in which DNA homology plays a part. Here we will focus on chromatin and chromatin-bound complexes which constitute the "mountains" that block resection, with a particular focus on how the breast and ovarian cancer predisposition protein-1 (BRCA1) contributes to repair outcomes through overcoming these blocks.
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Affiliation(s)
| | - Joanna R. Morris
- Birmingham Centre for Genome Biology, Institute of Cancer and Genomic Sciences, Medical and Dental Schools, University of Birmingham, Birmingham, United Kingdom
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13
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He J, Fu L, Li Q. Rsf‑1 regulates malignant melanoma cell viability and chemoresistance via NF‑κB/Bcl‑2 signaling. Mol Med Rep 2019; 20:3487-3498. [PMID: 31485613 PMCID: PMC6755232 DOI: 10.3892/mmr.2019.10610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022] Open
Abstract
Remodeling and spacing factor 1 (Rsf-1) has been reported as overexpressed in numerous cancers; however, its expression, biological functions and mechanisms in malignant melanoma remain unknown. In the present study, the expression of Rsf-1 was investigated in 50 cases of malignant melanoma samples using immunohistochemistry. The results revealed that Rsf-1 expression was elevated in 38% of specimens. MTT, colony formation, Transwell and flow cytometry assays were performed to investigate the functions of Rsf-1. Knockdown of Rsf-1 in the MV3 and A375 melanoma cell lines decreased the viability, invasion and cell cycle transition of cells. Conversely, overexpression of Rsf-1 in M14 cells with low endogenous Rsf-1 expression induced opposing effects. Further analysis revealed that Rsf-1 knockdown decreased matrix metalloproteinase-2, cyclin E and phosphorylated-IκB expression. Additionally, Rsf-1 depletion reduced cisplatin resistance and significantly increased the cisplatin-associated apoptotic rate, whereas Rsf-1 overexpression exhibited opposing effects. Rsf-1 also maintained the mitochondrial membrane potential following cisplatin treatment. Analysis of apoptosis-associated proteins revealed that Rsf-1 positively regulated B-cell lymphoma 2 (Bcl-2), cellular inhibitor of apoptosis 1 (cIAP1) and cIAP2, and downregulated Bcl-2-associated X protein expression. Nuclear factor κ-light-chain-enhancer of activated B-cells (NF-κB) inhibition reversed the effects of Rsf-1 on Bcl-2. In conclusion, Rsf-1 was overexpressed in malignant melanoma and may contribute to the malignant behaviors of melanoma cells, possibly via the regulation of NF-κB signaling. Therefore, Rsf-1 may be a potential therapeutic target in the treatment of malignant melanoma.
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Affiliation(s)
- Jiani He
- Department of Pathology, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Lin Fu
- Department of Pathology, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Qingchang Li
- Department of Pathology, China Medical University, Shenyang, Liaoning 110001, P.R. China
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14
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Jimeno S, Mejías-Navarro F, Prados-Carvajal R, Huertas P. Controlling the balance between chromosome break repair pathways. DNA Repair (Amst) 2019; 115:95-134. [DOI: 10.1016/bs.apcsb.2018.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Drissi R, Chauvin A, McKenna A, Lévesque D, Blais-Brochu S, Jean D, Boisvert FM. Destabilization of the MiniChromosome Maintenance (MCM) complex modulates the cellular response to DNA double strand breaks. Cell Cycle 2018; 17:2593-2609. [PMID: 30516086 PMCID: PMC6300108 DOI: 10.1080/15384101.2018.1553336] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA replication during S phase involves thousands of replication forks that must be coordinated to ensure that every DNA section is replicated only once. The minichromosome maintenance proteins, MCM2 to MCM7, form a heteromeric DNA helicase required for both the initiation and elongation of DNA replication. Although only two DNA helicase activities are necessary to establish a bidirectional replication fork from each replication origin, a large excess of MCM complexes is amassed and distributed along the chromatin. The function of the additional MCM complexes is not well understood, as most are displaced from the DNA during the S-phase, apparently without playing an active role in DNA replication. DNA damage response (DDR) kinases activated by stalled forks prevent the replication machinery from being activated, indicating a tight relationship between DDR and DNA replication. To investigate the role of MCM proteins in the cellular response to DNA damage, we used shRNA targeting MCM2 or MCM3 to determine the impact of a reduction in MCM complex. The alteration of MCM proteins induced a change in the activation of key factors of the DDR in response to Etoposide treatment. Etoposide-induced DNA damage affected the phosphorylation of γ-H2AX, CHK1 and CHK2 without affecting cell viability. Using assays measuring homologous recombination (HR) and non-homologous end-joining (NHEJ), we identified a decrease in both HR and NHEJ associated with a decrease in MCM complex.
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Affiliation(s)
- Romain Drissi
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Anaïs Chauvin
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Alyson McKenna
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Lévesque
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Simon Blais-Brochu
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - Dominique Jean
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
| | - François-Michel Boisvert
- a Department of Anatomy and Cell Biology , Université de Sherbrooke , 3201 Jean-Mignaul, Sherbrooke , Québec , Canada
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16
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Chromatin-remodeling factor, RSF1, controls p53-mediated transcription in apoptosis upon DNA strand breaks. Cell Death Dis 2018; 9:1079. [PMID: 30348983 PMCID: PMC6197202 DOI: 10.1038/s41419-018-1128-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/02/2018] [Accepted: 10/08/2018] [Indexed: 12/14/2022]
Abstract
Remodeling and spacing factor 1 (RSF1), which is one of chromatin-remodeling factors, has been linked to the DNA damage response (DDR) and DNA repair. However, the biological consequence of RSF1 deficiency in DDR in vivo and its molecular mechanisms remain unknown. Because defective DDR is related to neuropathological phenotypes, we developed neural-specific Rsf1 knockout mice. Rsf1 deficiency did not result in any neuropathological abnormalities, but prevented neural apoptosis triggered by excessive DNA strand breaks during neurogenesis. Likewise, cell death was significantly reduced in RSF1 deficient human cell lines after DNA damage, and the global transcriptome of these cells revealed that the expressions of p53 downstream genes were significantly reduced upon DNA strand breaks. Inactivation of these genes resulted from decreased binding of p53/p300 complex and subsequent reduction of H3 acetylation at their promoters. Our data show that RSF1 is necessary for p53-dependent gene expression in response to DNA strand breaks via controlling the accessibility of p53/p300 complex to its target genes and contributes to the maintenance of cellular integrity.
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17
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Lee HS, Lin Z, Chae S, Yoo YS, Kim BG, Lee Y, Johnson JL, Kim YS, Cantley LC, Lee CW, Yu H, Cho H. The chromatin remodeler RSF1 controls centromeric histone modifications to coordinate chromosome segregation. Nat Commun 2018; 9:3848. [PMID: 30242288 PMCID: PMC6155007 DOI: 10.1038/s41467-018-06377-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/20/2018] [Indexed: 01/20/2023] Open
Abstract
Chromatin remodelers regulate the nucleosome barrier during transcription, DNA replication, and DNA repair. The chromatin remodeler RSF1 is enriched at mitotic centromeres, but the functional consequences of this enrichment are not completely understood. Shugoshin (Sgo1) protects centromeric cohesion during mitosis and requires BuB1-dependent histone H2A phosphorylation (H2A-pT120) for localization. Loss of Sgo1 at centromeres causes chromosome missegregation. Here, we show that RSF1 regulates Sgo1 localization to centromeres through coordinating a crosstalk between histone acetylation and phosphorylation. RSF1 interacts with and recruits HDAC1 to centromeres, where it counteracts TIP60-mediated acetylation of H2A at K118. This deacetylation is required for the accumulation of H2A-pT120 and Sgo1 deposition, as H2A-K118 acetylation suppresses H2A-T120 phosphorylation by Bub1. Centromeric tethering of HDAC1 prevents premature chromatid separation in RSF1 knockout cells. Our results indicate that RSF1 regulates the dynamics of H2A histone modifications at mitotic centromeres and contributes to the maintenance of chromosome stability. The chromatin remodeler RSF1 is enriched at mitotic centromeres but its function there is poorly understood. Here, the authors show that RSF1 regulates H2A phosphorylation and acetylation at mitotic centromeres and contributes to chromosome stability.
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Affiliation(s)
- Ho-Soo Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Zhonghui Lin
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75930, USA.,College of Chemistry, Fuzhou University, 350116, Fujian, China
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Young-Suk Yoo
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, UNIST, Ulsan, 44919, Korea
| | - Youngsoo Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Jared L Johnson
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - You-Sun Kim
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Lewis C Cantley
- Meyer Cancer Center, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Chang-Woo Lee
- Department of Molecular Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Hongtao Yu
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, 75930, USA.
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon, 16499, Korea. .,Genomic Instability Research Center, Ajou University School of Medicine, Suwon, 16499, Korea.
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18
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Berger ND, Stanley FKT, Moore S, Goodarzi AA. ATM-dependent pathways of chromatin remodelling and oxidative DNA damage responses. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0283. [PMID: 28847820 DOI: 10.1098/rstb.2016.0283] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/14/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM) is a serine/threonine protein kinase with a master regulatory function in the DNA damage response. In this role, ATM commands a complex biochemical network that signals the presence of oxidative DNA damage, including the dangerous DNA double-strand break, and facilitates subsequent repair. Here, we review the current state of knowledge regarding ATM-dependent chromatin remodelling and epigenomic alterations that are required to maintain genomic integrity in the presence of DNA double-strand breaks and/or oxidative stress. We will focus particularly on the roles of ATM in adjusting nucleosome spacing at sites of unresolved DNA double-strand breaks within complex chromatin environments, and the impact of ATM on preserving the health of cells within the mammalian central nervous system.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- N Daniel Berger
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Fintan K T Stanley
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Shaun Moore
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Aaron A Goodarzi
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
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19
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Min S, Choi YW, Yun H, Jo S, Ji JH, Cho H. Post-Translational Regulation of the RSF1 Chromatin Remodeler under DNA Damage. Mol Cells 2018; 41:127-133. [PMID: 29385673 PMCID: PMC5824022 DOI: 10.14348/molcells.2018.2244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/21/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022] Open
Abstract
Chromatin remodeling factors are involved in many cellular processes such as transcription, replication, and DNA damage response by regulating chromatin structure. As one of chromatin remodeling factors, remodeling and spacing factor 1 (RSF1) is recruited at double strand break (DSB) sites and regulates ataxia telangiectasia mutated (ATM) -dependent checkpoint pathway upon DNA damage for the efficient repair. RSF1 is overexpressed in a variety of cancers, but regulation of RSF1 levels remains largely unknown. Here, we showed that protein levels of RSF1 chromatin remodeler are temporally upregulated in response to different DNA damage agents without changing the RSF1 mRNA level. In the absence of SNF2h, a binding partner of RSF1, the RSF1 protein level was significantly diminished. Intriguingly, the level of RSF1-3SA mutant lacking ATM-mediated phosphorylation sites significantly increased, and upregulation of RSF1 levels under DNA damage was not observed in cells overexpressing ATM kinase. Furthermore, failure in the regulation of RSF1 level caused a significant reduction in DNA repair, whereas reconstitution of RSF1, but not of RSF1-3SA mutants, restored DSB repair. Our findings reveal that temporal regulation of RSF1 levels at its post-translational modification by SNF2h and ATM is essential for efficient DNA repair.
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Affiliation(s)
- Sunwoo Min
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499,
Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon 16499,
Korea
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Yong Won Choi
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499,
Korea
- Department of Hematology and Oncology, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Hansol Yun
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499,
Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon 16499,
Korea
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Sujin Jo
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499,
Korea
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499,
Korea
- Department of Biomedical Sciences, Ajou University School of Medicine, Suwon 16499,
Korea
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499,
Korea
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20
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Kochan JA, Desclos EC, Bosch R, Meister L, Vriend LE, van Attikum H, Krawczyk PM. Meta-analysis of DNA double-strand break response kinetics. Nucleic Acids Res 2017; 45:12625-12637. [PMID: 29182755 PMCID: PMC5728399 DOI: 10.1093/nar/gkx1128] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
Most proteins involved in the DNA double-strand break response (DSBR) accumulate at the damage sites, where they perform functions related to damage signaling, chromatin remodeling and repair. Over the last two decades, studying the accumulation of many DSBR proteins provided information about their functionality and underlying mechanisms of action. However, comparison and systemic interpretation of these data is challenging due to their scattered nature and differing experimental approaches. Here, we extracted, analyzed and compared the available results describing accumulation of 79 DSBR proteins at sites of DNA damage, which can be further explored using Cumulus (http://www.dna-repair.live/cumulus/)-the accompanying interactive online application. Despite large inter-study variability, our analysis revealed that the accumulation of most proteins starts immediately after damage induction, occurs in parallel and peaks within 15-20 min. Various DSBR pathways are characterized by distinct accumulation kinetics with major non-homologous end joining proteins being generally faster than those involved in homologous recombination, and signaling and chromatin remodeling factors accumulating with varying speeds. Our meta-analysis provides, for the first time, comprehensive overview of the temporal organization of the DSBR in mammalian cells and could serve as a reference for future mechanistic studies of this complex process.
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Affiliation(s)
- Jakub A. Kochan
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C.B. Desclos
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Luna Meister
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E.M. Vriend
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Przemek M. Krawczyk
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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21
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Lee NS, Chang HR, Kim S, Ji JH, Lee J, Lee HJ, Seo Y, Kang M, Han JS, Myung K, Kim Y, Kim H. Ring finger protein 126 (RNF126) suppresses ionizing radiation-induced p53-binding protein 1 (53BP1) focus formation. J Biol Chem 2017; 293:588-598. [PMID: 29167269 PMCID: PMC5767864 DOI: 10.1074/jbc.m116.765602] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/19/2017] [Indexed: 11/06/2022] Open
Abstract
Cells have evolved sophisticated mechanisms to maintain genomic integrity in response to DNA damage. Ionizing radiation (IR)-induced DNA damage results in the formation of IR-induced foci (iRIF) in the nucleus. The iRIF formation is part of the DNA damage response (DDR), which is an essential signaling cascade that must be strictly regulated because either the loss of or an augmented DDR leads to loss of genome integrity. Accordingly, negative regulation of the DDR is as critical as its activation. In this study, we have identified ring finger protein 126 (RNF126) as a negative regulator of the DDR from a screen of iRIF containing 53BP1. RNF126 overexpression abolishes not only the formation of 53BP1 iRIF but also of RNF168, FK2, RAP80, and BRCA1. However, the iRIF formation of γH2AX, MDC1, and RNF8 is maintained, indicating that RNF126 acts between RNF8 and RNF168 during the DDR. In addition, RNF126 overexpression consistently results in the loss of RNF168-mediated H2A monoubiquitination at lysine 13/15 and inhibition of the non-homologous end joining capability. Taken together, our findings reveal that RNF126 is a novel factor involved in the negative regulation of DDR, which is important for sustaining genomic integrity.
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Affiliation(s)
- Nam Soo Lee
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hae Ryung Chang
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Soomi Kim
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jae-Hoon Ji
- the Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Republic of Korea
| | - Joorak Lee
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hyun Ji Lee
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yoojeong Seo
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Misun Kang
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea, and
| | - Joo Seok Han
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea, and
| | - Kyungjae Myung
- the Center for Genomic Integrity, Institute for Basic Science, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea, and
| | - Yonghwan Kim
- the Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea,
| | - Hongtae Kim
- From the Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea, .,the Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
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22
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Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing. Proc Natl Acad Sci U S A 2017; 114:E7949-E7958. [PMID: 28855339 PMCID: PMC5617306 DOI: 10.1073/pnas.1711158114] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Posttranslational histone modifications play important roles in regulating chromatin-based nuclear processes. Histone H2AK119 ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing. However, the underlying mechanism remains largely obscure. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF complex, as a H2Aub binding protein, which mediates the gene-silencing function of this histone modification. RSF1 associates specifically with H2Aub, but not H2Bub nucleosomes, through a previously uncharacterized and obligatory region designated as ubiquitinated H2A binding domain. In human and mouse cells, genes regulated by RSF1 overlap significantly with those controlled by RNF2/Ring1B, the subunit of Polycomb repressive complex 1 (PRC1) which catalyzes the ubiquitination of H2AK119. About 82% of H2Aub-enriched genes, including the classic PRC1 target Hox genes, are bound by RSF1 around their transcription start sites. Depletion of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. In contrast, RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but leads to derepression of H2Aub target genes, accompanied by changes in H2Aub chromatin organization and release of linker histone H1. The action of RSF1 in H2Aub-mediated gene silencing is further demonstrated by chromatin-based in vitro transcription. Finally, RSF1 and Ring1 act cooperatively to regulate mesodermal cell specification and gastrulation during Xenopus early embryonic development. Taken together, these data identify RSF1 as a H2Aub reader that contributes to H2Aub-mediated gene silencing by maintaining a stable nucleosome pattern at promoter regions.
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23
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Oppikofer M, Bai T, Gan Y, Haley B, Liu P, Sandoval W, Ciferri C, Cochran AG. Expansion of the ISWI chromatin remodeler family with new active complexes. EMBO Rep 2017; 18:1697-1706. [PMID: 28801535 DOI: 10.15252/embr.201744011] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
ISWI chromatin remodelers mobilize nucleosomes to control DNA accessibility. Complexes isolated to date pair one of six regulatory subunits with one of two highly similar ATPases. However, we find that each endogenously expressed ATPase co-purifies with every regulatory subunit, substantially increasing the diversity of ISWI complexes, and we additionally identify BAZ2B as a novel, seventh regulatory subunit. Through reconstitution of catalytically active human ISWI complexes, we demonstrate that the new interactions described here are stable and direct. Finally, we profile the nucleosome remodeling functions of the now expanded family of ISWI chromatin remodelers. By revealing the combinatorial nature of ISWI complexes, we provide a basis for better understanding ISWI function in normal settings and disease.
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Affiliation(s)
- Mariano Oppikofer
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Tianyi Bai
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yutian Gan
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Peter Liu
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrea G Cochran
- Department of Early Discovery Biochemistry, Genentech, Inc., South San Francisco, CA, USA
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24
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Koo GB, Ji JH, Cho H, Morgan MJ, Kim YS. Nuclear TRADD prevents DNA damage-mediated death by facilitating non-homologous end-joining repair. Sci Rep 2017; 7:3332. [PMID: 28611389 PMCID: PMC5469829 DOI: 10.1038/s41598-017-03211-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/26/2017] [Indexed: 11/18/2022] Open
Abstract
TNF receptor-associated death domain (TRADD) is an essential mediator of TNF receptor signaling, and serves as an adaptor to recruit other effectors. TRADD has been shown to cycle between the cytoplasm and nucleus due to its nuclear localization (NLS) and export sequences (NES). However, the underlying function of nuclear TRADD is poorly understood. Here we demonstrate that cytoplasmic TRADD translocates to DNA double-strand break sites (DSBs) during the DNA damage response (DDR). Deficiency of TRADD or its sequestration in cytosol leads to accumulation of γH2AX-positive foci in response to DNA damage, which is reversed by nuclear TRADD expression. TRADD facilitates non-homologous end-joining (NHEJ) by recruiting NHEJ repair factors 53BP1 and Ku70/80 complex, whereas TRADD is dispensable for homologous recombination (HR) repair. Finally, an impaired nuclear localization of TRADD triggers cell death through the persistent activation of JNK and accumulation of reactive oxygen species (ROS). Thus, our findings suggest that translocation of TRADD to DSBs into the nucleus contributes to cell survival in response to DNA damage through an activation of DNA damage repair.
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Affiliation(s)
- Gi-Bang Koo
- Department of Biochemistry, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biomedical Sciences, graduate School, Ajou University, Suwon, Gyeonggi, 16499, Republic of Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biomedical Sciences, graduate School, Ajou University, Suwon, Gyeonggi, 16499, Republic of Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea
| | - Michael J Morgan
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - You-Sun Kim
- Department of Biochemistry, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea. .,Department of Biomedical Sciences, graduate School, Ajou University, Suwon, Gyeonggi, 16499, Republic of Korea.
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25
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Ka NL, Na TY, Na H, Lee MH, Park HS, Hwang S, Kim IY, Seong JK, Lee MO. NR1D1 Recruitment to Sites of DNA Damage Inhibits Repair and Is Associated with Chemosensitivity of Breast Cancer. Cancer Res 2017; 77:2453-2463. [PMID: 28249904 DOI: 10.1158/0008-5472.can-16-2099] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/12/2016] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
Abstract
DNA repair capacity is critical for survival of cancer cells upon therapeutic DNA damage and thus is an important determinant of susceptibility to chemotherapy in cancer patients. In this study, we identified a novel function of nuclear receptor NR1D1 in DNA repair, which enhanced chemosensitivity in breast cancer cells. NR1D1 inhibited both nonhomologous end joining and homologous recombination double-strand breaks repair, and delayed the clearance of γH2AX DNA repair foci that formed after treatment of doxorubicin. PARylation of NR1D1 by PARP1 drove its recruitment to damaged DNA lesions. Deletion of the ligand binding domain of NR1D1 that interacted with PARP1, or treatment of 6-(5H)-phenanthridinone, an inhibitor of PARP1, suppressed the recruitment of NR1D1 to DNA damaged sites, indicating PARylation as a critical step for the NR1D1 recruitment. NR1D1 inhibited recruitment of the components of DNA damage response complex such as SIRT6, pNBS1, and BRCA1 to DNA lesions. Downregulation of NR1D1 in MCF7 cells resulted in resistance to doxorubicin, both in vitro and in vivo Analysis of four public patient data sets indicated that NR1D1 expression correlates positively with clinical outcome in breast cancer patients who received chemotherapy. Our findings suggest that NR1D1 and its ligands provide therapeutic options that could enhance the outcomes of chemotherapy in breast cancer patients. Cancer Res; 77(9); 2453-63. ©2017 AACR.
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Affiliation(s)
- Na-Lee Ka
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Tae-Young Na
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Hyelin Na
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Min-Ho Lee
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Han-Su Park
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Sewon Hwang
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea
| | - Il Yong Kim
- College of Veterinary Medicine, Seoul National University and Korea Mouse Phenotyping Center, Gwanak-gu, Seoul, Korea
| | - Je Kyung Seong
- College of Veterinary Medicine, Seoul National University and Korea Mouse Phenotyping Center, Gwanak-gu, Seoul, Korea
| | - Mi-Ock Lee
- College of Pharmacy and Bio-MAX Institute, Seoul National University, Gwanak-gu, Seoul, Korea.
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26
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Interaction of hepatitis B virus X protein with PARP1 results in inhibition of DNA repair in hepatocellular carcinoma. Oncogene 2016; 35:5435-5445. [PMID: 27041572 DOI: 10.1038/onc.2016.82] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/05/2016] [Accepted: 02/23/2016] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus X protein (HBx) contributes to the development of hepatocellular carcinoma (HCC), probably by regulating activities of many host or viral proteins through protein-protein interactions. In this study, we identified poly(ADP-ribose) polymerase (PARP1), a crucial factor in DNA repair, as an HBx-interacting protein using a proteomics approach. Coimmunoprecipitation and proximity ligation assays confirmed the binding and colocalization of HBx and PARP1 in the nucleus. The carboxyl-terminus of HBx protein bound to the catalytic domain of PARP1, and this binding reduced the enzymatic activity of PARP1 in both in vitro and in vivo assays. HBx interrupted the binding of PARP1 to Sirt6, which catalyzes the mono-ADP-ribosylation required for DNA repair. Consistently, overexpression of HBx inhibited the clearance of γH2AX DNA repair foci generated under oxidative stress in Chang liver cells. Recruitment of the DNA repair complex to the site-specific double-strand breaks was inhibited in the presence of HBx, when measured by laser microirradiation assay and damage-specific chromatin immunoprecipitation assays. Consequently, HBx increased signs of DNA damage such as accumulation of 8-hydroxy-2'-deoxyguanosine and comet formation, which were reversed by overexpression of PARP1 and/or Sirt6. Finally, the interaction between PARP1 and Sirt6 was markedly lower in the livers of HBx-transgenic mice and specimens obtained from HCC patients to compare with the corresponding control. Our data suggest that the physical interaction of HBx and PARP1 accelerates DNA damage by inhibiting recruitment of the DNA repair complex to the damaged DNA sites, which may lead to the onset of hepatocarcinogenesis.
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27
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ATM and SIRT6/SNF2H Mediate Transient H2AX Stabilization When DSBs Form by Blocking HUWE1 to Allow Efficient γH2AX Foci Formation. Cell Rep 2015; 13:2728-40. [DOI: 10.1016/j.celrep.2015.11.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 11/03/2015] [Accepted: 11/17/2015] [Indexed: 01/07/2023] Open
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28
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Jeggo PA, Downs JA. Roles of chromatin remodellers in DNA double strand break repair. Exp Cell Res 2014; 329:69-77. [PMID: 25278484 DOI: 10.1016/j.yexcr.2014.09.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 10/24/2022]
Abstract
Now that we have a good understanding of the DNA double strand break (DSB) repair mechanisms and DSB-induced damage signalling, attention is focusing on the changes to the chromatin environment needed for efficient DSB repair. Mutations in chromatin remodelling complexes have been identified in cancers, making it important to evaluate how they impact upon genomic stability. Our current understanding of the DSB repair pathways suggests that each one has distinct requirements for chromatin remodelling. Moreover, restricting the extent of chromatin modifications could be a significant factor regulating the decision of pathway usage. In this review, we evaluate the distinct DSB repair pathways for their potential need for chromatin remodelling and review the roles of ATP-driven chromatin remodellers in the pathways.
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Affiliation(s)
- Penny A Jeggo
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN19RQ, UK.
| | - Jessica A Downs
- Genome Damage and Stability Centre, Life Sciences, University of Sussex, Brighton BN19RQ, UK.
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29
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Vidi PA, Liu J, Salles D, Jayaraman S, Dorfman G, Gray M, Abad P, Moghe PV, Irudayaraj JM, Wiesmüller L, Lelièvre SA. NuMA promotes homologous recombination repair by regulating the accumulation of the ISWI ATPase SNF2h at DNA breaks. Nucleic Acids Res 2014; 42:6365-79. [PMID: 24753406 PMCID: PMC4041463 DOI: 10.1093/nar/gku296] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Chromatin remodeling factors play an active role in the DNA damage response by shaping chromatin to facilitate the repair process. The spatiotemporal regulation of these factors is key to their function, yet poorly understood. We report that the structural nuclear protein NuMA accumulates at sites of DNA damage in a poly[ADP-ribose]ylation-dependent manner and functionally interacts with the ISWI ATPase SNF2h/SMARCA5, a chromatin remodeler that facilitates DNA repair. NuMA coimmunoprecipitates with SNF2h, regulates its diffusion in the nucleoplasm and controls its accumulation at DNA breaks. Consistent with NuMA enabling SNF2h function, cells with silenced NuMA exhibit reduced chromatin decompaction after DNA cleavage, lesser focal recruitment of homologous recombination repair factors, impaired DNA double-strand break repair in chromosomal (but not in episomal) contexts and increased sensitivity to DNA cross-linking agents. These findings reveal a structural basis for the orchestration of chromatin remodeling whereby a scaffold protein promotes genome maintenance by directing a remodeler to DNA breaks.
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Affiliation(s)
- Pierre-Alexandre Vidi
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jing Liu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Daniela Salles
- Department of Obstetrics and Gynecology, University of Ulm, Prittwitzstrasse 43, D-89075 Ulm, Germany
| | - Swaathi Jayaraman
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - George Dorfman
- Department of Biomedical Engineering, and Chemical & Biochemical Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Matthew Gray
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Patricia Abad
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Prabhas V Moghe
- Department of Biomedical Engineering, and Chemical & Biochemical Engineering, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph M Irudayaraj
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, University of Ulm, Prittwitzstrasse 43, D-89075 Ulm, Germany
| | - Sophie A Lelièvre
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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