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Kovács ZJ, Harami GM, Pálinkás J, Kuljanishvili N, Hegedüs J, Harami‐Papp H, Mahmudova L, Khamisi L, Szakács G, Kovács M. DNA-dependent phase separation by human SSB2 (NABP1/OBFC2A) protein points to adaptations to eukaryotic genome repair processes. Protein Sci 2024; 33:e4959. [PMID: 38511671 PMCID: PMC10955726 DOI: 10.1002/pro.4959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all domains of life and play essential roles via stabilizing and protecting single-stranded (ss) DNA as well as organizing multiprotein complexes during DNA replication, recombination, and repair. Two mammalian SSB paralogs (hSSB1 and hSSB2 in humans) were recently identified and shown to be involved in various genome maintenance processes. Following our recent discovery of the liquid-liquid phase separation (LLPS) propensity of Escherichia coli (Ec) SSB, here we show that hSSB2 also forms LLPS condensates under physiologically relevant ionic conditions. Similar to that seen for EcSSB, we demonstrate the essential contribution of hSSB2's C-terminal intrinsically disordered region (IDR) to condensate formation, and the selective enrichment of various genome metabolic proteins in hSSB2 condensates. However, in contrast to EcSSB-driven LLPS that is inhibited by ssDNA binding, hSSB2 phase separation requires single-stranded nucleic acid binding, and is especially facilitated by ssDNA. Our results reveal an evolutionarily conserved role for SSB-mediated LLPS in the spatiotemporal organization of genome maintenance complexes. At the same time, differential LLPS features of EcSSB and hSSB2 point to functional adaptations to prokaryotic versus eukaryotic genome metabolic contexts.
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Affiliation(s)
- Zoltán J. Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gábor M. Harami
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - János Pálinkás
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Natalie Kuljanishvili
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - József Hegedüs
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Hajnalka Harami‐Papp
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lamiya Mahmudova
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Lana Khamisi
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
| | - Gergely Szakács
- HUN‐REN Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Academy of SciencesBudapestHungary
- Center for Cancer ResearchMedical University of ViennaWienAustria
| | - Mihály Kovács
- ELTE‐MTA “Momentum” Motor Enzymology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
- HUN‐REN–ELTE Motor Pharmacology Research Group, Department of BiochemistryEötvös Loránd UniversityBudapestHungary
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Xu C, Li C, Chen J, Xiong Y, Qiao Z, Fan P, Li C, Ma S, Liu J, Song A, Tao B, Xu T, Xu W, Chi Y, Xue J, Wang P, Ye D, Gu H, Zhang P, Wang Q, Xiao R, Cheng J, Zheng H, Yu X, Zhang Z, Wu J, Liang K, Liu YJ, Lu H, Chen FX. R-loop-dependent promoter-proximal termination ensures genome stability. Nature 2023; 621:610-619. [PMID: 37557913 PMCID: PMC10511320 DOI: 10.1038/s41586-023-06515-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 08/03/2023] [Indexed: 08/11/2023]
Abstract
The proper regulation of transcription is essential for maintaining genome integrity and executing other downstream cellular functions1,2. Here we identify a stable association between the genome-stability regulator sensor of single-stranded DNA (SOSS)3 and the transcription regulator Integrator-PP2A (INTAC)4-6. Through SSB1-mediated recognition of single-stranded DNA, SOSS-INTAC stimulates promoter-proximal termination of transcription and attenuates R-loops associated with paused RNA polymerase II to prevent R-loop-induced genome instability. SOSS-INTAC-dependent attenuation of R-loops is enhanced by the ability of SSB1 to form liquid-like condensates. Deletion of NABP2 (encoding SSB1) or introduction of cancer-associated mutations into its intrinsically disordered region leads to a pervasive accumulation of R-loops, highlighting a genome surveillance function of SOSS-INTAC that enables timely termination of transcription at promoters to constrain R-loop accumulation and ensure genome stability.
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Affiliation(s)
- Congling Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jiwei Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yan Xiong
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhibin Qiao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Pengyu Fan
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Conghui Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Shuangyu Ma
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Bolin Tao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tao Xu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Wei Xu
- Department of Orthopedic Oncology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yayun Chi
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jingyan Xue
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Pu Wang
- Huashan Hospital, Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Dan Ye
- Huashan Hospital, Fudan University, Shanghai Key Laboratory of Medical Epigenetics, Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Peng Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiong Wang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Hai Zheng
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Xiaoli Yu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhen Zhang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jiong Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yan-Jun Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China.
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Medical Epigenetics, Shanghai Key Laboratory of Radiation Oncology, Human Phenome Institute, Fudan University, Shanghai, China.
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.
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PARP1′s Involvement in RNA Polymerase II Elongation: Pausing and Releasing Regulation through the Integrator and Super Elongation Complex. Cells 2022; 11:cells11203202. [PMID: 36291070 PMCID: PMC9600911 DOI: 10.3390/cells11203202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/17/2022] Open
Abstract
RNA polymerase elongation along the gene body is tightly regulated to ensure proper transcription and alternative splicing events. Understanding the mechanism and factors critical in regulating the rate of RNA polymerase II elongation and processivity is clearly important. Recently we showed that PARP1, a well-known DNA repair protein, when bound to chromatin, regulates RNA polymerase II elongation. However, the mechanism by which it does so is not known. In the current study, we aimed to tease out how PARP1 regulates RNAPII elongation. We show, both in vivo and in vitro, that PARP1 binds directly to the Integrator subunit 3 (IntS3), a member of the elongation Integrator complex. The association between the two proteins is mediated via the C-terminal domain of PARP1 to the C-terminal domain of IntS3. Interestingly, the occupancy of IntS3 along two PARP1 target genes mimicked that of PARP1, suggesting a role in its recruitment/assembly of elongation factors. Indeed, the knockdown of PARP1 resulted in differential chromatin association and gene occupancy of IntS3 and other key elongation factors. Most of these PARP1-mediated effects were due to the physical presence of PARP1 rather than its PARylation activity. These studies argue that PARP1 controls the progressive RNAPII elongation complexes. In summary, we present a platform to begin to decipher PARP1′s role in recruiting/scaffolding elongation factors along the gene body regions during RNA polymerase II elongation and gene regulation.
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Wang Z, Wang H, Wu Q, Chen Y, Liu J, Liu Y, Sun D, Chen W. GATA2 promotes human vascular smooth muscle cell proliferation via mitofusin2-mediated Ras/Raf/MEK/ERK signaling pathway. Int J Cardiol 2022; 346:62-70. [PMID: 34774887 DOI: 10.1016/j.ijcard.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/18/2021] [Accepted: 11/07/2021] [Indexed: 01/05/2023]
Affiliation(s)
- Zuoguang Wang
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China.
| | - Hao Wang
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China
| | - Qiong Wu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China
| | - Yanyu Chen
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China
| | - Jielin Liu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China
| | - Ya Liu
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China
| | - Dongdong Sun
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China; Beijing Institute of Heart, Lung, Blood Vessel Diseases, Beijing, China
| | - Wenli Chen
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China
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Wu Q, Tang X, Zhu W, Li Q, Zhang X, Li H. The Potential Prognostic Role of Oligosaccharide-Binding Fold-Containing Protein 2A (OBFC2A) in Triple-Negative Breast Cancer. Front Oncol 2021; 11:751430. [PMID: 34868954 PMCID: PMC8634334 DOI: 10.3389/fonc.2021.751430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Patients with triple-negative breast cancer (TNBC) have poor overall survival. The present study aimed to investigate the potential prognostics of TNBC by analyzing breast cancer proteomic and transcriptomic datasets. METHODS Candidate proteins selected from CPTAC (the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium) were validated using datasets from METABRIC (Molecular Taxonomy of Breast Cancer International Consortium). Kaplan-Meier analysis and ROC (receiver operating characteristic) curve analysis were performed to explore the prognosis of candidate genes. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis were performed on the suspected candidate genes. Single-cell RNA-seq (scRNA-seq) data from GSE118389 were used to analyze the cell clusters in which OBFC2A (Oligosaccharide-Binding Fold-Containing Protein 2A) was mainly distributed. TIMER (Tumor Immune Estimation Resource) was used to verify the correlation between OBFC2A expression and immune infiltration. Clone formation assays and wound healing assays were used to detect the role of OBFC2A expression on the proliferation, invasion, and migration of breast cancer cells. Flow cytometry was used to analyze the effects of silencing OBFC2A on breast cancer cell cycle and apoptosis. RESULTS Six candidate proteins were found to be differentially expressed in non-TNBC and TNBC groups from CPTAC. However, only OBFC2A was identified as an independently poor prognostic gene marker in METABRIC (HR=3.658, 1.881-7.114). And OBFC2A was associated with immune functions in breast cancer. Biological functional experiments showed that OBFC2A might promote the proliferation and migration of breast cancer cells. The inhibition of OBFC2A expression blocked the cell cycle in G1 phase and inhibited the transformation from G1 phase to S phase. Finally, downregulation of OBFC2A also increased the total apoptosis rate of cells. CONCLUSION On this basis, OBFC2A may be a potential prognostic biomarker for TNBC.
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Affiliation(s)
- Qianxue Wu
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xin Tang
- Department of Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Wenming Zhu
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Qing Li
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Xiang Zhang
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
| | - Hongyuan Li
- Department of the Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing Medical University, Chongqing, China
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Pfleiderer MM, Galej WP. Emerging insights into the function and structure of the Integrator complex. Transcription 2021; 12:251-265. [PMID: 35311473 PMCID: PMC9006982 DOI: 10.1080/21541264.2022.2047583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
The Integrator was originally discovered as a specialized 3'-end processing endonuclease complex required for maturation of RNA polymerase II (RNAPII)-dependent small nuclear RNAs (snRNAs). Since its discovery, Integrator's spectrum of substrates was significantly expanded to include non-polyadenylated long noncoding RNAs (lncRNA), enhancer RNAs (eRNAs), telomerase RNA (tertRNA), several Herpesvirus transcripts, and messenger RNAs (mRNAs). Recently emerging transcriptome-wide studies reveled an important role of the Integrator in protein-coding genes, where it contributes to gene expression regulation through promoter-proximal transcription attenuation. These new functional data are complemented by several structures of Integrator modules and higher-order complexes, providing mechanistic insights into Integrator-mediated processing events. In this work, we summarize recent progress in our understanding of the structure and function of the Integrator complex.
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Jia Y, Cheng Z, Bharath SR, Sun Q, Su N, Huang J, Song H. Crystal structure of the INTS3/INTS6 complex reveals the functional importance of INTS3 dimerization in DSB repair. Cell Discov 2021; 7:66. [PMID: 34400606 PMCID: PMC8368002 DOI: 10.1038/s41421-021-00283-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/17/2021] [Indexed: 11/23/2022] Open
Abstract
SOSS1 is a single-stranded DNA (ssDNA)-binding protein complex that plays a critical role in double-strand DNA break (DSB) repair. SOSS1 consists of three subunits: INTS3, SOSSC, and hSSB1, with INTS3 serving as a scaffold to stabilize this complex. Moreover, the integrator complex subunit 6 (INTS6) participates in the DNA damage response through direct binding to INTS3, but how INTS3 interacts with INTS6, thereby impacting DSB repair, is not clear. Here, we determined the crystal structure of the C-terminus of INTS3 (INTS3c) in complex with the C-terminus of INTS6 (INTS6c) at a resolution of 2.4 Å. Structural analysis revealed that two INTS3c subunits dimerize and interact with INTS6c via conserved residues. Subsequent biochemical analyses confirmed that INTS3c forms a stable dimer and INTS3 dimerization is important for recognizing the longer ssDNA. Perturbation of INTS3c dimerization and disruption of the INTS3c/INTS6c interaction impair the DSB repair process. Altogether, these results unravel the underappreciated role of INTS3 dimerization and the molecular basis of INTS3/INTS6 interaction in DSB repair.
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Affiliation(s)
- Yu Jia
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zixiu Cheng
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sakshibeedu R Bharath
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore City, Singapore
| | - Qiangzu Sun
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Nannan Su
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Huang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Haiwei Song
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China. .,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore City, Singapore. .,Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore City, Singapore.
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8
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Li J, Ma X, Banerjee S, Baruah S, Schnicker NJ, Roh E, Ma W, Liu K, Bode AM, Dong Z. Structural basis for multifunctional roles of human Ints3 C-terminal domain. J Biol Chem 2021; 296:100112. [PMID: 33434574 PMCID: PMC7948952 DOI: 10.1074/jbc.ra120.016393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 11/06/2022] Open
Abstract
Proper repair of damaged DNA is critical for the maintenance of genome stability. A complex composed of Integrator subunit 3 (Ints3), single-stranded DNA-binding protein 1 (SSB1), and SSB-interacting protein 1 (SSBIP1) is required for efficient homologous recombination-dependent repair of double-strand breaks (DSBs) and ataxia-telangiectasia mutated (ATM)-dependent signaling pathways. It is known that in this complex the Ints3 N-terminal domain scaffolds SSB1 and SSBIP1. However, the molecular basis for the function of the Ints3 C-terminal domain remains unclear. Here, we present the crystal structure of the Ints3 C-terminal domain, uncovering a HEAT-repeat superhelical fold. Using structure and mutation analysis, we show that the C-terminal domain exists as a stable dimer. A basic groove and a cluster of conserved residues on two opposite sides of the dimer bind single-stranded RNA/DNA (ssRNA/ssDNA) and Integrator complex subunit 6 (Ints6), respectively. Dimerization is required for nucleic acid binding, but not for Ints6 binding. Additionally, in vitro experiments using HEK 293T cells demonstrate that Ints6 interaction is critical for maintaining SSB1 protein level. Taken together, our findings establish the structural basis of a multifunctional Ints3 C-terminal module, allowing us to propose a novel mode of nucleic acid recognition by helical repeat protein and paving the way for future mechanistic studies.
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Affiliation(s)
- Jian Li
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Xinli Ma
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Surajit Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA
| | - Sankar Baruah
- Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Nicholas J Schnicker
- Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eunmiri Roh
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA; Department of Cosmetic Science, Kwangju Women's University, Gwangju, Republic of Korea
| | - Weiya Ma
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Kangdong Liu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China; College of Medicine, Zhengzhou University, Zhengzhou, Henan, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Zigang Dong
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China; College of Medicine, Zhengzhou University, Zhengzhou, Henan, China.
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Andrade S, Morais T, Sandovici I, Seabra AL, Constância M, Monteiro MP. Adipose Tissue Epigenetic Profile in Obesity-Related Dysglycemia - A Systematic Review. Front Endocrinol (Lausanne) 2021; 12:681649. [PMID: 34290669 PMCID: PMC8288106 DOI: 10.3389/fendo.2021.681649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Obesity is a major risk factor for dysglycemic disorders, including type 2 diabetes (T2D). However, there is wide phenotypic variation in metabolic profiles. Tissue-specific epigenetic modifications could be partially accountable for the observed phenotypic variability. SCOPE The aim of this systematic review was to summarize the available data on epigenetic signatures in human adipose tissue (AT) that characterize overweight or obesity-related insulin resistance (IR) and dysglycemia states and to identify potential underlying mechanisms through the use of unbiased bioinformatics approaches. METHODS Original data published in the last decade concerning the comparison of epigenetic marks in human AT of individuals with metabolically unhealthy overweight/obesity (MUHO) versus normal weight individuals or individuals with metabolically healthy overweight/obesity (MHO) was assessed. Furthermore, association of these epigenetic marks with IR/dysglycemic traits, including T2D, was compiled. RESULTS We catalogued more than two thousand differentially methylated regions (DMRs; above the cut-off of 5%) in the AT of individuals with MUHO compared to individuals with MHO. These DNA methylation changes were less likely to occur around the promoter regions and were enriched at loci implicated in intracellular signaling (signal transduction mediated by small GTPases, ERK1/2 signaling and intracellular trafficking). We also identified a network of seven transcription factors that may play an important role in targeting DNA methylation changes to specific genes in the AT of subjects with MUHO, contributing to the pathogeny of obesity-related IR/T2D. Furthermore, we found differentially methylated CpG sites at 8 genes that were present in AT and whole blood, suggesting that DMRs in whole blood could be potentially used as accessible biomarkers of MUHO. CONCLUSIONS The overall evidence linking epigenetic alterations in key tissues such AT to metabolic complications in human obesity is still very limited, highlighting the need for further studies, particularly those focusing on epigenetic marks other than DNA methylation. Our initial analysis suggests that DNA methylation patterns can potentially discriminate between MUHO from MHO and provide new clues into why some people with obesity are less susceptible to dysglycemia. Identifying AT-specific epigenetic targets could also lead to novel approaches to modify the progression of individuals with obesity towards metabolic disease. SYSTEMATIC REVIEW REGISTRATION PROSPERO, identifier CRD42021227237.
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Affiliation(s)
- Sara Andrade
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Tiago Morais
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Ionel Sandovici
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre L. Seabra
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Miguel Constância
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, Addenbrookes Hospital, Cambridge, United Kingdom
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- National Institute of Health Research, Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Mariana P. Monteiro
- Endocrine and Metabolic Research, Unit for Multidisciplinary Research in Biomedicine (UMIB), University of Porto, Porto, Portugal
- Department of Anatomy, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- *Correspondence: Mariana P. Monteiro,
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10
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Hu Y, Xiao T, Wang Q, Liang B, Zhang A. Effects of Essential Trace Elements and Oxidative Stress on Endemic Arsenism Caused by Coal Burning in PR China. Biol Trace Elem Res 2020; 198:25-36. [PMID: 31960276 DOI: 10.1007/s12011-020-02047-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/15/2020] [Indexed: 12/12/2022]
Abstract
Few studies have investigated the association between essential trace elements and oxidative stress in environmental media and populations with endemic arsenism caused by coal burning. Element contents and oxidative stress indicators were measured. Moreover, the expression of genes related to the nuclear factor E2-related factor 2 (Nrf2)/Kelch-like ECH-associated protein 1 (Keap1)-antioxidant response element (ARE) signaling pathway and Nrf2-ARE binding ability is detected. The results show that the contents of arsenic, copper, iron, and chromium were increased in environmental media from the arsenism area compared with the control area; however, the selenium content decreased. The arsenic, iron, chromium, and copper contents and the copper/zinc ratio were also increased in the arsenic-exposed population; however, the selenium content decreased. The results also show that the concentrations of arsenic, iron, and chromium and the copper/zinc ratio increased gradually with the severity of arsenism. However, selenium concentrations decreased gradually with the severity of arsenism. The contents of malondialdehyde, 8-hydroxyldeoxyguanosine, and protein carbonyl in plasma increased, while the levels of sulfhydryl, thioredoxin reductase (TrxR), glutathione peroxidase (Gpx), and superoxide dismutase 1 (SOD1) decreased. The mRNA expression of Keap1 and TrxR1 decreased in the blood, while the mRNA expression of Nrf2, GPx1, and SOD1 increased. Moreover, the Nrf2 protein content and Nrf2-ARE binding ability increased, and the Keap1 protein content decreased. In conclusion, our data suggest that the increased arsenic content in environmental media and populations was accompanied by abnormal levels of essential trace elements. Insufficient selenium intake, copper, and chromium overload and a high copper/zinc ratio might be some of the causes of arsenism, which might be related to the Nrf2/Keap1-ARE signaling pathway.
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Affiliation(s)
- Yong Hu
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Tingting Xiao
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Qi Wang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Bing Liang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Aihua Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, People's Republic of China.
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11
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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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12
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Trubnykova M, Bazalar Montoya J, La Serna-Infantes J, Vásquez Sotomayor F, Castro Mujica MDC, Abarca Barriga HH. GATAD2B Gene Microdeletion Causing Intellectual Disability Autosomal Dominant Type 18: Case Report and Review of the Literature. Mol Syndromol 2019; 10:186-194. [PMID: 31602190 DOI: 10.1159/000499209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2019] [Indexed: 12/15/2022] Open
Abstract
Pathogenic variants of the GATAD2B gene (1q21.3) are linked to intellectual disability autosomal dominant type 18 (MRD18; MIM 615074), characterized by dysmorphic features, psychomotor and language delay. We present an 11-year-old female patient with intellectual disability and typical clinical characteristics of MRD18. Chromosomal microarray analysis (CMA) revealed a novel CNV, approximately 200 kb in size and showed that the INTS3 and SLC27A3 genes are completely deleted along with the first 10 exons of the GATAD2B gene. INTS3 encodes the integrator complex subunit 3 and is part of the complex that maintains genome stability; SLC27A3 encodes a fatty acid transporter and has been associated with autism spectrum disorder. GATAD2B haploinsufficiency is associated with the phenotype. Furthermore, the girl had other clinical characteristics not previously described, such as emotional instability, calf hypotrophy, hypoplastic digit pads, tapered thumbs, and anterior earlobe crease. This study highlights the importance of the phenotype-genotype correlation using molecular diagnostic techniques, such as CMA, and its impact on precise diagnosis, treatment, prognosis, and genetic counseling for patients and their families.
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Affiliation(s)
- Milana Trubnykova
- Servicio de Genética & Errores Innatos del Metabolismo (EIM), Instituto Nacional de Salud del Niño-Breña
| | - Jeny Bazalar Montoya
- Unidad de Genética & Biología Molecular, Instituto Nacional de Enfermedades Neoplásicas
| | | | - Flor Vásquez Sotomayor
- Servicio de Genética & Errores Innatos del Metabolismo (EIM), Instituto Nacional de Salud del Niño-Breña
| | | | - Hugo Hernán Abarca Barriga
- Servicio de Genética & Errores Innatos del Metabolismo (EIM), Instituto Nacional de Salud del Niño-Breña.,Facultad de Medicina Humana, Universidad Ricardo Palma.,Facultad de Odontología, Universidad Científica del Sur, Lima, Peru
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13
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Lawson T, El-Kamand S, Kariawasam R, Richard DJ, Cubeddu L, Gamsjaeger R. A Structural Perspective on the Regulation of Human Single-Stranded DNA Binding Protein 1 (hSSB1, OBFC2B) Function in DNA Repair. Comput Struct Biotechnol J 2019; 17:441-446. [PMID: 30996823 PMCID: PMC6451162 DOI: 10.1016/j.csbj.2019.03.014] [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: 02/27/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Single-stranded DNA binding (SSB) proteins are essential to protect singe-stranded DNA (ssDNA) that exists as a result of several important DNA repair pathways in living cells. In humans, besides the well-characterised Replication Protein A (RPA) we have described another SSB termed human SSB1 (hSSB1, OBFC2B) and have shown that this protein is an important player in the maintenance of the genome. In this review we define the structural and biophysical details of how hSSB1 interacts with both DNA and other essential proteins. While the presence of the oligonucleotide/oligosaccharide (OB) domain ensures ssDNA binding by hSSB1, it has also been shown to self-oligomerise as well as interact with and being modified by several proteins highlighting the versatility that hSSB1 displays in the context of DNA repair. A detailed structural understanding of these processes will likely lead to the designs of tailored hSSB1 inhibitors as anti-cancer drugs in the near future.
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Affiliation(s)
- Teegan Lawson
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Serene El-Kamand
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Derek J Richard
- Genome Stability Laboratory, Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland 4102, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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