1
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Zhang F, Xiong Q, Wang M, Cao X, Zhou C. FUBP1 in human cancer: Characteristics, functions, and potential applications. Transl Oncol 2024; 48:102066. [PMID: 39067088 DOI: 10.1016/j.tranon.2024.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/04/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
Far upstream element-binding protein 1 (FUBP1) is a single-stranded nucleic acid-binding protein that binds to the Far Upstream Element (FUSE) sequence and is involved in important biological processes, including DNA transcription, RNA biogenesis, and translation. Recent studies have highlighted the significance of aberrant expression or mutations in FUBP1 in the development of various tumors, with FUBP1 overexpression often indicating oncogenic roles in different tumor types. However, it is worth noting that recent research has discovered its tumor-suppressive role in cancer, which is not yet fully understood and appears to be tissue- or context-dependent. This review summarizes the association between FUBP1 and diverse cancers and discusses the functions of FUBP1 in cancer. In addition, this review proposes potential clinical implications and outlines future research directions to pave the way for the development of targeted therapeutic strategies focusing on FUBP1.
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Affiliation(s)
- Fan Zhang
- Department of Oncology, Shaanxi Provincial People's Hospital, No 256 Youyi West Road, Xi'an, 710068, Shaanxi, China
| | - Qunli Xiong
- Department of Abdominal Oncology, West China Hospital, Sichuan University, No 37 Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Min Wang
- Department of Science and Education, Xi'an Children's Hospital Affiliated of Xi'an Jiaotong University, No 69 Xijuyuan lane, Xi'an, 710002, Shaanxi, China
| | - Ximing Cao
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, No 256 Youyi West Road, Xi'an, 710068, Shaanxi, China
| | - Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, No 256 Youyi West Road, Xi'an, 710068, Shaanxi, China.
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2
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An H, Wang X, Li J, Sun H, Zhu S, Ge J, Han L, Shen B, Wang Q. KAS-seq profiling captures transcription dynamics during oocyte maturation. J Ovarian Res 2024; 17:23. [PMID: 38267939 PMCID: PMC10807090 DOI: 10.1186/s13048-023-01342-8] [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: 11/03/2023] [Accepted: 12/31/2023] [Indexed: 01/26/2024] Open
Abstract
In fully grown oocytes, the genome is considered to be globally transcriptionally silenced. However, this conclusion is primarily derived from the results obtained through immunofluorescence staining or inferred from the highly condensed state of chromosomes, lacking more direct evidence. Here, by using a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, we investigated the landscape of single-strand DNA (ssDNA) throughout the genome and provided a readout of the activity and dynamics of transcription during oocyte meiotic maturation. In non-surrounded nucleolus (NSN) oocytes, we observed a robust KAS-seq signal, indicating the high transcriptional activity. In surrounded nucleolus (SN) oocytes, the presence of ssDNA still persists although the KAS-seq signal was relatively weak, suggesting the presence of transcription. Accompanying with the meiotic resumption, the transcriptional activity gradually decreased, and global repression was detected in matured oocytes. Moreover, we preformed the integrative genomics analysis to dissect the transcriptional dynamics during mouse oocyte maturation. In sum, the present study delineates the detailed transcriptional activity during mammalian oocyte maturation.
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Affiliation(s)
- Huiqing An
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Xiuwan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Jiashuo Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Hongzheng Sun
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Shuai Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Juan Ge
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Longsen Han
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China
| | - Qiang Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 101 Longmian Rd, Nanjing, 211166, China.
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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3
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Xi Z, Huang H, Hu J, Yu Y, Ma X, Xu M, Ming J, Li L, Zhang H, Chen H, Huang T. LINC00571 drives tricarboxylic acid cycle metabolism in triple-negative breast cancer through HNRNPK/ILF2/IDH2 axis. J Exp Clin Cancer Res 2024; 43:22. [PMID: 38238853 PMCID: PMC10795234 DOI: 10.1186/s13046-024-02950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer is a complex breast malignancy subtype characterized by poor prognosis. The pursuit of effective therapeutic approaches for this subtype is considerably challenging. Notably, recent research has illuminated the key role of the tricarboxylic acid cycle in cancer metabolism and the complex landscape of tumor development. Concurrently, an emerging body of evidence underscores the noteworthy role that long non-coding RNAs play in the trajectory of breast cancer development. Despite this growing recognition, the exploration of whether long non-coding RNAs can influence breast cancer progression by modulating the tricarboxylic acid cycle has been limited. Moreover, the underlying mechanisms orchestrating these interactions have not been identified. METHODS The expression levels of LINC00571 and IDH2 were determined through the analysis of the public TCGA dataset, transcriptome sequencing, qRT‒PCR, and Western blotting. The distribution of LINC00571 was assessed using RNA fluorescence in situ hybridization. Alterations in biological effects were evaluated using CCK-8, colony formation, EdU, cell cycle, and apoptosis assays and a tumor xenograft model. To elucidate the interaction between LINC00571, HNRNPK, and ILF2, RNA pull-down, mass spectrometry, coimmunoprecipitation, and RNA immunoprecipitation assays were performed. The impacts of LINC00571 and IDH2 on tricarboxylic acid cycle metabolites were investigated through measurements of the oxygen consumption rate and metabolite levels. RESULTS This study revealed the complex interactions between a novel long non-coding RNA (LINC00571) and tricarboxylic acid cycle metabolism. We validated the tumor-promoting role of LINC00571. Mechanistically, LINC00571 facilitated the interaction between HNRNPK and ILF2, leading to reduced ubiquitination and degradation of ILF2, thereby stabilizing its expression. Furthermore, ILF2 acted as a transcription factor to enhance the expression of its downstream target gene IDH2. CONCLUSIONS Our study revealed that the LINC00571/HNRNPK/ILF2/IDH2 axis promoted the progression of triple-negative breast cancer by regulating tricarboxylic acid cycle metabolites. This discovery provides a novel theoretical foundation and new potential targets for the clinical treatment of triple-negative breast cancer.
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Affiliation(s)
- Zihan Xi
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Haohao Huang
- Department of Neurosurgery, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, 430070, China
- General Hospital Of Central Theater Command and Hubei Key Laboratory of Central Nervous System Tumor and Intervention, Wuhan, China
| | - Jin Hu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yuanhang Yu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xianxiong Ma
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ming Xu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jie Ming
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Hengyu Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, China.
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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4
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Cho E, Che X, Ang MJ, Cheon S, Lee J, Kim KS, Lee CH, Lee SY, Yang HY, Moon C, Park C, Choi JY, Lee TH. Peroxiredoxin 5 regulates osteogenic differentiation through interaction with hnRNPK during bone regeneration. eLife 2023; 12:80122. [PMID: 36735291 PMCID: PMC9897727 DOI: 10.7554/elife.80122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
Peroxiredoxin 5 (Prdx5) is involved in pathophysiological regulation via the stress-induced cellular response. However, its function in the bone remains largely unknown. Here, we show that Prdx5 is involved in osteoclast and osteoblast differentiation, resulting in osteoporotic phenotypes in Prdx5 knockout (Prdx5Ko) male mice. To investigate the function of Prdx5 in the bone, osteoblasts were analyzed through immunoprecipitation (IP) and liquid chromatography combined with tandem mass spectrometry (LC-MS/MS) methods, while osteoclasts were analyzed through RNA-sequencing. Heterogeneous nuclear ribonucleoprotein K (hnRNPK) was identified as a potential binding partner of Prdx5 during osteoblast differentiation in vitro. Prdx5 acts as a negative regulator of hnRNPK-mediated osteocalcin (Bglap) expression. In addition, transcriptomic analysis revealed that in vitro differentiated osteoclasts from the bone marrow-derived macrophages of Prdx5Ko mice showed enhanced expression of several osteoclast-related genes. These findings indicate that Prdx5 might contribute to the maintenance of bone homeostasis by regulating osteoblast differentiation. This study proposes a new function of Prdx5 in bone remodeling that may be used in developing therapeutic strategies for bone diseases.
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Affiliation(s)
- Eunjin Cho
- Department of Oral Biochemistry, Korea Mouse Phenotype Center (KMPC), Dental Science Research Institute, School of Dentistry, Chonnam National UniversityGwangjuRepublic of Korea
| | - Xiangguo Che
- Department of Biochemistry and Cell Biology, BK21 Plus KNU Biomedical Convergence Program, Skeletal Diseases Analysis Center, Korea Mouse Phenotyping Center (KMPC), School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Mary Jasmin Ang
- Department of Basic Veterinary Sciences, College of Veterinary Medicine, University of the Philippines Los BañosLos BañosPhilippines
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National UniversityGwangjuRepublic of Korea,Proteomics Core Facility, Biomedical Research Institute, Seoul National University HospitalSeoulRepublic of Korea
| | - Jinkyung Lee
- Department of Oral Biochemistry, Korea Mouse Phenotype Center (KMPC), Dental Science Research Institute, School of Dentistry, Chonnam National UniversityGwangjuRepublic of Korea
| | - Kwang Soo Kim
- Department of Microbiology, Department of Molecular Medicine (BK21plus), Chonnam National University Medical SchoolGwangjuRepublic of Korea
| | - Chang Hoon Lee
- Therapeutic & Biotechnology Division, Drug Discovery Platform Research Center, Research Institute of Chemical Technology (KRICT)DaejeonRepublic of Korea
| | - Sang-Yeop Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science InstituteOchangRepublic of Korea
| | - Hee-Young Yang
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation FoundationDaeguRepublic of Korea
| | - Changjong Moon
- Department of Veterinary Anatomy and Animal Behavior, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National UniversityGwangjuRepublic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National UniversityGwangjuRepublic of Korea
| | - Je-Yong Choi
- Department of Biochemistry and Cell Biology, BK21 Plus KNU Biomedical Convergence Program, Skeletal Diseases Analysis Center, Korea Mouse Phenotyping Center (KMPC), School of Medicine, Kyungpook National UniversityDaeguRepublic of Korea
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Korea Mouse Phenotype Center (KMPC), Dental Science Research Institute, School of Dentistry, Chonnam National UniversityGwangjuRepublic of Korea
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5
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Mechanistic insights into poly(C)-binding protein hnRNP K resolving i-motif DNA secondary structures. J Biol Chem 2022; 298:102670. [PMID: 36334628 PMCID: PMC9709238 DOI: 10.1016/j.jbc.2022.102670] [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: 06/28/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 11/27/2022] Open
Abstract
I-motifs are four-strand noncanonical secondary structures formed by cytosine (C)-rich sequences in living cells. The structural dynamics of i-motifs play essential roles in many cellular processes, such as telomerase inhibition, DNA replication, and transcriptional regulation. In cells, the structural dynamics of the i-motif can be modulated by the interaction of poly(C)-binding proteins (PCBPs), and the interaction is closely related to human health, through modulating the transcription of oncogenes and telomere stability. Therefore, the mechanisms of how PCBPs interact with i-motif structures are fundamentally important. However, the underlying mechanisms remain elusive. I-motif structures in the promoter of the c-MYC oncogene can be unfolded by heterogeneous nuclear ribonucleoprotein K (hnRNP K), a PCBP, to activate its transcription. Here, we selected this system as an example to comprehensively study the unfolding mechanisms. We found that the promoter sequence containing 5 C-runs preferred folding into type-1245 to type-1234 i-motif structures based on their folding stability, which was further confirmed by single-molecule FRET. In addition, we first revealed that the c-MYC i-motif structure was discretely resolved by hnRNP K through two intermediate states, which were assigned to the opposite hairpin and neighboring hairpin, as further confirmed by site mutations. Furthermore, we found all three KH (hnRNP K homology) domains of hnRNP K could unfold the c-MYC i-motif structure, and KH2 and KH3 were more active than KH1. In conclusion, this study may deepen our understanding of the interactions between i-motifs and PCBPs and may be helpful for drug development.
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6
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Guo JT, Malik F. Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches. Biomolecules 2022; 12:biom12091187. [PMID: 36139026 PMCID: PMC9496475 DOI: 10.3390/biom12091187] [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: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).
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7
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Cheng J, Morselli M, Huang WL, Heo YJ, Pinheiro-Ferreira T, Li F, Wei F, Chia D, Kim Y, He HJ, Cole KD, Su WC, Pellegrini M, Wong DT. Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA. iScience 2022; 25:104554. [PMID: 35800774 PMCID: PMC9254344 DOI: 10.1016/j.isci.2022.104554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/25/2022] [Accepted: 06/02/2022] [Indexed: 12/28/2022] Open
Abstract
Plasma cell-free DNA is being widely explored as a biomarker for clinical screening. Currently, methods are optimized for the extraction and detection of double-stranded mononucleosomal cell-free DNA of ∼160bp in length. We introduce uscfDNA-seq, a single-stranded cell-free DNA next-generation sequencing pipeline, which bypasses previous limitations to reveal a population of ultrashort single-stranded cell-free DNA in human plasma. This species has a modal size of 50nt and is distinctly separate from mononucleosomal cell-free DNA. Treatment with single-stranded and double-stranded specific nucleases suggests that ultrashort cell-free DNA is primarily single-stranded. It is distributed evenly across chromosomes and has a similar distribution profile over functional elements as the genome, albeit with an enrichment over promoters, exons, and introns, which may be suggestive of a terminal state of genome degradation. The examination of this cfDNA species could reveal new features of cell death pathways or it can be used for cell-free DNA biomarker discovery.
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Affiliation(s)
- Jordan Cheng
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Marco Morselli
- Department of Molecular, Cellular & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Wei-Lun Huang
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 704, Taiwan
| | - You Jeong Heo
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea
| | | | - Feng Li
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - David Chia
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Kenneth D. Cole
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Wu-Chou Su
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Matteo Pellegrini
- Department of Molecular, Cellular & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - David T.W. Wong
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
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8
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Roth Weizman E, Glick Azaria A, Garini Y. Conformation of Ring Single-Stranded DNA Measured by DNA Origami Structures. Biophys J 2022; 121:2127-2134. [PMID: 35490298 DOI: 10.1016/j.bpj.2022.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/17/2021] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Measuring the mechanical properties of single-stranded DNA (ssDNA) is a complex challenge that has been addressed lately by different methods. We measured the persistence length of ring ssDNA using a combination of special DNA origami structure, a self-avoiding ring-polymer simulation model and a non-parametric estimation statistics. The method overcomes the complexities set forth by previously used methods. We designed the DNA origami nano structures and measured the ring ssDNA polymer conformations using atomic force microscopy. We then calculated its radius of gyration, which was used as a fitting parameter for finding the persistence length. As there is no simple formulation for the radius of gyration distribution, we developed a simulation program consisting of a self-avoiding ring polymer to fit the persistence length to the experimental data. ssDNA naturally forms stem loops, which should be taken into account in fitting a model to the experimental measurement. To overcome that hurdle, we found the possible loops using minimal energy considerations and used it in our fitting procedure of the persistence length. Due to the statistical nature of the loops formation, we calculated the persistence length for different percentages of loops that are formed. In the range of 25-75% loop formation, we found the persistence length to be 1.9-4.4 nm and for 50% loop formation we get a persistence length of 2.83±0.63nm. This estimation narrows the previously known persistence length, and provides tools for finding the conformations of ssDNA.
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Affiliation(s)
- Efrat Roth Weizman
- Physics Depsartment & Institute for Nanotechnology, Bar Ilan University, Ramat Gan, Israel.
| | - Alex Glick Azaria
- Physics Depsartment & Institute for Nanotechnology, Bar Ilan University, Ramat Gan, Israel
| | - Yuval Garini
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
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9
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Puvvula PK, Buczkowski S, Moon AM. hnRNPK-derived cell-penetrating peptide inhibits cancer cell survival. Mol Ther Oncolytics 2021; 23:342-354. [PMID: 34820504 PMCID: PMC8586514 DOI: 10.1016/j.omto.2021.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
hnRNPK is a multifunctional protein that plays an important role in cancer cell proliferation and metastasis via its RNA- and DNA-binding properties. Previously we showed that cell-penetrating peptides derived from the RGG RNA-binding domain of SAFA (hnRNPU) disrupt cancer cell proliferation and survival. Here we explore the efficacy of a peptide derived from the RGG domain of hnRNPK. This peptide acts in a dominant-negative manner on several hnRNPK functions to induce death of multiple types of cancer cells. The peptide phenocopies the effect of hnRNPK knockdown on its mRNA-stability targets such as KLF4 and EGR1 and alters the levels and locations of long non-coding RNAs (lncRNAs) and proteins required for nuclear and paraspeckle formation and function. The RGG-derived peptide also decreases euchromatin as evidenced by loss of active marks and polymerase II occupancy. Our findings reveal the potential therapeutic utility of the hnRNPK RGG-derived peptide in a range of cancers.
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Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Corresponding author: Pavan Kumar Puvvula, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
| | - Stephanie Buczkowski
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
| | - Anne M. Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, USA
- Corresponding author: Anne M. Moon, MD, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
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10
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Kwon PK, Kim HM, Kang B, Kim SW, Hwang SM, Im SH, Roh TY, Kim KT. hnRNP K supports the maintenance of RORγ circadian rhythm through ERK signaling. FASEB J 2021; 35:e21507. [PMID: 33724572 DOI: 10.1096/fj.202002076r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 11/11/2022]
Abstract
Retinoic acid-related orphan receptor γ (RORγ) maintains the circadian rhythms of its downstream genes. However, the mechanism behind the transcriptional activation of RORγ itself remains unclear. Here, we demonstrate that transcription of RORγ is activated by heterogeneous nuclear ribonucleoprotein K (hnRNP K) via the poly(C) motif within its proximal promoter. Interestingly, we confirmed the binding of endogenous hnRNP K within RORγ1 and RORγ2 promoter along with the recruitment of RNA polymerase 2 through chromatin immunoprecipitation (ChIP). Furthermore, an assay for transposase accessible chromatin (ATAC)-qPCR showed that hnRNP K induced higher chromatin accessibility within the RORγ1 and RORγ2 promoter. Then we found that the knockdown of hnRNP K lowers RORγ mRNA oscillation amplitude in both RORγ and RORγ-dependent metabolic genes. Moreover, we demonstrated that time-dependent extracellular signal-regulated kinase (ERK) activation controls mRNA oscillation of RORγ and RORγ-dependent metabolic genes through hnRNP K. Taken together, our results provide new insight into the regulation of RORγ by hnRNP K as a transcriptional activator, along with its physiological significance in metabolism.
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Affiliation(s)
- Paul Kwangho Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Hyo-Min Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Byunghee Kang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sung Wook Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sung-Min Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kyong-Tai Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
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11
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Ray S, Tillo D, Durell SR, Khund-Sayeed S, Vinson C. REL Domain of NFATc2 Binding to Five Types of DNA Using Protein Binding Microarrays. ACS OMEGA 2021; 6:4147-4154. [PMID: 33644537 PMCID: PMC7906578 DOI: 10.1021/acsomega.0c04069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
NFATc2 is a DNA binding protein in the Rel family transcription factors, which binds a CGGAA motif better when both cytosines in the CG dinucleotide are methylated. Using protein binding microarrays (PBMs), we examined the DNA binding of NFATc2 to three additional types of DNA: single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with either 5-methylcytosine (5mC, M) or 5-hydroxymethylcytosine (5hmC, H) in one strand and a cytosine in the second strand. ATTTCCAC, the complement of the core GGAA motif, is better bound as ssDNA compared to dsDNA. dsDNA containing the 5-mer CGGAA with either 5mC or 5hmC in one DNA strand is bound stronger than CGGAA. In contrast, the reverse complement TTCCG is bound weaker when it contains 5mC. Analysis of the available NFATc2:dsDNA complexes rationalizes these PBM data.
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Affiliation(s)
- Sreejana Ray
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, 37 Convent Drive, Building 37, Room 5000, Bethesda, Maryland 20892, United States
| | - Desiree Tillo
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, 37 Convent Drive, Building 37, Room 5000, Bethesda, Maryland 20892, United States
| | - Stewart R. Durell
- Laboratory
of Cell Biology, National Cancer Institute,
National Institutes of Health, 37 Convent Drive, Building 37, Room 5000, Bethesda, Maryland 20892, United States
| | - Syed Khund-Sayeed
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, 37 Convent Drive, Building 37, Room 5000, Bethesda, Maryland 20892, United States
| | - Charles Vinson
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, 37 Convent Drive, Building 37, Room 5000, Bethesda, Maryland 20892, United States
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12
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Yadav M, Singh RS, Hogan D, Vidhyasagar V, Yang S, Chung IYW, Kusalik A, Dmitriev OY, Cygler M, Wu Y. The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase. J Biol Chem 2021; 296:100085. [PMID: 33199368 PMCID: PMC7949032 DOI: 10.1074/jbc.ra120.015824] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins. Recently, we found that the DEAD-box helicase DDX43 contains a KH domain in its N-terminus; however, its function remains unknown. Here, we purified recombinant DDX43 KH domain protein and found that it prefers binding ssDNA and ssRNA. Electrophoretic mobility shift assay and NMR revealed that the KH domain favors pyrimidines over purines. Mutational analysis showed that the GXXG loop in the KH domain is involved in pyrimidine binding. Moreover, we found that an alanine residue adjacent to the GXXG loop is critical for binding. Systematic evolution of ligands by exponential enrichment, chromatin immunoprecipitation-seq, and cross-linking immunoprecipitation-seq showed that the KH domain binds C-/T-rich DNA and U-rich RNA. Bioinformatics analysis suggested that the KH domain prefers to bind promoters. Using 15N-heteronuclear single quantum coherence NMR, the optimal binding sequence was identified as TTGT. Finally, we found that the full-length DDX43 helicase prefers DNA or RNA substrates with TTGT or UUGU single-stranded tails and that the KH domain is critically important for sequence specificity and unwinding processivity. Collectively, our results demonstrated that the KH domain facilitates the substrate specificity and processivity of the DDX43 helicase.
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Affiliation(s)
- Manisha Yadav
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ravi Shankar Singh
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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13
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Zheng KW, Zhang JY, He YD, Gong JY, Wen CJ, Chen JN, Hao YH, Zhao Y, Tan Z. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res 2020; 48:11706-11720. [PMID: 33045726 PMCID: PMC7672459 DOI: 10.1093/nar/gkaa841] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123 000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ∼70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
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Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Jia-yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Jia-yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Cui-jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Juan-nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Yu-hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Yong Zhao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
- Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P.R. China
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14
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Xu Y, Wu W, Han Q, Wang Y, Li C, Zhang P, Xu H. Post-translational modification control of RNA-binding protein hnRNPK function. Open Biol 2020; 9:180239. [PMID: 30836866 PMCID: PMC6451366 DOI: 10.1098/rsob.180239] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK), a ubiquitously occurring RNA-binding protein (RBP), can interact with numerous nucleic acids and various proteins and is involved in a number of cellular functions including transcription, translation, splicing, chromatin remodelling, etc. Through its abundant biological functions, hnRNPK has been implicated in cellular events including proliferation, differentiation, apoptosis, DNA damage repair and the stress and immune responses. Thus, it is critical to understand the mechanism of hnRNPK regulation and its downstream effects on cancer and other diseases. A number of recent studies have highlighted that several post-translational modifications (PTMs) possibly play an important role in modulating hnRNPK function. Phosphorylation is the most widely occurring PTM in hnRNPK. For example, in vivo analyses of sites such as S116 and S284 illustrate the purpose of PTM of hnRNPK in altering its subcellular localization and its ability to bind target nucleic acids or proteins. Other PTMs such as methylation, ubiquitination, sumoylation, glycosylation and proteolytic cleavage are increasingly implicated in the regulation of DNA repair, cellular stresses and tumour growth. In this review, we describe the PTMs that impact upon hnRNPK function on gene expression programmes and different disease states. This knowledge is key in allowing us to better understand the mechanism of hnRNPK regulation.
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Affiliation(s)
- Yongjie Xu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Wei Wu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Qiu Han
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Yaling Wang
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Cencen Li
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Pengpeng Zhang
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
| | - Haixia Xu
- College of Life Science, Xinyang Normal University , Xinyang 464000 , People's Republic of China
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15
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hnRNP K Supports High-Amplitude D Site-Binding Protein mRNA ( Dbp mRNA) Oscillation To Sustain Circadian Rhythms. Mol Cell Biol 2020; 40:MCB.00537-19. [PMID: 31907279 DOI: 10.1128/mcb.00537-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/20/2019] [Indexed: 01/24/2023] Open
Abstract
Circadian gene expression is defined by the gene-specific phase and amplitude of daily oscillations in mRNA and protein levels. D site-binding protein mRNA (Dbp mRNA) shows high-amplitude oscillation; however, the underlying mechanism remains elusive. Here, we demonstrate that heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a key regulator that activates Dbp transcription via the poly(C) motif within its proximal promoter. Biochemical analyses identified hnRNP K as a specific protein that directly associates with the poly(C) motif in vitro Interestingly, we further confirmed the rhythmic binding of endogenous hnRNP K within the Dbp promoter through chromatin immunoprecipitation as well as the cycling expression of hnRNP K. Finally, knockdown of hnRNP K decreased mRNA oscillation in both Dbp and Dbp-dependent clock genes. Taken together, our results show rhythmic protein expression of hnRNP K and provide new insights into its function as a transcriptional amplifier of Dbp.
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16
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Liu W, Lin C, Wu G, Dai J, Chang TC, Yang D. Structures of 1:1 and 2:1 complexes of BMVC and MYC promoter G-quadruplex reveal a mechanism of ligand conformation adjustment for G4-recognition. Nucleic Acids Res 2019; 47:11931-11942. [PMID: 31740959 PMCID: PMC7145684 DOI: 10.1093/nar/gkz1015] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/11/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
BMVC is the first fluorescent probe designed to detect G-quadruplexes (G4s) in vivo. The MYC oncogene promoter forms a G4 (MycG4) which acts as a transcription silencer. Here, we report the high-affinity and specific binding of BMVC to MycG4 with unusual slow-exchange rates on the NMR timescale. We also show that BMVC represses MYC in cancer cells. We determined the solution structures of the 1:1 and 2:1 BMVC-MycG4 complexes. BMVC first binds the 5'-end of MycG4 to form a 1:1 complex with a well-defined structure. At higher ratio, BMVC also binds the 3'-end to form a second complex. In both complexes, the crescent-shaped BMVC recruits a flanking DNA residue to form a BMVC-base plane stacking over the external G-tetrad. Remarkably, BMVC adjusts its conformation to a contracted form to match the G-tetrad for an optimal stacking interaction. This is the first structural example showing the importance of ligand conformational adjustment in G4 recognition. BMVC binds the more accessible 5'-end with higher affinity, whereas sequence specificity is present at the weaker-binding 3'-site. Our structures provide insights into specific recognition of MycG4 by BMVC and useful information for design of G4-targeted anticancer drugs and fluorescent probes.
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Affiliation(s)
- Wenting Liu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Ave, West Lafayette, IN 47907, USA
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Clement Lin
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Ave, West Lafayette, IN 47907, USA
| | - Guanhui Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Ave, West Lafayette, IN 47907, USA
| | - Jixun Dai
- College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-166, Taipei 106, Taiwan ROC
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Ave, West Lafayette, IN 47907, USA
- Purdue Center for Cancer Research, West Lafayette, IN 47906, USA
- Purdue Institute for Drug Discovery, West Lafayette, IN 47907, USA
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17
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Mondal M, Bhattacharyya D, Gao YQ. Structural properties and influence of solvent on the stability of telomeric four-stranded i-motif DNA. Phys Chem Chem Phys 2019; 21:21549-21560. [PMID: 31536074 DOI: 10.1039/c9cp03253c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Repetitive cytosine rich i-motif forming sequences are abundant in the telomere, centromere and promoters of several oncogenes and in some instances are known to regulate transcription and gene expression. The in vivo existence of i-motif structures demands further insight into the factors affecting their formation and stability and development of better understanding of their gene regulatory functions. Most prior studies characterizing the conformational dynamics of i-motifs are based on i-motif forming synthetic constructs. Here, we present a systematic study on the stability and structural properties of biologically relevant i-motifs of telomeric and centromeric repeat fragments. Our results based on molecular dynamics simulations and quantum chemical calculations indicate that along with base pairing interactions within the i-motif core the overall folded conformation is associated with the stable C-HO sugar "zippers" in the narrow grooves and structured water molecules along the wide grooves. The stacked geometry of the hemi-protonated cytosine pairs within the i-motif core is mainly governed by the repulsive base stacking interaction. The loop sequence can affect the structural dynamics of the i-motif by altering the loop motion and backbone conformation. Overall this study provides microscopic insight into the i-motif structure that will be helpful to understand the structural aspect of mechanisms of gene regulation by i-motif DNA.
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Affiliation(s)
- Manas Mondal
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.
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18
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DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation. Proc Natl Acad Sci U S A 2019; 116:20453-20461. [PMID: 31548374 DOI: 10.1073/pnas.1909047116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) are noncanonical secondary structures formed in guanine-rich DNA and RNA sequences. MYC, one of the most critical oncogenes, forms a DNA G4 in its proximal promoter region (MycG4) that functions as a transcriptional silencer. However, MycG4 is highly stable in vitro and its regulatory role would require active unfolding. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, is extremely proficient at unfolding MycG4-DNA. Our results show that DDX5 is a highly active G4-resolvase that does not require a single-stranded overhang and that ATP hydrolysis is not directly coupled to G4-unfolding of DDX5. The chromatin binding sites of DDX5 are G-rich sequences. In cancer cells, DDX5 is enriched at the MYC promoter and activates MYC transcription. The DDX5 interaction with the MYC promoter and DDX5-mediated MYC activation is inhibited by G4-interactive small molecules. Our results uncover a function of DDX5 in resolving DNA and RNA G4s and suggest a molecular target to suppress MYC for cancer intervention.
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19
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Molnar M, Liddell SC, Wadkins RM. Effects of Polyamine Binding on the Stability of DNA i-Motif Structures. ACS OMEGA 2019; 4:8967-8973. [PMID: 31459985 PMCID: PMC6648627 DOI: 10.1021/acsomega.9b00784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/13/2019] [Indexed: 05/12/2023]
Abstract
B-form DNA can adopt alternative structures under conditions such as superhelical duress. Alternative DNA structures are favored when there is asymmetric distribution of guanosine and cytosine on complimentary DNA strands. A guanosine-rich strand can form a four-stranded structure known as a quadruplex (G4). The complimentary cytosine-rich strand can utilize intercalating cytosine-cytosine base pairing to form a four-stranded structure known as the i-motif (iM). Both secondary structures are energetically uphill from double-strand DNA (dsDNA), meaning that additional factors are needed for their formation. Most iMs require slightly acidic conditions for structure stabilization. However, crowding agents such as polyethylene glycols and dextrans can shift the pK a of the iM to near-physiological pH ≈ 7. Nucleic acids have long been known to be bound and stabilized by polyamines such as putrescine, spermidine, and spermine. Polyamines have very high concentrations in cells (0.1-30 mM), and their binding to DNA is driven by electrostatic interactions. Polyamines typically bind in the minor groove of DNA. However, because of the unusual structure of iMs, it was unknown whether polyamines might also bind and stabilize iMs. The study described here was undertaken to analyze polyamine-iM interactions. The thermal stability and pH dependence of iM structures were determined in the presence of polyamines. In contrast to dsDNA, our results suggest that polyamines have considerably weaker interactions with iMs, as demonstrated by the minimal change in iM pH dependence and thermal stability. Our results suggest that polyamines are unlikely to provide a significant source of iM stabilization in vivo.
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Affiliation(s)
- Michael
M. Molnar
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Shelby C. Liddell
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Randy M. Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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20
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i‐Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Manish Debnath
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Khushnood Fatma
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of Science Jadavpur Kolkata- 700032 India
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21
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Debnath M, Fatma K, Dash J. Chemical Regulation of DNA i-Motifs for Nanobiotechnology and Therapeutics. Angew Chem Int Ed Engl 2019; 58:2942-2957. [PMID: 30600876 DOI: 10.1002/anie.201813288] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/27/2018] [Indexed: 12/20/2022]
Abstract
DNA sequences rich in cytosine have the propensity, under acidic pH, to fold into four-stranded intercalated DNA structures called i-motifs. Recent studies have provided significant breakthroughs that demonstrate how chemists can manipulate these structures for nanobiotechnology and therapeutics. The first section of this Minireview discusses the development of advanced functional nanostructures by synthetic conjugation of i-motifs with organic scaffolds and metal nanoparticles and their role in therapeutics. The second section highlights the therapeutic targeting of i-motifs with chemical scaffolds and their significance in biology. For this, first we shed light on the long-lasting debate regarding the stability of i-motifs under physiological conditions. Next, we present a comparative analysis of recently reported small molecules for specifically targeting i-motifs over other abundant DNA structures and modulating their function in cellular systems. These advances provide new insights into i-motif-targeted regulation of gene expression, telomere maintenance, and therapeutic applications.
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Affiliation(s)
- Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Khushnood Fatma
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-, 700032, India
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22
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Debaize L, Troadec MB. The master regulator FUBP1: its emerging role in normal cell function and malignant development. Cell Mol Life Sci 2019; 76:259-281. [PMID: 30343319 PMCID: PMC11105487 DOI: 10.1007/s00018-018-2933-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/06/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022]
Abstract
The human Far Upstream Element (FUSE) Binding Protein 1 (FUBP1) is a multifunctional DNA- and RNA-binding protein involved in diverse cellular processes. FUBP1 is a master regulator of transcription, translation, and RNA splicing. FUBP1 has been identified as a potent pro-proliferative and anti-apoptotic factor by modulation of complex networks. FUBP1 is also described either as an oncoprotein or a tumor suppressor. Especially, FUBP1 overexpression is observed in a growing number of cancer and leads to a deregulation of targets that includes the fine-tuned MYC oncogene. Moreover, recent loss-of-function analyses of FUBP1 establish its essential functions in hematopoietic stem cell maintenance and survival. Therefore, FUBP1 appears as an emerging suspect in hematologic disorders in addition to solid tumors. The scope of the present review is to describe the advances in our understanding of the molecular basis of FUBP1 functions in normal cells and carcinogenesis. We also delineate the recent progresses in the understanding of the master role of FUBP1 in normal and pathological hematopoiesis. We conclude that FUBP1 is not only worth studying biologically but is also of clinical relevance through its pivotal role in regulating multiple cellular processes and its involvement in oncogenesis.
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Affiliation(s)
- Lydie Debaize
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, F-35000, Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)-UMR 6290, F-35000, Rennes, France.
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200, Brest, France.
- CHRU de Brest, laboratoire de cytogénétique, F-29200, Brest, France.
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23
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Abstract
G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5'- and 3'-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.
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Affiliation(s)
- Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, IN USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN USA
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24
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Shu B, Zeng P, Kang S, Li PH, Hu D, Kuang G, Cao J, Li X, Zhang M, An LK, Huang ZS, Li D. Syntheses and evaluation of new Quinoline derivatives for inhibition of hnRNP K in regulating oncogene c-myc transcription. Bioorg Chem 2018; 85:1-17. [PMID: 30599408 DOI: 10.1016/j.bioorg.2018.12.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/22/2022]
Abstract
Aberrant overexpression of heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a key feature in oncogenesis and progression of many human cancers. hnRNP K has been found to be a transcriptional activator to up-regulate c-myc gene transcription, a critical proto-oncogene for regulation of cell growth and differentiation. Therefore, down-regulation of c-myc transcription by inhibiting hnRNP K through disrupting its binding to c-myc gene promoter is a potential approach for cancer therapy. In the present study, we synthesized and screened a series of Quinoline derivatives and evaluated their binding affinity for hnRNP K. Among these derivatives, (E)-1-(4-methoxyphenyl)-3-(4-morpholino-6-nitroquinolin-2-yl)prop-2-en-1-one (compound 25) was determined to be the first-reported hnRNP K binding ligand with its KD values of 4.6 and 2.6 μM measured with SPR and MST, respectively. Subsequent evaluation showed that the binding of compound 25 to hnRNP K could disrupt its unfolding of c-myc promoter i-motif, resulting in down-regulation of c-myc transcription. Compound 25 showed a selective anti-proliferative effect on human cancer cell lines with IC50 values ranged from 1.36 to 3.59 μM. Compound 25 exhibited good tumor growth inhibition in a Hela xenograft tumor model, which might be related to its binding with hnRNP K. These findings illustrated that inhibition of DNA-binding protein hnRNP K by compound 25 could be a new and selective strategy of regulating oncogene transcription instead of targeting promoter DNA secondary structures such as G-quadruplexes or i-motifs.
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Affiliation(s)
- Bing Shu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ping Zeng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Shuangshuang Kang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Peng-Hui Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Dexuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Guotao Kuang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Jiaojiao Cao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Xiaoya Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Meiling Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, 132 Waihuan East Road, Guangzhou 510006, PR China.
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25
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Calabrese DR, Chen X, Leon EC, Gaikwad SM, Phyo Z, Hewitt WM, Alden S, Hilimire TA, He F, Michalowski AM, Simmons JK, Saunders LB, Zhang S, Connors D, Walters KJ, Mock BA, Schneekloth JS. Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex. Nat Commun 2018; 9:4229. [PMID: 30315240 PMCID: PMC6185959 DOI: 10.1038/s41467-018-06315-w] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/16/2018] [Indexed: 01/06/2023] Open
Abstract
G-quadruplexes (G4s) are noncanonical DNA structures that frequently occur in the promoter regions of oncogenes, such as MYC, and regulate gene expression. Although G4s are attractive therapeutic targets, ligands capable of discriminating between different G4 structures are rare. Here, we describe DC-34, a small molecule that potently downregulates MYC transcription in cancer cells by a G4-dependent mechanism. Inhibition by DC-34 is significantly greater for MYC than other G4-driven genes. We use chemical, biophysical, biological, and structural studies to demonstrate a molecular rationale for the recognition of the MYC G4. We solve the structure of the MYC G4 in complex with DC-34 by NMR spectroscopy and illustrate specific contacts responsible for affinity and selectivity. Modification of DC-34 reveals features required for G4 affinity, biological activity, and validates the derived NMR structure. This work advances the design of quadruplex-interacting small molecules to control gene expression in therapeutic areas such as cancer. Targeting noncoding nucleic acids with small molecules represents an important and significant challenge in chemical biology and drug discovery. Here the authors characterize DC-34, a small molecule that exhibits selective binding to specific G4 structures, and provide a structural basis for its selectivity
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Affiliation(s)
- David R Calabrese
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Xiang Chen
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Elena C Leon
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Snehal M Gaikwad
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Zaw Phyo
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - William M Hewitt
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Stephanie Alden
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Thomas A Hilimire
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Fahu He
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | | | - John K Simmons
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lindsey B Saunders
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shuling Zhang
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Daniel Connors
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Kylie J Walters
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Beverly A Mock
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA.
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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26
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Rocca R, Moraca F, Costa G, Talarico C, Ortuso F, Da Ros S, Nicoletto G, Sissi C, Alcaro S, Artese A. In Silico Identification of Piperidinyl-amine Derivatives as Novel Dual Binders of Oncogene c-myc/c-Kit G-quadruplexes. ACS Med Chem Lett 2018; 9:848-853. [PMID: 30128079 DOI: 10.1021/acsmedchemlett.8b00275] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/10/2018] [Indexed: 12/15/2022] Open
Abstract
In the last years, it has been shown that the DNA secondary structure known as G-quadruplex is also involved in the regulation of oncogenes transcription, such as c-myc, c-Kit, KRAS, Bcl-2, VEGF, and PDGF. DNA G-quadruplexes, formed in the promoter region of these proto-oncogenes, are considered alternative anticancer targets since their stabilization causes a reduction of the related oncoprotein overexpression. In this study, a structure-based virtual screening toward the experimental DNA G-quadruplex structures of c-myc and c-Kit was performed by using Glide for the docking analysis of a commercial library of approximately 693 000 compounds. The best hits were submitted to thermodynamic and biophysical studies, highlighting the effective stabilization of both G-quadruplex oncogene promoter structures for three N-(4-piperidinylmethyl)amine derivatives, thus proposed as a new class of dual G-quadruplex binders.
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Affiliation(s)
- Roberta Rocca
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Carmine Talarico
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Silvia Da Ros
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Giulia Nicoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università “Magna Graecia” di Catanzaro, Campus “Salvatore Venuta”, Viale Europa, 88100 Catanzaro, Italy
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27
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Kar A, Jones N, Arat NÖ, Fishel R, Griffith JD. Long repeating (TTAGGG) n single-stranded DNA self-condenses into compact beaded filaments stabilized by G-quadruplex formation. J Biol Chem 2018; 293:9473-9485. [PMID: 29674319 PMCID: PMC6005428 DOI: 10.1074/jbc.ra118.002158] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/04/2018] [Indexed: 11/06/2022] Open
Abstract
Conformations adopted by long stretches of single-stranded DNA (ssDNA) are of central interest in understanding the architecture of replication forks, R loops, and other structures generated during DNA metabolism in vivo This is particularly so if the ssDNA consists of short nucleotide repeats. Such studies have been hampered by the lack of defined substrates greater than ∼150 nt and the absence of high-resolution biophysical approaches. Here we describe the generation of very long ssDNA consisting of the mammalian telomeric repeat (5'-TTAGGG-3') n , as well as the interrogation of its structure by EM and single-molecule magnetic tweezers (smMT). This repeat is of particular interest because it contains a run of three contiguous guanine residues capable of forming G quartets as ssDNA. Fluorescent-dye exclusion assays confirmed that this G-strand ssDNA forms ubiquitous G-quadruplex folds. EM revealed thick bead-like filaments that condensed the DNA ∼12-fold. The bead-like structures were 5 and 8 nm in diameter and linked by thin filaments. The G-strand ssDNA displayed initial stability to smMT force extension that ultimately released in steps that were multiples ∼28 nm at forces between 6 and 12 pN, well below the >20 pN required to unravel G-quadruplexes. Most smMT steps were consistent with the disruption of the beads seen by EM. Binding by RAD51 distinctively altered the force extension properties of the G-strand ssDNA, suggesting a stochastic G-quadruplex-dependent condensation model that is discussed.
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Affiliation(s)
- Anirban Kar
- From the Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599
| | - Nathan Jones
- the Department of Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio 43210
- the Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210, and
| | - N Özlem Arat
- From the Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599
- the Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Richard Fishel
- the Department of Cancer Biology and Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio 43210,
- the Interdisciplinary Biophysics Graduate Program, Ohio State University, Columbus, Ohio 43210, and
| | - Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599,
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28
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Zaytseva O, Quinn LM. DNA Conformation Regulates Gene Expression: The MYC Promoter and Beyond. Bioessays 2018; 40:e1700235. [PMID: 29504137 DOI: 10.1002/bies.201700235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/29/2018] [Indexed: 01/07/2023]
Abstract
Emerging evidence suggests that DNA topology plays an instructive role in cell fate control through regulation of gene expression. Transcription produces torsional stress, and the resultant supercoiling of the DNA molecule generates an array of secondary structures. In turn, local DNA architecture is harnessed by the cell, acting within sensory feedback mechanisms to mediate transcriptional output. MYC is a potent oncogene, which is upregulated in the majority of cancers; thus numerous studies have focused on detailed understanding of its regulation. Dissection of regulatory regions within the MYC promoter provided the first hint that intimate feedback between DNA topology and associated DNA remodeling proteins is critical for moderating transcription. As evidence of such regulation is also found in the context of many other genes, here we expand on the prototypical example of the MYC promoter, and also explore DNA architecture in a genome-wide context as a global mechanism of transcriptional control.
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Affiliation(s)
- Olga Zaytseva
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
| | - Leonie M Quinn
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, ACT 2600, Canberra City, Australia.,School of Biomedical Sciences, University of Melbourne, 3010, Parkville, Australia
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29
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Bhat J, Mondal S, Sengupta P, Chatterjee S. In Silico Screening and Binding Characterization of Small Molecules toward a G-Quadruplex Structure Formed in the Promoter Region of c-MYC Oncogene. ACS OMEGA 2017; 2:4382-4397. [PMID: 30023722 PMCID: PMC6044917 DOI: 10.1021/acsomega.6b00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/20/2017] [Indexed: 06/08/2023]
Abstract
Overexpression of c-MYC oncogene is associated with cancer pathology. Expression of c-MYC is regulated by the G-quadruplex structure formed in the G-rich segment of nuclease hypersensitive element (NHE III1), that is, "Pu27", which is localized in the promoter region. Ligand-induced stabilization of the Pu27 structure has been identified as a novel target for cancer therapeutics. Here, we have explored the library of synthetic compounds against the predefined binding site of Pu27. Three compounds were selected based on the docking analyses; they were further scrutinized using all atom molecular dynamics simulations in an explicit water model. Simulated trajectories were scrutinized for conformational stability and ligand binding free energy estimation; essential dynamic behavior was determined using principal component analysis. One of the molecules, "TPP (1-(3-(4-(1,2,3-thiadiazol-4-yl)phenoxy)-2-hydroxypropyl)-4-carbamoylpiperidinium)", with the best results was considered for further evaluation. The theoretical observations are supported well by biophysical analysis using circular dichroism, isothermal titration calorimetry, and high-resolution NMR spectroscopy indicating association of TPP with Pu27. The in vitro studies were then translated into c-MYC overexpression in the T47D breast cancer cell line. Biological evaluation through the MTT assay, flow cytometric assay, RT-PCR, and reporter luciferase assay suggests that TPP downregulates the expression of c-MYC oncogene by arresting its promoter region. In silico and in vitro observations cumulatively suggest that the novel skeleton of TPP could be a potential anticancer agent by stabilizing the G-quadruplex formed in the Pu27 and consequently downregulating the expression of c-MYC oncogene. Derivation of new molecules on its skeleton may confer anticancer therapeutics for the next generation.
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30
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Kshirsagar R, Khan K, Joshi MV, Hosur RV, Muniyappa K. Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks. Biophys J 2017; 112:2056-2074. [PMID: 28538144 DOI: 10.1016/j.bpj.2017.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/13/2017] [Accepted: 04/19/2017] [Indexed: 12/29/2022] Open
Abstract
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.
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Affiliation(s)
- Rucha Kshirsagar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Krishnendu Khan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Mamata V Joshi
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Ramakrishna V Hosur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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31
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Kaiser CE, Van Ert NA, Agrawal P, Chawla R, Yang D, Hurley LH. Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. J Am Chem Soc 2017; 139:8522-8536. [PMID: 28570076 PMCID: PMC5978000 DOI: 10.1021/jacs.7b02046] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.
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Affiliation(s)
- Christine E. Kaiser
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalie A. Van Ert
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Prashansa Agrawal
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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32
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Zeng DY, Kuang GT, Wang SK, Peng W, Lin SL, Zhang Q, Su XX, Hu MH, Wang H, Tan JH, Huang ZS, Gu LQ, Ou TM. Discovery of Novel 11-Triazole Substituted Benzofuro[3,2-b]quinolone Derivatives as c-myc G-Quadruplex Specific Stabilizers via Click Chemistry. J Med Chem 2017; 60:5407-5423. [PMID: 28514170 DOI: 10.1021/acs.jmedchem.7b00016] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The specificity of nucleic acids' binders is crucial for developing this kind of drug, especially for novel G-quadruplexes' binders. Quindoline derivatives have been developed as G-quadruplex stabilizers with good interactive activities. In order to improve the selectivity and binding affinity of quindoline derivatives as c-myc G-quadruplex binding ligands, novel triazole containing benzofuroquinoline derivatives (T-BFQs) were designed and synthesized by using the 1,3-dipolar cycloaddition of a series of alkyne and azide building blocks. The selectivity toward c-myc G-quadruplex DNA of these novel T-BFQs was significantly improved, together with an obvious increase on binding affinity. Further cellular and in vivo experiments indicated that the T-BFQs showed inhibitory activity on tumor cells' proliferation, presumably through the down-regulation of transcription of c-myc gene. Our findings broadened the modification strategies of specific G-quadruplex stabilizers.
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Affiliation(s)
- De-Ying Zeng
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Guo-Tao Kuang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Shi-Ke Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Wang Peng
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Shu-Ling Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Qi Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Xiao-Xuan Su
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Ming-Hao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Honggen Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, People's Republic of China
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33
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Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome. Cell Syst 2017; 4:344-356.e7. [PMID: 28237796 DOI: 10.1016/j.cels.2017.01.013] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 09/06/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022]
Abstract
DNA in cells is predominantly B-form double helix. Though certain DNA sequences in vitro may fold into other structures, such as triplex, left-handed Z form, or quadruplex DNA, the stability and prevalence of these structures in vivo are not known. Here, using computational analysis of sequence motifs, RNA polymerase II binding data, and genome-wide potassium permanganate-dependent nuclease footprinting data, we map thousands of putative non-B DNA sites at high resolution in mouse B cells. Computational analysis associates these non-B DNAs with particular structures and indicates that they form at locations compatible with an involvement in gene regulation. Further analyses support the notion that non-B DNA structure formation influences the occupancy and positioning of nucleosomes in chromatin. These results suggest that non-B DNAs contribute to the control of a variety of critical cellular and organismal processes.
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34
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Sutherland C, Cui Y, Mao H, Hurley LH. A Mechanosensor Mechanism Controls the G-Quadruplex/i-Motif Molecular Switch in the MYC Promoter NHE III1. J Am Chem Soc 2016; 138:14138-14151. [DOI: 10.1021/jacs.6b09196] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Caleb Sutherland
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
| | - Yunxi Cui
- Department
of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department
of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Laurence H. Hurley
- University of Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, United States
- University of Arizona, College of Pharmacy, 1703 East Mabel Street, Tucson, Arizona 85721, United States
- BIO5 Institute, 1657 East
Helen Street, Tucson, Arizona 85721, United States
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35
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Bhat J, Chatterjee S. Skeleton selectivity in complexation of chelerythrine and chelerythrine-like natural plant alkaloids with the G-quadruplex formed at the promoter of c-MYC oncogene: in silico exploration. RSC Adv 2016. [DOI: 10.1039/c6ra04671a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chelerythrine binds at the 5′ end and arrests the G-quadruplex formed in the promoter region ofc-MYConcogene thus restrict thec-MYCexpression. Position of methoxy group over the core skeleton of chelerythrine determines the binding pattern of ligand.
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Affiliation(s)
- Jyotsna Bhat
- Department of Biophysics
- Bose Institute
- Kolkata
- India
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36
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Li Y, Hennig M. (1)H, (15)N and (13)C backbone resonance assignments of the N-terminal, tandem KH domains of human hnRNP E1. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:431-434. [PMID: 26143480 PMCID: PMC4570482 DOI: 10.1007/s12104-015-9624-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) can be divided into subgroups based on their RNA-binding characteristics. One subgroup in mammalian cells are the Poly(C)-binding proteins (PCBPs) comprised of hnRNP K/J and hnRNP E1-4 [the latter also known as PCBP 1-4 or α-complex proteins (α-CP) 1-4]. Each subgroup member has three K homology (KH) nucleic acid-binding domains. Individual KH domains bind short single-stranded (ss), poly-pyrimidine-rich nucleic acid sequences with rather weak affinity. In this study, we report the (1)H, (13)C and (15)N backbone resonance assignments of the first and second KH domains of hnRNP E1, which plays a pivotal role in posttranscriptional and translational regulation of RNA targets. Our NMR assignments lay the foundation for a detailed investigation of the dynamic cooperation of the tandem KH1 and KH2 domains to bind nucleic acids.
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Affiliation(s)
- Yang Li
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Mirko Hennig
- Department of Nutrition, University of North Carolina at Chapel Hill/Nutrition Research Institute, Room 3151, 500 Laureate Way, Kannapolis, NC, 28081, USA.
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37
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Reilly SM, Lyons DF, Wingate SE, Wright RT, Correia JJ, Jameson DM, Wadkins RM. Folding and hydrodynamics of a DNA i-motif from the c-MYC promoter determined by fluorescent cytidine analogs. Biophys J 2015; 107:1703-11. [PMID: 25296324 DOI: 10.1016/j.bpj.2014.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/05/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022] Open
Abstract
The four-stranded i-motif (iM) conformation of cytosine-rich DNA has importance to a wide variety of biochemical systems that range from their use in nanomaterials to potential roles in oncogene regulation. The iM structure is formed at slightly acidic pH, where hemiprotonation of cytosine results in a stable C-C(+) basepair. Here, we performed fundamental studies to examine iM formation from a C-rich strand from the promoter of the human c-MYC gene. We used a number of biophysical techniques to characterize both the hydrodynamic properties and folding kinetics of a folded iM. Our hydrodynamic studies using fluorescence anisotropy decay and analytical ultracentrifugation show that the iM structure has a compact size in solution and displays the rigidity of a double strand. By studying the rates of circular dichroism spectral changes and quenching of fluorescent cytidine analogs, we also established a mechanism for the folding of a random coil oligo into the iM. In the course of determining this folding pathway, we established that the fluorescent dC analogs tC° and PdC can be used to monitor individual residues of an iM structure and to determine the pKa of an iM. We established that the C-C(+) hydrogen bonding of certain bases initiates the folding of the iM structure. We also showed that substitutions in the loop regions of iMs give a distinctly different kinetic signature during folding compared with bases that are intercalated. Our data reveal that the iM passes through a distinct intermediate form between the unfolded and folded forms. Taken together, our results lay the foundation for using fluorescent dC analogs to follow structural changes during iM formation. Our technique may also be useful for examining folding and structural changes in more complex iMs.
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Affiliation(s)
- Samantha M Reilly
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi
| | - Daniel F Lyons
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - Sara E Wingate
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi
| | - Robert T Wright
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - John J Correia
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Randy M Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi.
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38
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Moritz B, Lilie H, Naarmann-de Vries IS, Urlaub H, Wahle E, Ostareck-Lederer A, Ostareck DH. Biophysical and biochemical analysis of hnRNP K: arginine methylation, reversible aggregation and combinatorial binding to nucleic acids. Biol Chem 2015; 395:837-53. [PMID: 25003387 DOI: 10.1515/hsz-2014-0146] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/20/2014] [Indexed: 12/17/2022]
Abstract
Abstract Analysis of arginine methylation, which affects specific protein interactions in eukaryotic cells, requires access to methylated protein for biophysical and biochemical studies. Methylation of heterogeneous nuclear ribonucleoprotein K (hnRNP K) upon co-expression with protein arginine methyltransferase 1 in E. coli was monitored by mass spectrometry and found to be identical to the modification of hnRNP K purified from mammalian cells. Recombinant non-methylated and arginine-methylated hnRNP K (MethnRNP K) were used to characterize self-aggregation and nucleic acid binding. Analytical ultracentrifugation and static light scattering experiments revealed that hnRNP K methylation does not impact reversible self-aggregation, which can be prevented by high ionic strength and organic additives. Filter binding assays were used to compare the binding of non-methylated and MethnRNP K to the pyrimidine repeat-containing differentiation control element (DICE) of reticulocyte 15-lipoxygenase mRNA 3' UTR. No affinity differences were detected for both hnRNP K variants. A series of oligonucleotides carrying various numbers of C4 motifs at different positions was used in steady state competition assays with fluorescently-labeled functional differentiation control element (2R). Quantitative evaluation indicated that all hnRNP K homology domains of hnRNP K contribute differentially to RNA binding, with KH1-KH2 acting as a tandem domain and KH3 as an individual binding domain.
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39
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Quadruplex forming promoter region of c-myc oncogene as a potential target for a telomerase inhibitory plant alkaloid, chelerythrine. Biochem Biophys Res Commun 2015; 459:75-80. [DOI: 10.1016/j.bbrc.2015.02.072] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 02/14/2015] [Indexed: 11/20/2022]
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40
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Structure-based virtual screening of novel natural alkaloid derivatives as potential binders of h-telo and c-myc DNA G-quadruplex conformations. Molecules 2014; 20:206-23. [PMID: 25547724 PMCID: PMC6272608 DOI: 10.3390/molecules20010206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/15/2014] [Indexed: 01/08/2023] Open
Abstract
Several ligands can bind to the non-canonical G-quadruplex DNA structures thereby stabilizing them. These molecules can act as effective anticancer agents by stabilizing the telomeric regions of DNA or by regulating oncogene expression. In order to better interact with the quartets of G-quadruplex structures, G-binders are generally characterized by a large aromatic core involved in π-π stacking. Some natural flexible cyclic molecules from Traditional Chinese Medicine have shown high binding affinity with G-quadruplex, such as berbamine and many other alkaloids. Using the structural information available on G-quadruplex structures, we performed a high throughput in silico screening of commercially available alkaloid derivative databases by means of a structure-based approach based on docking and molecular dynamics simulations against the human telomeric sequence d[AG3(T2AG3)3] and the c-myc promoter structure. We identified 69 best hits reporting an improved theoretical binding affinity with respect to the active set. Among them, a berberine derivative, already known to remarkably inhibit telomerase activity, was related to a better theoretical affinity versusc-myc.
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41
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Buket ONEL, Clement LIN, DanZhou YANG. DNA G-quadruplex and its potential as anticancer drug target. Sci China Chem 2014; 57:1605-1614. [PMID: 27182219 PMCID: PMC4863707 DOI: 10.1007/s11426-014-5235-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
G-quadruplex secondary structures are four-stranded globular nucleic acid structures form in the specific DNA and RNA G-rich sequences with biological significance such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5' and 3'-untranslated (UTR) regions. The non-canonical G-quadruplex secondary structures can readily form under physiologically relevant ionic conditions and are considered to be new molecular target for cancer therapeutics. This review discusses the essential progress in our lab related to the structures and functions of biologically relevant DNA G-quadruplexes in human gene promoters and telomeres, and the opportunities presented for the development of G-quadruplex-targeted small- molecule drugs.
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Affiliation(s)
- ONEL Buket
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - LIN Clement
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721, USA
| | - YANG DanZhou
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- The Arizona Cancer Center, Tucson, AZ 85724, USA
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42
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Lu L, Han H, Tian Y, Li W, Zhang J, Feng M, Li Y. Aurora kinase A mediates c-Myc's oncogenic effects in hepatocellular carcinoma. Mol Carcinog 2014; 54:1467-79. [PMID: 25284017 DOI: 10.1002/mc.22223] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 08/09/2014] [Accepted: 08/13/2014] [Indexed: 12/13/2022]
Abstract
Dysregulation of c-Myc (Myc) has been shown to contribute to progression of hepatocellular carcinoma, however, the detailed molecular mechanism remains poorly understood. Here, we report that Myc binds to the Aurora kinase A (Aurka) promoter and induces expression of Aurka in HCC cells. Increased expression of Aurka correlates with that of Myc in HCC. Nuclear accumulation of Aurka was confirmed by subcellular protein fractionation and immunoblot experiments in HCC cells. Myc inhibition decreases the nuclear accumulation of Aurka in HCC cells. Also Aurka accumulating in the nucleus up-regulates Myc transcription by binding the Myc promoter containing the highly conserved CCCTCCCCA in the NHE region of the CpG islands. Inhibition of Myc or Aurka diminishes the malignant phenotypes of HCC cells by down-regulating some common target genes. Also Aurka and Myc mediates the effects of each other, at least partially, on proliferation, anchorage-independent soft agar growth, and ATP production. Blocking Aurka in an orthotopic model significantly impairs tumor growth in mice. These results identify a Myc-Aurka feedback loop in which Myc and Aurka regulate expression of each other at the transcriptional level and both play an important role in hepatocarcinogenesis.
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Affiliation(s)
- Longfeng Lu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Han Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuan Tian
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Wenjuan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinxiang Zhang
- Department of Surgery, Wuhan Union Hospital, Wuhan, China
| | - Maohui Feng
- Department of Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Youjun Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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43
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Kang HJ, Kendrick S, Hecht SM, Hurley LH. The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules. J Am Chem Soc 2014; 136:4172-85. [PMID: 24559432 PMCID: PMC3985447 DOI: 10.1021/ja4109352] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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In a companion paper (DOI: 10.021/ja410934b) we demonstrate that the C-rich
strand of the cis-regulatory element in the BCL2 promoter element
is highly dynamic in nature and can form either an i-motif or a flexible
hairpin. Under physiological conditions these two secondary DNA structures
are found in an equilibrium mixture, which can be shifted by the addition
of small molecules that trap out either the i-motif (IMC-48) or the
flexible hairpin (IMC-76). In cellular experiments we demonstrate
that the addition of these molecules has opposite effects on BCL2 gene expression and furthermore that these effects
are antagonistic. In this contribution we have identified a transcriptional
factor that recognizes and binds to the BCL2 i-motif
to activate transcription. The molecular basis for the recognition
of the i-motif by hnRNP LL is determined, and we demonstrate that
the protein unfolds the i-motif structure to form a stable single-stranded
complex. In subsequent experiments we show that IMC-48 and IMC-76
have opposite, antagonistic effects on the formation of the hnRNP
LL–i-motif complex as well as on the transcription factor occupancy
at the BCL2 promoter. For the first time we propose
that the i-motif acts as a molecular switch that controls gene expression
and that small molecules that target the dynamic equilibrium of the
i-motif and the flexible hairpin can differentially modulate gene
expression.
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Affiliation(s)
- Hyun-Jin Kang
- College of Pharmacy and §BIO5 Institute, University of Arizona , Tucson, Arizona 85721, United States
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44
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Cui J, Waltman P, Le VH, Lewis EA. The effect of molecular crowding on the stability of human c-MYC promoter sequence I-motif at neutral pH. Molecules 2013; 18:12751-67. [PMID: 24132198 PMCID: PMC6270392 DOI: 10.3390/molecules181012751] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/26/2013] [Accepted: 10/10/2013] [Indexed: 12/20/2022] Open
Abstract
We have previously shown that c-MYC promoter sequences can form stable i-motifs in acidic solution (pH 4.5-5.5). In terms of drug targeting, the question is whether c-MYC promoter sequence i-motifs will exist in the nucleus at neutral pH. In this work, we have investigated the stability of a mutant c-MYC i-motif in solutions containing a molecular crowding agent. The crowded nuclear environment was modeled by the addition of up to 40% w/w polyethylene glycols having molecular weights up to 12,000 g/mol. CD and DSC were used to establish the presence and stability of c-MYC i-motifs in buffer solutions over the pH range 4 to 7. We have shown that the c-MYC i-motif can exist as a stable structure at pH values as high as 6.7 in crowded solutions. Generic dielectric constant effects, e.g., a shift in the pKa of cytosine by more than 2 units (e.g., 4.8 to 7.0), or the formation of non-specific PEG/DNA complexes appear to contribute insignificantly to i-motif stabilization. Molecular crowding, largely an excluded volume effect of added PEG, having a molecular weight in excess of 1,000 g/mol, appears to be responsible for stabilizing the more compact i-motif over the random coil at higher pH values.
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Affiliation(s)
- Jingjing Cui
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA.
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45
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Molecular basis of recognition of quadruplexes human telomere and c-myc promoter by the putative anticancer agent sanguinarine. Biochim Biophys Acta Gen Subj 2013; 1830:4189-201. [DOI: 10.1016/j.bbagen.2013.03.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/19/2013] [Accepted: 03/26/2013] [Indexed: 01/24/2023]
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46
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Ma DL, He HZ, Leung KH, Chan DSH, Leung CH. Bioactive Luminescent Transition-Metal Complexes for Biomedical Applications. Angew Chem Int Ed Engl 2013; 52:7666-7682. [DOI: 10.1002/anie.201208414] [Citation(s) in RCA: 293] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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47
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Ma DL, He HZ, Leung KH, Chan DSH, Leung CH. Bioaktive lumineszierende Übergangsmetallkomplexe für biomedizinische Anwendungen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208414] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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48
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Preferential binding of hot spot mutant p53 proteins to supercoiled DNA in vitro and in cells. PLoS One 2013; 8:e59567. [PMID: 23555710 PMCID: PMC3608670 DOI: 10.1371/journal.pone.0059567] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 02/19/2013] [Indexed: 11/21/2022] Open
Abstract
Hot spot mutant p53 (mutp53) proteins exert oncogenic gain-of-function activities. Binding of mutp53 to DNA is assumed to be involved in mutp53-mediated repression or activation of several mutp53 target genes. To investigate the importance of DNA topology on mutp53-DNA recognition in vitro and in cells, we analyzed the interaction of seven hot spot mutp53 proteins with topologically different DNA substrates (supercoiled, linear and relaxed) containing and/or lacking mutp53 binding sites (mutp53BS) using a variety of electrophoresis and immunoprecipitation based techniques. All seven hot spot mutp53 proteins (R175H, G245S, R248W, R249S, R273C, R273H and R282W) were found to have retained the ability of wild-type p53 to preferentially bind circular DNA at native negative superhelix density, while linear or relaxed circular DNA was a poor substrate. The preference of mutp53 proteins for supercoiled DNA (supercoil-selective binding) was further substantiated by competition experiments with linear DNA or relaxed DNA in vitro and ex vivo. Using chromatin immunoprecipitation, the preferential binding of mutp53 to a sc mutp53BS was detected also in cells. Furthermore, we have shown by luciferase reporter assay that the DNA topology influences p53 regulation of BAX and MSP/MST1 promoters. Possible modes of mutp53 binding to topologically constrained DNA substrates and their biological consequences are discussed.
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49
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Wei PC, Wang ZF, Lo WT, Su MI, Shew JY, Chang TC, Lee WH. A cis-element with mixed G-quadruplex structure of NPGPx promoter is essential for nucleolin-mediated transactivation on non-targeting siRNA stress. Nucleic Acids Res 2013; 41:1533-43. [PMID: 23241391 PMCID: PMC3561993 DOI: 10.1093/nar/gks1232] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 12/16/2022] Open
Abstract
We reported that non-targeting siRNA (NT-siRNA) stress induces non-selenocysteine containing phospholipid hydroperoxide glutathione peroxidase (NPGPx) expression to cooperate with exoribonuclease XRN2 for releasing the stress [Wei,P.C., Lo,W.T., Su,M.I., Shew,J.Y. and Lee,W.H. (2011) Non-targeting siRNA induces NPGPx expression to cooperate with exoribonuclease XRN2 for releasing the stress. Nucleic Acids Res., 40, 323-332]. However, how NT-siRNA stress inducing NPGPx expression remains elusive. In this communication, we showed that the proximal promoter of NPGPx contained a mixed G-quadruplex (G4) structure, and disrupting the structure diminished NT-siRNA induced NPGPx promoter activity. We also demonstrated that nucleolin (NCL) specifically bonded to the G4-containing sequences to replace the originally bound Sp1 at the NPGPx promoter on NT-siRNA stress. Consistently, overexpression of NCL further increased NPGPx promoter activity, whereas depletion of NCL desensitized NPGPx promoter to NT-siRNA stress. These results suggest that the cis-element with mixed G4 structure at the NPGPx promoter plays an essential role for its transactivation mediated by NCL to release cells from NT-siRNA stress.
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Affiliation(s)
- Pei-Chi Wei
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Zi-Fu Wang
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Wen-Ting Lo
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Mei-I Su
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Jin-Yuh Shew
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Ta-Chau Chang
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
| | - Wen-Hwa Lee
- Graduate Institute of Life Sciences, National Defense Medical Center, 11490 Taipei, Taiwan, Genomics Research Center, 11529 Taipei, Institute of Atomic and Molecular Sciences, Academia Sinica, 11529 Taipei, Department of Chemistry, National Taiwan University, 11529 Taipei, Institute of Biological Chemistry, Academia Sinica, 11529 Taipei, Taiwan and Department of Biological Chemistry, University of California, Irvine, California, USA
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50
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Moumen A, Magill C, Dry KL, Jackson SP. ATM-dependent phosphorylation of heterogeneous nuclear ribonucleoprotein K promotes p53 transcriptional activation in response to DNA damage. Cell Cycle 2013; 12:698-704. [PMID: 23343766 PMCID: PMC3594270 DOI: 10.4161/cc.23592] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Previous work has established that heterogeneous nuclear ribonucleoprotein K (hnRNP K) is stabilized in an ATM-dependent manner in response to DNA damage and acts as a cofactor for p53-mediated transcription. Here, we show that in response to DNA damage caused by ionizing radiation, hnRNP K is phosphorylated in an ATM-dependent manner. Furthermore, our data indicate that ATM-dependent hnRNP K phosphorylation is required for its stabilization and its function as a p53 transcriptional cofactor in response to DNA damage. These findings thereby establish hnRNP K as an ATM target and help define how ATM orchestrates p53-dependent transcriptional responses in response to genotoxic stress.
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Affiliation(s)
- Abdeladim Moumen
- DNA Damage Response Group, Basic Medical Science Department, St. George's University of London, London, UK
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