1
|
Zhu Y, Li X, Zhang Q, Yang X, Sun X, Pan Y, Yuan X, Ma Y, Xu B, Yang Z. Aptamer AS411 interacts with the KRAS promoter/hnRNP A1 complex and shows increased potency against drug-resistant lung cancer. RSC Med Chem 2024; 15:1515-1526. [PMID: 38784467 PMCID: PMC11110790 DOI: 10.1039/d3md00752a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/15/2024] [Accepted: 02/22/2024] [Indexed: 05/25/2024] Open
Abstract
G-quadruplex (G4) aptamers that can competitively binding protein with oncogene promoter G4 hold promise for cancer treatment. In this study, a neutral cytidinyl lipid, DNCA, was shown to transfect and deliver G4 aptamers (AS1411, TBA) into tumour cells, including multidrug-resistant tumour cells, and their nuclear localizations were clearly detected. Both AS1411/DNCA and TBA/DNCA showed excellent antitumour efficacies in the drug-resistant non-small cell lung cancer cell line A549/TXL at a low concentration (100 nM). Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) was identified as a new target of AS1411 and TBA. The binding affinities were measured, and the Kd values of AS1411/hnRNP A1 and TBA/hnRNP A1 were 17.5 nM and 21.1 nM, respectively. Then the expression of KRAS mRNA in A549/TXL cells was found to be higher than that in A549 cells, and KRAS mRNA was reduced by approximately 40% after administration of AS1411 or TBA in A549/TXL cells. Further, it was confirmed for the first time that AS1411 targeted not only hnRNP A1 but also the KRAS promoter/hnRNP A1 complexes. And although TBA cannot target the KRAS promoter/hnRNP A1 complexes, the biolayer interferometry (BLI) experiment showed that TBA and AS1411 have similar effects on several key proteins in tumour cells, especially hnRNP A1. Molecular docking and molecular dynamics simulation showed that AS1411 and the KRAS promoter bound to the same domain of hnRNP A1 protein, while TBA bound to another domain.
Collapse
Affiliation(s)
- Yuejie Zhu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiang Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Qi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
- School of Pharmacy, Chengdu Medical College 783 Xindu Avenue, Xindu District Chengdu 610500 China
| | - Xudong Sun
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yi Pan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Xia Yuan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Yuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Bo Xu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China +86 10 82802503 +86 10 82802503
| |
Collapse
|
2
|
Taha MS, Ahmadian MR. Fragile X Messenger Ribonucleoprotein Protein and Its Multifunctionality: From Cytosol to Nucleolus and Back. Biomolecules 2024; 14:399. [PMID: 38672417 PMCID: PMC11047961 DOI: 10.3390/biom14040399] [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: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Silencing of the fragile X messenger ribonucleoprotein 1 (FMR1) gene and a consequent lack of FMR protein (FMRP) synthesis are associated with fragile X syndrome, one of the most common inherited intellectual disabilities. FMRP is a multifunctional protein that is involved in many cellular functions in almost all subcellular compartments under both normal and cellular stress conditions in neuronal and non-neuronal cell types. This is achieved through its trafficking signals, nuclear localization signal (NLS), nuclear export signal (NES), and nucleolar localization signal (NoLS), as well as its RNA and protein binding domains, and it is modulated by various post-translational modifications such as phosphorylation, ubiquitination, sumoylation, and methylation. This review summarizes the recent advances in understanding the interaction networks of FMRP with a special focus on FMRP stress-related functions, including stress granule formation, mitochondrion and endoplasmic reticulum plasticity, ribosome biogenesis, cell cycle control, and DNA damage response.
Collapse
Affiliation(s)
- Mohamed S. Taha
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
- Research on Children with Special Needs Department, Institute of Medical Research and Clinical Studies, National Research Centre, Cairo 12622, Egypt
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| |
Collapse
|
3
|
Chen X, Haribowo AG, Baik AH, Fossati A, Stevenson E, Chen YR, Reyes NS, Peng T, Matthay MA, Traglia M, Pico AR, Jarosz DF, Buchwalter A, Ghaemmaghami S, Swaney DL, Jain IH. In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response. SCIENCE ADVANCES 2023; 9:eadj4884. [PMID: 38064566 PMCID: PMC10708181 DOI: 10.1126/sciadv.adj4884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
Abstract
Oxygen deprivation and excess are both toxic. Thus, the body's ability to adapt to varying oxygen tensions is critical for survival. While the hypoxia transcriptional response has been well studied, the post-translational effects of oxygen have been underexplored. In this study, we systematically investigate protein turnover rates in mouse heart, lung, and brain under different inhaled oxygen tensions. We find that the lung proteome is the most responsive to varying oxygen tensions. In particular, several extracellular matrix (ECM) proteins are stabilized in the lung under both hypoxia and hyperoxia. Furthermore, we show that complex 1 of the electron transport chain is destabilized in hyperoxia, in accordance with the exacerbation of associated disease models by hyperoxia and rescue by hypoxia. Moreover, we nominate MYBBP1A as a hyperoxia transcriptional regulator, particularly in the context of rRNA homeostasis. Overall, our study highlights the importance of varying oxygen tensions on protein turnover rates and identifies tissue-specific mediators of oxygen-dependent responses.
Collapse
Affiliation(s)
- Xuewen Chen
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Augustinus G. Haribowo
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan H. Baik
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Fossati
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Erica Stevenson
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yiwen R. Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Nabora S. Reyes
- Department of Medicine and Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Tien Peng
- Department of Medicine and Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California San Francisco, San Francisco, CA, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Michael A. Matthay
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Departments of Medicine and Anesthesia, University of California San Francisco, San Francisco, CA, USA
| | - Michela Traglia
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Alexander R. Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Daniel F. Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, CA, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sina Ghaemmaghami
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, NY, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Danielle L. Swaney
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Isha H. Jain
- Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Bakar Aging Research Institute, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
4
|
Zhang C, Guo Q, Chen L, Wu Z, Yan XJ, Zou C, Zhang Q, Tan J, Fang T, Rao Q, Li Y, Shen S, Deng M, Wang L, Gao H, Yu J, Li H, Zhang C, Nowsheen S, Kloeber J, Zhao F, Yin P, Teng C, Lin Z, Song K, Yao S, Yao L, Wu L, Zhang Y, Cheng X, Gao Q, Yuan J, Lou Z, Zhang JS. A ribosomal gene panel predicting a novel synthetic lethality in non-BRCAness tumors. Signal Transduct Target Ther 2023; 8:183. [PMID: 37160887 PMCID: PMC10170152 DOI: 10.1038/s41392-023-01401-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/04/2023] [Accepted: 02/27/2023] [Indexed: 05/11/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors are one of the most exciting classes of targeted therapy agents for cancers with homologous recombination (HR) deficiency. However, many patients without apparent HR defects also respond well to PARP inhibitors/cisplatin. The biomarker responsible for this mechanism remains unclear. Here, we identified a set of ribosomal genes that predict response to PARP inhibitors/cisplatin in HR-proficient patients. PARP inhibitor/cisplatin selectively eliminates cells with high expression of the eight genes in the identified panel via DNA damage (ATM) signaling-induced pro-apoptotic ribosomal stress, which along with ATM signaling-induced pro-survival HR repair constitutes a new model to balance the cell fate in response to DNA damage. Therefore, the combined examination of the gene panel along with HR status would allow for more precise predictions of clinical response to PARP inhibitor/cisplatin. The gene panel as an independent biomarker was validated by multiple published clinical datasets, as well as by an ovarian cancer organoids library we established. More importantly, its predictive value was further verified in a cohort of PARP inhibitor-treated ovarian cancer patients with both RNA-seq and WGS data. Furthermore, we identified several marketed drugs capable of upregulating the expression of the genes in the panel without causing HR deficiency in PARP inhibitor/cisplatin-resistant cell lines. These drugs enhance PARP inhibitor/cisplatin sensitivity in both intrinsically resistant organoids and cell lines with acquired resistance. Together, our study identifies a marker gene panel for HR-proficient patients and reveals a broader application of PARP inhibitor/cisplatin in cancer therapy.
Collapse
Affiliation(s)
- Chao Zhang
- Beijing Institute of Basic Medical Sciences, 100850, Beijing, China
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qiang Guo
- School of Pharmaceutical Sciences, Wenzhou Medical University, 325035, Wenzhou, Zhejiang, China
| | - Lifeng Chen
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Zhejiang Provincial People's Hospital, 310014, Hangzhou, Zhejiang, China
- Department of Gynecology, Zhejiang Provincial People's Hospital, 310014, Hangzhou, Zhejiang, China
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiao-Jian Yan
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China
| | - Chengyang Zou
- Department of Gynecology, the First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China
| | - Qiuxue Zhang
- Wuhan Kingwise Biotechnology Co., Ltd., 430206, Wuhan, Hubei, China
| | - Jiahong Tan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Tian Fang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Qunxian Rao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, 310006, Hangzhou, Zhejiang, China
| | - Shizhen Shen
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, 310006, Hangzhou, Zhejiang, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Somaira Nowsheen
- Department of Dermatology, University of California San Diego, San Diego, CA, 92122, USA
| | - Jake Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Chunbo Teng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, 150040, Harbin, China
| | - Zhongqiu Lin
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 510120, Guangzhou, Guangdong, China
| | - Kun Song
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 250012, Jinan, Shandong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-Sen University, 510080, Guangzhou, Guangdong, China
| | - Liangqing Yao
- Department of Gynecologic Oncology, Obstetrics and Gynecology Hospital of Fudan University, 200090, Shanghai, China
| | - Lingying Wu
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yong Zhang
- Department of Radiation Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xiaodong Cheng
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Reproductive Health Research, 310006, Hangzhou, Zhejiang, China.
- Department of Gynecologic Oncology, Women's Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, Zhejiang, China.
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, 200120, Shanghai, China.
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, 200120, Shanghai, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, 324000, Quzhou, Zhejiang, China.
- Medical Research Center, and Key Laboratory of Interventional Pulmonology of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang, China.
| |
Collapse
|
5
|
Regulation of RNA Polymerase I Stability and Function. Cancers (Basel) 2022; 14:cancers14235776. [PMID: 36497261 PMCID: PMC9737084 DOI: 10.3390/cancers14235776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
RNA polymerase I is a highly processive enzyme with fast initiation and elongation rates. The structure of Pol I, with its in-built RNA cleavage ability and incorporation of subunits homologous to transcription factors, enables it to quickly and efficiently synthesize the enormous amount of rRNA required for ribosome biogenesis. Each step of Pol I transcription is carefully controlled. However, cancers have highjacked these control points to switch the enzyme, and its transcription, on permanently. While this provides an exceptional benefit to cancer cells, it also creates a potential cancer therapeutic vulnerability. We review the current research on the regulation of Pol I transcription, and we discuss chemical biology efforts to develop new targeted agents against this process. Lastly, we highlight challenges that have arisen from the introduction of agents with promiscuous mechanisms of action and provide examples of agents with specificity and selectivity against Pol I.
Collapse
|
6
|
Li J, Cheng C, Xu J, Zhang T, Tokat B, Dolios G, Ramakrishnan A, Shen L, Wang R, Xu PX. The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and REST-binding sequences to maintain nephron progenitor identity. Nucleic Acids Res 2022; 50:10343-10359. [PMID: 36130284 PMCID: PMC9561260 DOI: 10.1093/nar/gkac760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 11/15/2022] Open
Abstract
Eya1 is critical for establishing and maintaining nephron progenitor cells (NPCs). It belongs to a family of proteins called phosphatase-transcriptional activators but without intrinsic DNA-binding activity. However, the spectrum of the Eya1-centered networks is underexplored. Here, we combined transcriptomic, genomic and proteomic approaches to characterize gene regulation by Eya1 in the NPCs. We identified Eya1 target genes, associated cis-regulatory elements and partner proteins. Eya1 preferentially occupies promoter sequences and interacts with general transcription factors (TFs), RNA polymerases, different types of TFs, chromatin-remodeling factors with ATPase or helicase activity, and DNA replication/repair proteins. Intriguingly, we identified REST-binding motifs in 76% of Eya1-occupied sites without H3K27ac-deposition, which were present in many Eya1 target genes upregulated in Eya1-deficient NPCs. Eya1 copurified REST-interacting chromatin-remodeling factors, histone deacetylase/lysine demethylase, and corepressors. Coimmunoprecipitation validated physical interaction between Eya1 and Rest/Hdac1/Cdyl/Hltf in the kidneys. Collectively, our results suggest that through interactions with chromatin-remodeling factors and specialized DNA-binding proteins, Eya1 may modify chromatin structure to facilitate the assembly of regulatory complexes that regulate transcription positively or negatively. These findings provide a mechanistic basis for how Eya1 exerts its activity by forming unique multiprotein complexes in various biological processes to maintain the cellular state of NPCs.
Collapse
Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Chunming Cheng
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Bengu Tokat
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Georgia Dolios
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | | | - Li Shen
- Department of Neurosciences, New York, NY 10029, USA
| | - Rong Wang
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, New York, NY 10029, USA.,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
7
|
Abaji R, Roux V, Yssaad IR, Kalegari P, Gagné V, Gioia R, Ferbeyre G, Beauséjour C, Krajinovic M. Characterization of the impact of the MYBBP1A gene and rs3809849 on asparaginase sensitivity and cellular functions. Pharmacogenomics 2022; 23:415-430. [PMID: 35485735 DOI: 10.2217/pgs-2022-0010] [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] [Indexed: 11/21/2022] Open
Abstract
Aims: To investigate the role of MYBBP1A gene and rs3809849 in pancreatic cancer (PANC1) and lymphoblastic leukemia (NALM6) cell lines and their response to asparaginase treatment. Materials & methods: The authors applied CRISPR-Cas9 to produce MYBBP1A knock-out (KO) and rs3809849 knock-in (KI) cell lines. The authors also interrogated rs3809849's impact on PANC1 cells through allele-specific overexpression. Results: PANC1 MYBBP1A KO cells exhibited lower proliferation capacity (p ≤ 0.05), higher asparaginase sensitivity (p = 0.01), reduced colony-forming potential (p = 0.001), cell cycle blockage in S phase, induction of apoptosis and remarkable morphology changes suggestive of an epithelial-mesenchymal transition. Overexpression of the wild-type (but not the mutant) allele of MYBBP1A-rs3809849 in PANC1 cells increased asparaginase sensitivity. NALM6 MYBBP1A KO displayed resistance to asparaginase (p < 0.0001), whereas no effect for rs3809849 KI was noted. Conclusions:MYBBP1A is important for regulating various cellular functions, and it plays, along with its rs3809849 polymorphism, a tissue-specific role in asparaginase treatment response.
Collapse
Affiliation(s)
- Rachid Abaji
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Department of Pharmacology & Physiology, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Vincent Roux
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
| | - Ismahène Reguieg Yssaad
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Department of Pharmacology & Physiology, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Paloma Kalegari
- Department of Biochemistry & Molecular Medicine, University of Montreal, Montreal, QC, H3T 1J4, Canada
- University of Montreal Hospital Research Centre (CRCHUM), University of Montreal, Montreal, QC, H2X 0A9, Canada
| | - Vincent Gagné
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
| | - Romain Gioia
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
| | - Gerardo Ferbeyre
- Department of Biochemistry & Molecular Medicine, University of Montreal, Montreal, QC, H3T 1J4, Canada
- University of Montreal Hospital Research Centre (CRCHUM), University of Montreal, Montreal, QC, H2X 0A9, Canada
| | - Christian Beauséjour
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Department of Pharmacology & Physiology, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Maja Krajinovic
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Department of Pharmacology & Physiology, University of Montreal, Montreal, QC, H3T 1J4, Canada
- Department of Pediatrics, University of Montreal, Montreal, QC, H3T 1C5, Canada
| |
Collapse
|
8
|
Bora P, Gahurova L, Hauserova A, Stiborova M, Collier R, Potěšil D, Zdráhal Z, Bruce AW. DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification. Open Biol 2021; 11:210092. [PMID: 34255976 PMCID: PMC8277471 DOI: 10.1098/rsob.210092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Successful navigation of the mouse preimplantation stages of development, during which three distinct blastocyst lineages are derived, represents a prerequisite for continued development. We previously identified a role for p38-mitogen-activated kinases (p38-MAPK) regulating blastocyst inner cell mass (ICM) cell fate, specifically primitive endoderm (PrE) differentiation, that is intimately linked to rRNA precursor processing, polysome formation and protein translation regulation. Here, we develop this work by assaying the role of DEAD-box RNA helicase 21 (DDX21), a known regulator of rRNA processing, in the context of p38-MAPK regulation of preimplantation mouse embryo development. We show nuclear DDX21 protein is robustly expressed from the 16-cell stage, becoming exclusively nucleolar during blastocyst maturation, a localization dependent on active p38-MAPK. siRNA-mediated clonal Ddx21 knockdown within developing embryos is associated with profound cell-autonomous and non-autonomous proliferation defects and reduced blastocyst volume, by the equivalent peri-implantation blastocyst stage. Moreover, ICM residing Ddx21 knockdown clones express the EPI marker NANOG but rarely express the PrE differentiation marker GATA4. These data contribute further significance to the emerging importance of lineage-specific translation regulation, as identified for p38-MAPK, during mouse preimplantation development.
Collapse
Affiliation(s)
- Pablo Bora
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Lenka Gahurova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Andrea Hauserova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Martina Stiborova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Rebecca Collier
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Alexander W Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| |
Collapse
|
9
|
p38-MAPK-mediated translation regulation during early blastocyst development is required for primitive endoderm differentiation in mice. Commun Biol 2021; 4:788. [PMID: 34172827 PMCID: PMC8233355 DOI: 10.1038/s42003-021-02290-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Successful specification of the two mouse blastocyst inner cell mass (ICM) lineages (the primitive endoderm (PrE) and epiblast) is a prerequisite for continued development and requires active fibroblast growth factor 4 (FGF4) signaling. Previously, we identified a role for p38 mitogen-activated protein kinases (p38-MAPKs) during PrE differentiation, but the underlying mechanisms have remained unresolved. Here, we report an early blastocyst window of p38-MAPK activity that is required to regulate ribosome-related gene expression, rRNA precursor processing, polysome formation and protein translation. We show that p38-MAPK inhibition-induced PrE phenotypes can be partially rescued by activating the translational regulator mTOR. However, similar PrE phenotypes associated with extracellular signal-regulated kinase (ERK) pathway inhibition targeting active FGF4 signaling are not affected by mTOR activation. These data indicate a specific role for p38-MAPKs in providing a permissive translational environment during mouse blastocyst PrE differentiation that is distinct from classically reported FGF4-based mechanisms.
Collapse
|
10
|
Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. Sci Rep 2021; 11:346. [PMID: 33431961 PMCID: PMC7801731 DOI: 10.1038/s41598-020-79436-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians or sea cucumbers, cellular processes of intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Comparisons of differential expression were made using the mesentery as a reference against 24 h and 3 days regenerating intestine, revealing a large number of differentially expressed transcripts. Gene ontology and pathway enrichment analysis showed evidence of increasing transcriptional activity. Further analysis of transcripts associated with transcription factors revealed diverse expression patterns with mechanisms involving developmental and cancer-related activity that could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
Collapse
|
11
|
Hsieh A, Pitarresi JR, Lerner J, Donahue G, Hsiehchen D, Rustgi AK, Zaret K. Growth of pancreatic cancers with hemizygous chromosomal 17p loss of MYBBP1A can be preferentially targeted by PARP inhibitors. SCIENCE ADVANCES 2020; 6:eabc4517. [PMID: 33277249 PMCID: PMC7821900 DOI: 10.1126/sciadv.abc4517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/21/2020] [Indexed: 05/02/2023]
Abstract
Here, we selectively target pancreatic ductal adenocarcinoma (PDAC) cells harboring a hemizygous gene essential for cell growth. MYB binding protein 1A (MYBBP1A), encoding a chromatin-bound protein, is hemizygous in most of the PDAC due to a chromosome 17p deletion that also spans TP53 We find that hemizygous MYBBP1A loss in isogenic PDAC cells promotes tumorigenesis but, paradoxically, homozygous MYBBP1A loss is associated with impaired cell growth and decreased tumorigenesis. Poly-adenosine 5'-diphosphate-ribose polymerase 1 (PARP1) interacts with MYBBP1A and displaces it from chromatin. Small molecules, such as olaparib, that trap PARP1 to chromatin are able to evict the minimal pool of chromatin-bound MYBBP1A protein in MYBBP1A hemizygous cells and impair cell growth, greater than its impact on wild-type cells. Our findings reveal how a cell essential gene with one allele lost in cancer cells can be preferentially susceptible to a specific molecular therapy, when compared to wild-type cells.
Collapse
Affiliation(s)
- Antony Hsieh
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5157, USA
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5157, USA
| | - Jason R Pitarresi
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5157, USA
| | - Jonathan Lerner
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5157, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5157, USA
| | - David Hsiehchen
- Division of Hematology and Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital, New York City, NY 10032, USA
| | - Kenneth Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5157, USA.
| |
Collapse
|
12
|
Rudenok M, Alieva A, Starovatykh J, Nesterov M, Stanishevskaya V, Kolacheva A, Ugryumov M, Slominsky P, Shadrina M. Expression analysis of genes involved in mitochondrial biogenesis in mice with MPTP-induced model of Parkinson's disease. Mol Genet Metab Rep 2020; 23:100584. [PMID: 32280590 PMCID: PMC7139113 DOI: 10.1016/j.ymgmr.2020.100584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/23/2023] Open
Abstract
The mitochondrion is an extremely important organelle that performs various functions in the cell: e.g. energy production, regulation of respiration processes and maintenance of calcium homeostasis. Disruption of the biogenesis and functioning of this organelle can lead to cell damage and cell death. Mitochondrial dysfunction has been shown to possibly be involved in the pathogenesis of Parkinson's disease. However, the role of genes associated with mitochondrial biogenesis in the early stages of disease remains poorly understood. The objective of the present study was to analyze changes in the expression of activator (Nrf1, Ppargc1a, Prkn, and Kif1b) and repressor (Zfp746 and Mybbp1a) genes of mitochondrial biogenesis in the early stages of the development of neurodegeneration in an MPTP-induced model of presymptomatic and early symptomatic stages of PD. Statistically significant changes in expression at the mRNA level were detected for all studied genes. There was mainly a decrease in the expression of activator genes (Nrf1, Ppargc1a, Prkn, and Kif1b) at all stages of neurodegeneration, which seemed to be associated with impaired mitochondrial biogenesis and the development of neurodegeneration processes. A predominant decrease in the expression was detected for the Zfp746 and Mybbp1a repressor genes of mitochondrial biogenesis. However, in this case, it was associated with the emergence of compensatory mechanisms during the development of Parkinson's disease. The largest number of statistically significant changes was detected for the Nrf1 activator gene and the Mybbp1a repressor gene. Apparently, these two genes play the most important role in this disease.
Collapse
Affiliation(s)
- M.M. Rudenok
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - A.Kh. Alieva
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - J.S. Starovatykh
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - M.S. Nesterov
- Bioanalytical Research Laboratory, Scientific Center of Biomedical Technologies of the Federal Medical and Biological Agency of Russia, Moscow, Russia
| | - V.A. Stanishevskaya
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - A.A. Kolacheva
- Laboratory of Nervous and Neuro-endocrine Regulations, Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - M.V. Ugryumov
- Laboratory of Nervous and Neuro-endocrine Regulations, Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - P.A. Slominsky
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - M.I. Shadrina
- Laboratory of Molecular Genetics of Hereditary Diseases, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
13
|
Dangelmaier E, Lal A. Adaptor proteins in long noncoding RNA biology. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194370. [DOI: 10.1016/j.bbagrm.2019.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/11/2022]
|
14
|
Braun CM, Hackert P, Schmid CE, Bohnsack MT, Bohnsack KE, Perez-Fernandez J. Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit. Nucleic Acids Res 2020; 48:405-420. [PMID: 31745560 PMCID: PMC7145529 DOI: 10.1093/nar/gkz1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/24/2023] Open
Abstract
More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5' external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5' ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.
Collapse
Affiliation(s)
- Christina M Braun
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Catharina E Schmid
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| |
Collapse
|
15
|
The Tumor Suppressor Roles of MYBBP1A, a Major Contributor to Metabolism Plasticity and Stemness. Cancers (Basel) 2020; 12:cancers12010254. [PMID: 31968688 PMCID: PMC7017249 DOI: 10.3390/cancers12010254] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/18/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
The MYB binding protein 1A (MYBBP1A, also known as p160) acts as a co-repressor of multiple transcription factors involved in many physiological processes. Therefore, MYBBP1A acts as a tumor suppressor in multiple aspects related to cell physiology, most of them very relevant for tumorigenesis. We explored the different roles of MYBBP1A in different aspects of cancer, such as mitosis, cellular senescence, epigenetic regulation, cell cycle, metabolism plasticity and stemness. We especially reviewed the relationships between MYBBP1A, the inhibitory role it plays by binding and inactivating c-MYB and its regulation of PGC-1α, leading to an increase in the stemness and the tumor stem cell population. In addition, MYBBP1A causes the activation of PGC-1α directly and indirectly through c-MYB, inducing the metabolic change from glycolysis to oxidative phosphorylation (OXPHOS). Therefore, the combination of these two effects caused by the decreased expression of MYBBP1A provides a selective advantage to tumor cells. Interestingly, this only occurs in cells lacking pVHL. Finally, the loss of MYBBP1A occurs in 8%–9% of renal tumors. tumors, and this subpopulation could be studied as a possible target of therapies using inhibitors of mitochondrial respiration.
Collapse
|
16
|
Deubiquitinase USP29 Governs MYBBP1A in the Brains of Parkinson's Disease Patients. J Clin Med 2019; 9:jcm9010052. [PMID: 31878357 PMCID: PMC7019889 DOI: 10.3390/jcm9010052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 11/16/2022] Open
Abstract
The inactivation of parkin by mutation or post-translational modification contributes to dopaminergic neuronal death in Parkinson's disease (PD). The substrates of parkin, FBP1 and AIMP2, are accumulated in the postmortem brains of PD patients, and it was recently suggested that these parkin substrates transcriptionally activate deubiquitinase USP29. Herein, we newly identified 160 kDa myb-binding protein (MYBBP1A) as a novel substrate of USP29. Knockdown of parkin increased the level of AIMP2, leading to ultimately USP29 and MYBBP1A accumulation in SH-SY5Y cells. Notably, MYBBP1A was downregulated in the ventral midbrain (VM) of Aimp2 knockdown mice, whereas the upregulation of MYBBP1A was observed in the VM of inducible AIMP2 transgenic mice, as well as in the substantia nigra of sporadic PD patients. These results suggest that AIMP2 upregulates USP29 and MYBBP1A in the absence of parkin activity, contributing to PD pathogenesis.
Collapse
|
17
|
Ramos-Sáenz A, González-Álvarez D, Rodríguez-Galán O, Rodríguez-Gil A, Gaspar SG, Villalobo E, Dosil M, de la Cruz J. Pol5 is an essential ribosome biogenesis factor required for 60S ribosomal subunit maturation in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2019; 25:1561-1575. [PMID: 31413149 PMCID: PMC6795146 DOI: 10.1261/rna.072116.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
In Saccharomyces cerevisiae, more than 250 trans-acting factors are involved in the maturation of 40S and 60S ribosomal subunits. The expression of most of these factors is transcriptionally coregulated to ensure correct ribosome production under a wide variety of environmental and intracellular conditions. Here, we identified the essential nucleolar Pol5 protein as a novel trans-acting factor required for the synthesis of 60S ribosomal subunits. Pol5 weakly and/or transiently associates with early to medium pre-60S ribosomal particles. Depletion of and temperature-sensitive mutations in Pol5 result in a deficiency of 60S ribosomal subunits and accumulation of half-mer polysomes. Both processing of 27SB pre-rRNA to mature 25S rRNA and release of pre-60S ribosomal particles from the nucle(ol)us to the cytoplasm are impaired in the Pol5-depleted strain. Moreover, we identified the genes encoding ribosomal proteins uL23 and eL27A as multicopy suppressors of the slow growth of a temperature-sensitive pol5 mutant. These results suggest that Pol5 could function in ensuring the correct folding of 25S rRNA domain III; thus, favoring the correct assembly of these two ribosomal proteins at their respective binding sites into medium pre-60S ribosomal particles. Pol5 is homologous to the human tumor suppressor Myb-binding protein 1A (MYBBP1A). However, expression of MYBBP1A failed to complement the lethal phenotype of a pol5 null mutant strain though interfered with 60S ribosomal subunit biogenesis.
Collapse
Affiliation(s)
- Ana Ramos-Sáenz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012, Seville, Spain
| | - Daniel González-Álvarez
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012, Seville, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012, Seville, Spain
| | - Alfonso Rodríguez-Gil
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013, Seville, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, E-37007, Salamanca, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), CSIC-Universidad de Salamanca, E-37007, Salamanca, Spain
| | - Eduardo Villalobo
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013, Seville, Spain
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, E-41012, Seville, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, E-37007, Salamanca, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), CSIC-Universidad de Salamanca, E-37007, Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, E-37007, Salamanca, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012, Seville, Spain
| |
Collapse
|
18
|
Corsini NS, Peer AM, Moeseneder P, Roiuk M, Burkard TR, Theussl HC, Moll I, Knoblich JA. Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation. Cell Stem Cell 2019; 22:543-558.e12. [PMID: 29625069 DOI: 10.1016/j.stem.2018.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 01/05/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Stem cell-specific transcriptional networks are well known to control pluripotency, but constitutive cellular processes such as mRNA splicing and protein synthesis can add complex layers of regulation with poorly understood effects on cell-fate decisions. Here, we show that the RNA binding protein HTATSF1 controls embryonic stem cell differentiation by regulating multiple aspects of RNA processing during ribosome biogenesis. HTATSF1, in a complex with splicing factor SF3B1, controls intron removal from ribosomal protein transcripts and regulates ribosomal RNA transcription and processing, thereby controlling 60S ribosomal abundance and protein synthesis. HTATSF1-dependent protein synthesis is essential for naive pre-implantation epiblast to transition into post-implantation epiblast, a stage with transiently low protein synthesis, and further differentiation toward neuroectoderm. Together, these results identify coordinated regulation of ribosomal RNA and protein synthesis by HTATSF1 and show that this essential mechanism controls protein synthesis during early mammalian embryogenesis.
Collapse
Affiliation(s)
- Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Angela M Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Paul Moeseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Mykola Roiuk
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Hans-Christian Theussl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
19
|
Kovacevic J, Palm D, Jooss D, Bublak D, Simm S, Schleiff E. Co-orthologues of ribosome biogenesis factors in A. thaliana are differentially regulated by transcription factors. PLANT CELL REPORTS 2019; 38:937-949. [PMID: 31087154 DOI: 10.1007/s00299-019-02416-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/29/2019] [Indexed: 06/09/2023]
Abstract
Different genes coding for one ribosome biogenesis factor are differentially expressed and are likely under the control of distinct transcription factors, which contributes to the regulatory space for ribosome maturation. Maturation of ribosomes including rRNA processing and modification, rRNA folding and ribosome protein association requires the function of many ribosome biogenesis factors (RBFs). Recent studies document plant-specific variations of the generally conserved process of ribosome biogenesis. For instance, distinct rRNA maturation pathways and intermediates have been identified, the existence of plant specific RBFs has been proposed and several RBFs are encoded by multiple genes. The latter in combination with the discussed ribosome heterogeneity points to a possible function of the different proteins representing one RBF in diversification of ribosomal compositions. Such factor-based regulation would require a differential regulation of their expression, may be even controlled by different transcription factors. We analyzed the expression profiles of genes coding for putative RBFs and transcription factors. Most of the genes coding for RBFs are expressed in a comparable manner, while different genes coding for a single RBF are often differentially expressed. Based on a selected set of genes we document a function of the transcription factors AtMYC1, AtMYC2, AtbHLH105 and AtMYB26 on the regulation of different RBFs. Moreover, on the example of the RBFs LSG1 and BRX1, both encoded by two genes, we give a first hint on a differential transcription factor dependence of expression. Consistent with this observation, the phenotypic analysis of RBF mutants suggests a relation between LSG1-1 and BRX1-1 expression and the transcription factor MYC1. In summary, we propose that the multiple genes coding for one RBF are required to enlarge the regulatory space for ribosome biogenesis.
Collapse
Affiliation(s)
- Jelena Kovacevic
- Institute for Molecular Biosciences, Goethe University, Biocenter/Max von Laue Straße 9/N200/R3.02, 60438, Frankfurt am Main, Germany
| | - Denise Palm
- Institute for Molecular Biosciences, Goethe University, Biocenter/Max von Laue Straße 9/N200/R3.02, 60438, Frankfurt am Main, Germany
| | - Domink Jooss
- Institute for Molecular Biosciences, Goethe University, Biocenter/Max von Laue Straße 9/N200/R3.02, 60438, Frankfurt am Main, Germany
| | - Daniela Bublak
- Institute for Molecular Biosciences, Goethe University, Biocenter/Max von Laue Straße 9/N200/R3.02, 60438, Frankfurt am Main, Germany
| | - Stefan Simm
- Institute for Molecular Biosciences, Goethe University, Biocenter/Max von Laue Straße 9/N200/R3.02, 60438, Frankfurt am Main, Germany
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University, Biocenter/Max von Laue Straße 9/N200/R3.02, 60438, Frankfurt am Main, Germany.
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany.
| |
Collapse
|
20
|
Gallagher JEG. Proteins and RNA sequences required for the transition of the t-Utp complex into the SSU processome. FEMS Yeast Res 2019; 19:5184469. [PMID: 30445532 DOI: 10.1093/femsyr/foy120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Ribosomes are synthesized by large ribonucleoprotein complexes cleaving and properly assembling highly structured rRNAs with ribosomal proteins. Transcription and processing of pre-rRNAs are linked by the transcription-Utp sub-complex (t-Utps), a sub-complex of the small subunit (SSU) processome and prompted the investigations for the requirements of t-Utp formation and transition into the SSU processome. The rDNA promoter, the first 44 nucleotides of the 5΄ETS, and active transcription by pol I were sufficient to recruit the t-Utps to the rDNA. Pol5, accessory factor, dissociated as t-Utps matured into the UtpA complex which permitted later recruitment of the UtpB, U3 snoRNP and the Mpp10 complex into the SSU processome. The t-Utp complex associated with short RNAs 121 and 138 nucleotides long transcribed from the 5΄ETS. These transcripts were not present when pol II transcribed the rDNA or in nondividing cells. Depletion of a t-Utp, but not of other SSU processome components led to decreased levels of the short transcripts. However, ectopic expression of the short transcripts slowed the growth of yeast with impaired rDNA transcription. These results provide insight into how transcription of the rRNA primes the assemble of t-Utp complex with the pre-rRNA into the UtpA complex and the later association of SSU processome components.
Collapse
|
21
|
Weng X, Wu J, Lv Z, Peng C, Chen J, Zhang C, He B, Tong R, Hu W, Ding C, Cao L, Chen D, Wu J, Zheng S. Targeting Mybbp1a suppresses HCC progression via inhibiting IGF1/AKT pathway by CpG islands hypo-methylation dependent promotion of IGFBP5. EBioMedicine 2019; 44:225-236. [PMID: 31109829 PMCID: PMC6606930 DOI: 10.1016/j.ebiom.2019.05.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/10/2019] [Accepted: 05/10/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Myb-binding protein 1A (Mybbp1a) is a nucleolar protein that can regulate rRNA metabolism, the stress response and carcinogenesis. However, the function of Mybbp1a in the progression of hepatocellular carcinoma (HCC) is unclear. We aimed to determine the role of Mybbp1a in HCC and the underlying mechanism. METHODS We investigated the function of Mybbp1a in HCC cell models and the xenograft mouse model. The relationship between Mybbp1a and IGFBP5 was found through expression profile chip. The molecular mechanism of Mybbp1a regulating IGFBP5 was proved through CO-IP, CHIP, Bisulfite Sequencing and Pyrosequencing. FINDINGS In this study, we observed that Mybbp1a was overexpressed in HCC tissues and associated with the poor prognosis of HCC patients. Suppression of Mybbp1a led to a reduction in the proliferation and migration ability of HCC cells through inhibiting the IGF1/AKT signaling pathway. Further study found that Mybbp1a could form a complex with DNMT1 and induce aberrant hyper-methylation of CpG islands of IGFBP5, which inhibits secretion of IGFBP5 and then activates IGF1/AKT signaling pathway. INTERPRETATION These findings extend our understanding of the function of Mybbp1a in the progression of HCC. The newly identified Mybbp1a may provide a novel biomarker for developing potential therapeutic targets of HCC. FUND: Science Technology Department of Zhejiang Province (No. 2015C03034), National Health and Family Planning Commission of China (No. 2016138643), Innovative Research Groups of National Natural Science Foundation of China (No. 81721091), Major program of National Natural Science Foundation of China (No. 91542205).
Collapse
Affiliation(s)
- Xiaoyu Weng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Jingbang Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Zhen Lv
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Chuanhui Peng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Junru Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Cheng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Bin He
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Rongliang Tong
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Wendi Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Chaofeng Ding
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Linping Cao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Diyu Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China; The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China.
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Key Lab of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou 310003, China; The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China.
| |
Collapse
|
22
|
Li XL, Subramanian M, Jones MF, Chaudhary R, Singh DK, Zong X, Gryder B, Sindri S, Mo M, Schetter A, Wen X, Parvathaneni S, Kazandjian D, Jenkins LM, Tang W, Elloumi F, Martindale JL, Huarte M, Zhu Y, Robles AI, Frier SM, Rigo F, Cam M, Ambs S, Sharma S, Harris CC, Dasso M, Prasanth KV, Lal A. Long Noncoding RNA PURPL Suppresses Basal p53 Levels and Promotes Tumorigenicity in Colorectal Cancer. Cell Rep 2018; 20:2408-2423. [PMID: 28877474 DOI: 10.1016/j.celrep.2017.08.041] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/21/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
Basal p53 levels are tightly suppressed under normal conditions. Disrupting this regulation results in elevated p53 levels to induce cell cycle arrest, apoptosis, and tumor suppression. Here, we report the suppression of basal p53 levels by a nuclear, p53-regulated long noncoding RNA that we termed PURPL (p53 upregulated regulator of p53 levels). Targeted depletion of PURPL in colorectal cancer cells results in elevated basal p53 levels and induces growth defects in cell culture and in mouse xenografts. PURPL associates with MYBBP1A, a protein that binds to and stabilizes p53, and inhibits the formation of the p53-MYBBP1A complex. In the absence of PURPL, MYBBP1A interacts with and stabilizes p53. Silencing MYBBP1A significantly rescues basal p53 levels and proliferation in PURPL-deficient cells, suggesting that MYBBP1A mediates the effect of PURPL in regulating p53. These results reveal a p53-PURPL auto-regulatory feedback loop and demonstrate a role for PURPL in maintaining basal p53 levels.
Collapse
Affiliation(s)
- Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Murugan Subramanian
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Matthew F Jones
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Ritu Chaudhary
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA
| | - Deepak K Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Berkley Gryder
- Oncogenomics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sivasish Sindri
- Oncogenomics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Min Mo
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Aaron Schetter
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Xinyu Wen
- Oncogenomics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Swetha Parvathaneni
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Dickran Kazandjian
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Wei Tang
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Office of Science and Technology Resources, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Jennifer L Martindale
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH, Baltimore, MD 21224, USA
| | - Maite Huarte
- Center for Applied Medical Research, Department of Gene Therapy and Regulation of Gene Expression, University of Navarra, 31008 Pamplona, Spain
| | - Yuelin Zhu
- Molecular Genetics Section, Genetics Branch, CCR, NCI, NIH, Bethesda, MD 28092, USA
| | - Ana I Robles
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Maggie Cam
- Office of Science and Technology Resources, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Stefan Ambs
- Molecular Epidemiology Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC 20059, USA
| | - Curtis C Harris
- Molecular Genetics and Carcinogenesis Section, Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Mary Dasso
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
23
|
Liu Y, Mattila J, Ventelä S, Yadav L, Zhang W, Lamichane N, Sundström J, Kauko O, Grénman R, Varjosalo M, Westermarck J, Hietakangas V. PWP1 Mediates Nutrient-Dependent Growth Control through Nucleolar Regulation of Ribosomal Gene Expression. Dev Cell 2017; 43:240-252.e5. [PMID: 29065309 DOI: 10.1016/j.devcel.2017.09.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/01/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022]
Abstract
Ribosome biogenesis regulates animal growth and is controlled by nutrient-responsive mTOR signaling. How ribosome biogenesis is regulated during the developmental growth of animals and how nutrient-responsive signaling adjusts ribosome biogenesis in this setting have remained insufficiently understood. We uncover PWP1 as a chromatin-associated regulator of developmental growth with a conserved role in RNA polymerase I (Pol I)-mediated rRNA transcription. We further observed that PWP1 epigenetically maintains the rDNA loci in a transcription-competent state. PWP1 responds to nutrition in Drosophila larvae via mTOR signaling through gene expression and phosphorylation, which controls the nucleolar localization of dPWP1. Our data further imply that dPWP1 acts synergistically with mTOR signaling to regulate the nucleolar localization of TFIIH, a known elongation factor of Pol I. Ribosome biogenesis is often deregulated in cancer, and we demonstrate that high PWP1 levels in human head and neck squamous cell carcinoma tumors are associated with poor prognosis.
Collapse
Affiliation(s)
- Ying Liu
- Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Jaakko Mattila
- Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Sami Ventelä
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Leena Yadav
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Wei Zhang
- Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Nicole Lamichane
- Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Jari Sundström
- Department of Pathology, University of Turku, 20520 Turku, Finland; Department of Pathology, Turku University Hospital, 20521 Turku, Finland
| | - Otto Kauko
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Pathology, University of Turku, 20520 Turku, Finland
| | - Reidar Grénman
- Department of Otorhinolaryngology - Head and Neck Surgery and Department of Medical Biochemistry and Genetics, University of Turku and Turku University Hospital, 20521 Turku, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Jukka Westermarck
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Pathology, University of Turku, 20520 Turku, Finland
| | - Ville Hietakangas
- Department of Biosciences, University of Helsinki, 00790 Helsinki, Finland; Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland.
| |
Collapse
|
24
|
Chen Z, Cao H, Lu Y, Ren Q, Sun L. DNA polymerase 5 acetylation by Eso1 is essential for Schizosaccharomyces pombe viability. Int J Mol Med 2017; 40:1907-1913. [PMID: 29039458 DOI: 10.3892/ijmm.2017.3192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 07/24/2017] [Indexed: 11/05/2022] Open
Abstract
Eco1/Eso1 protein plays an important role in chromosome segregation, DNA repair and gene regulation. Eco1 mutation induces Roberts syndrome clinically and rDNA transcription disorders in vivo. In this study, we examined the role of Eso1 protein binding to polymerase 5 (Pol5) and the acetylation of Pol5 protein in the regulation of Schizosaccharomyces pombe (S. pombe) viability. Immunoprecipitation and mass spectrometry assays identified Eso1 protein binding to Cdc2, Pol5 and Cdc21, as well as other proteins. Pol5 protein specifically bound to Eso1 protein, but not to the Rad30 part or Rad30 part plus the additional zinc finger domain of Eco1 protein. Mass spectrometry data further identified several acetylation or trimethylation modification sites in the lysine residues of the Pol5 protein. However, the mutation of the Pol5 K47 site to arginine was lethal to S. pombe. Eso1 protein was able to acetylate Pol5 protein and mediate S. pombe viability. On the whole, our data indicate that the Eso1 interaction with Pol5 which acetylates Pol5 protein is essential for S. pombe viability.
Collapse
Affiliation(s)
- Zhiming Chen
- Department of Forensic Pathology, Basic Medical College, The First Hospital, Jilin University, Jilin 130021, P.R. China
| | - Hongshi Cao
- Department of Neurosurgery, The First Hospital, Jilin University, Jilin 130021, P.R. China
| | - Yingqiang Lu
- Department of Forensic Pathology, Basic Medical College, The First Hospital, Jilin University, Jilin 130021, P.R. China
| | - Qiang Ren
- Department of Forensic Pathology, Basic Medical College, The First Hospital, Jilin University, Jilin 130021, P.R. China
| | - Liankun Sun
- Department of Forensic Pathology, Basic Medical College, The First Hospital, Jilin University, Jilin 130021, P.R. China
| |
Collapse
|
25
|
Komatsu T, Robinson DR, Hisaoka M, Ueshima S, Okuwaki M, Nagata K, Wodrich H. Tracking adenovirus genomes identifies morphologically distinct late DNA replication compartments. Traffic 2016; 17:1168-1180. [PMID: 27492875 DOI: 10.1111/tra.12429] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023]
Abstract
In adenoviral virions, the genome is organized into a chromatin-like structure by viral basic core proteins. Consequently viral DNAs must be replicated, chromatinized and packed into progeny virions in infected cells. Although viral DNA replication centers can be visualized by virtue of viral and cellular factors, the spatiotemporal regulation of viral genomes during subsequent steps remains to be elucidated. In this study, we used imaging analyses to examine the fate of adenoviral genomes and to track newly replicated viral DNA as well as replication-related factors. We show de novo formation of a subnuclear domain, which we termed Virus-induced Post-Replication (ViPR) body, that emerges concomitantly with or immediately after disintegration of initial replication centers. Using a nucleoside analogue, we show that viral genomes continue being synthesized in morphologically distinct replication compartments at the periphery of ViPR bodies and are then transported inward. In addition, we identified a nucleolar protein Mybbp1a as a molecular marker for ViPR bodies, which specifically associated with viral core protein VII. In conclusion, our work demonstrates the formation of previously uncharacterized viral DNA replication compartments specific for late phases of infection that produce progeny viral genomes accumulating in ViPR bodies.
Collapse
Affiliation(s)
- Tetsuro Komatsu
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France.,Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Derrick R Robinson
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Miharu Hisaoka
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shuhei Ueshima
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mitsuru Okuwaki
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, Université de Bordeaux, Bordeaux, France.
| |
Collapse
|
26
|
Conrad T, Albrecht AS, de Melo Costa VR, Sauer S, Meierhofer D, Ørom UA. Serial interactome capture of the human cell nucleus. Nat Commun 2016; 7:11212. [PMID: 27040163 PMCID: PMC4822031 DOI: 10.1038/ncomms11212] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/02/2016] [Indexed: 11/15/2022] Open
Abstract
Novel RNA-guided cellular functions are paralleled by an increasing number of RNA-binding proteins (RBPs). Here we present 'serial RNA interactome capture' (serIC), a multiple purification procedure of ultraviolet-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with high specificity. We apply serIC to the nuclei of proliferating K562 cells to obtain the first human nuclear RNA interactome. The domain composition of the 382 identified nuclear RBPs markedly differs from previous IC experiments, including few factors without known RNA-binding domains that are in good agreement with computationally predicted RNA binding. serIC extends the number of DNA-RNA-binding proteins (DRBPs), and reveals a network of RBPs involved in p53 signalling and double-strand break repair. serIC is an effective tool to couple global RBP capture with additional selection or labelling steps for specific detection of highly purified RBPs.
Collapse
Affiliation(s)
- Thomas Conrad
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany
| | - Anne-Susann Albrecht
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany
- Department of Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Veronica Rodrigues de Melo Costa
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany
- Department of Informatics, Free University of Berlin, 14195 Berlin, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany
- CU Systems Medicine, 97080 Würzburg 14195, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Core Facility, 14195 Berlin, Germany
| | - Ulf Andersson Ørom
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany
| |
Collapse
|
27
|
Hu G, Gong AY, Wang Y, Ma S, Chen X, Chen J, Su CJ, Shibata A, Strauss-Soukup JK, Drescher KM, Chen XM. LincRNA-Cox2 Promotes Late Inflammatory Gene Transcription in Macrophages through Modulating SWI/SNF-Mediated Chromatin Remodeling. THE JOURNAL OF IMMUNOLOGY 2016; 196:2799-2808. [PMID: 26880762 DOI: 10.4049/jimmunol.1502146] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022]
Abstract
Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (>200 nt) from the intergenic regions of annotated protein-coding genes. One of the most highly induced lincRNAs in macrophages upon TLR ligation is lincRNA-Cox2, which was recently shown to mediate the activation and repression of distinct classes of immune genes in innate immune cells. We report that lincRNA-Cox2, located at chromosome 1 proximal to the PG-endoperoxide synthase 2 (Ptgs2/Cox2) gene, is an early-primary inflammatory gene controlled by NF-κB signaling in murine macrophages. Functionally, lincRNA-Cox2 is required for the transcription of NF-κB-regulated late-primary inflammatory response genes stimulated by bacterial LPS. Specifically, lincRNA-Cox2 is assembled into the switch/sucrose nonfermentable (SWI/SNF) complex in cells after LPS stimulation. This resulting lincRNA-Cox2/SWI/SNF complex can modulate the assembly of NF-κB subunits to the SWI/SNF complex, and ultimately, SWI/SNF-associated chromatin remodeling and transactivation of the late-primary inflammatory-response genes in macrophages in response to microbial challenge. Therefore, our data indicate a new regulatory role for NF-κB-induced lincRNA-Cox2 as a coactivator of NF-κB for the transcription of late-primary response genes in innate immune cells through modulation of epigenetic chromatin remodeling.
Collapse
Affiliation(s)
- Guoku Hu
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Ai-Yu Gong
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Yang Wang
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Shibin Ma
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Xiqiang Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Jing Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Chun-Jen Su
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Annemarie Shibata
- Department of Biology, Creighton University College of Arts and Sciences, Omaha, NE 68178, USA
| | - Juliane K Strauss-Soukup
- Department of Chemistry, Creighton University College of Arts and Sciences, Omaha, NE 68178, USA
| | - Kristen M Drescher
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| |
Collapse
|
28
|
Kleszcz R, Paluszczak J, Baer-Dubowska W. Targeting aberrant cancer metabolism - The role of sirtuins. Pharmacol Rep 2015; 67:1068-80. [PMID: 26481524 DOI: 10.1016/j.pharep.2015.03.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 12/23/2022]
Abstract
Cancer cells, as opposed to normal cells, generate energy by increasing aerobic glycolysis, which is a phenomenon called "the Warburg effect". An altered energy metabolism supporting continuous cell growth and proliferation was pointed to as the new "hallmark" of cancer cells. Several hypotheses have been proposed to explain the maintenance of this seemingly wasteful catabolic state. The epigenetic mechanisms which depend on the covalent modifications of both DNA and histones have recently emerged as important players in the regulation of glucose metabolism. The sirtuin family of histone deacetylases has emerged as important regulators of diverse physiological and pathological events, including cancer metabolism. Sirtuins 1-7 (SIRT1-7) belong to class III of histone deacetylase enzymes which are dependent on NAD(+) for activity. It was recently demonstrated that SIRT6 is a tumor suppressor that modulates aerobic glycolysis by repressing HIF1 transcription. Members of this family of enzymes are considered promising pharmaceutical targets for cancer treatment. This review highlights the major functions of sirtuins in relation to cancer metabolism and the possibilities of their activation and inhibition by small molecule drugs.
Collapse
Affiliation(s)
- Robert Kleszcz
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
| | - Jarosław Paluszczak
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
| | - Wanda Baer-Dubowska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland.
| |
Collapse
|
29
|
Hajjawi OS. Ribonucleic acid (RNA) biosynthesis in human cancer. Cancer Cell Int 2015; 15:22. [PMID: 25717284 PMCID: PMC4339644 DOI: 10.1186/s12935-015-0167-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/20/2015] [Indexed: 12/28/2022] Open
Abstract
In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article, we review malignant tumor, with stem like properties, and recent technical advances into the phenomenon of micro-particles and micro-vesicles containing cell-free nucleic acids that circulate plasma. New areas of research have been opened into screening tumor telomerase progression, prognosis of aptamers targeting cell surface, monitoring the efficacy of anticancer therapies, oncogenic transformation of host cell, and RNA polymerases role in the cell cycle progression and differentiation.
Collapse
Affiliation(s)
- Omar S Hajjawi
- Department of Biology, Arab American University, P. O. Box 240, Jenin, Israeli Occupied Territories of Palestine
| |
Collapse
|
30
|
Regulation and function of Myb-binding protein 1A (MYBBP1A) in cellular senescence and pathogenesis of head and neck cancer. Cancer Lett 2014; 358:191-199. [PMID: 25543088 DOI: 10.1016/j.canlet.2014.12.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 11/20/2022]
Abstract
Myb-binding protein 1A (MYBBP1A) is a nucleolar protein implicated in stress response and carcinogenesis; however, its functional contribution to senescence remains elusive. In this study we show decreased MYBBP1A protein levels in tumor cells after treatment with etoposide, a potent inducer of DNA damage. Although silencing of MYBBP1A expression was not sufficient to induce senescence, it significantly increased the relative abundance of senescent cells after DNA damage. We found an inverse regulation of MYBBP1A and AKT phosphorylation (pAKT(Ser473)), which was characteristic for the pre-senescent state after etoposide administration in vitro. Tissue microarrays with tumor specimens from primary oropharyngeal squamous cell carcinoma (OPSCC) patients (n = 61) by immunohistochemistry revealed a significant correlation between MYBBP1A(low)pAKT(Ser473)(high) staining pattern and shorter progression-free (p = 0.007) or overall survival (p < 0.001). Multivariate analysis showed that MYBBP1A(low)pAKT(Ser473)(high) staining pattern is an independent prognosticator for OPSCC. Taken together, our study points to a critical role of MYBBP1A in the regulation of senescence under genotoxic stress and that a MYBBP1A(low)AKT(Ser473)(high) staining pattern serves not only as a marker for the pre-senescent stage but also as an indicator of OPSCC patients at high risk for treatment failure.
Collapse
|
31
|
Kang H, Shin JH. Repression of rRNA transcription by PARIS contributes to Parkinson's disease. Neurobiol Dis 2014; 73:220-8. [PMID: 25315684 DOI: 10.1016/j.nbd.2014.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/23/2014] [Accepted: 10/01/2014] [Indexed: 11/26/2022] Open
Abstract
The nucleolus is a compartment for the transcription of ribosomal RNA (rRNA) and assembly of ribosome subunits. Dysregulation of the nucleolus is considered to be a cellular stress event associated with aging and neurodegenerative disease, including Parkinson's disease (PD). We previously demonstrated that PARIS (PARkin Interacting Substrate, ZNF746) transcriptionally suppresses peroxisome proliferator-activated receptor gamma (PPARγ) coactivator-1α (PGC-1α) in PD and its accumulation results in selective dopaminergic neuronal death. However, functional knowledge of PARIS is limited, and no other studies have been performed to elucidate its function. Here, we used tandem-affinity purification to identify the binding partners of PARIS, showing that PARIS interacts with 160-kDa Myb-binding protein 1α (MYBBP1A), which suppresses rRNA transcription and the rRNA editing process. Interestingly, PARIS was also found to interact with the components of RNA polymerase I, occupied the promoter of rDNA, and suppressed rDNA transcription in vivo. Accordingly, we observed a reduction of rRNA levels and increased expression of p53, a molecular marker of nucleolar stress, in the substantia nigra of conditional parkin knockout mice, AAV-mediated PARIS overexpression mice, and in patients with sporadic PD. Together, our results suggest that dysfunction of the Parkin-PARIS pathway may play a deleterious role in rRNA transcription and contribute to PD pathogenesis.
Collapse
Affiliation(s)
- Hojin Kang
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi-do 440-746, Republic of Korea
| | - Joo-Ho Shin
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi-do 440-746, Republic of Korea; Mass Spectrometry, Research Core Facility, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Gyeonggi-do 440-746, Republic of Korea.
| |
Collapse
|
32
|
Cong R, Das S, Douet J, Wong J, Buschbeck M, Mongelard F, Bouvet P. macroH2A1 histone variant represses rDNA transcription. Nucleic Acids Res 2014; 42:181-92. [PMID: 24071584 PMCID: PMC3874179 DOI: 10.1093/nar/gkt863] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/30/2013] [Accepted: 09/04/2013] [Indexed: 01/21/2023] Open
Abstract
The regulation of ribosomal DNA transcription is an important step for the control of cell growth. Epigenetic marks such as DNA methylation and posttranslational modifications of canonical histones have been involved in this regulation, but much less is known about the role of histone variants. In this work, we show that the histone variant macroH2A1 is present on the promoter of methylated rDNA genes. The inhibition of the expression of macroH2A1 in human HeLa and HepG2 cells and in a mouse ES cell line resulted in an up to 5-fold increase of pre-rRNA levels. This increased accumulation of pre-rRNA is accompanied by an increase of the loading of RNA polymerase I and UBF on the rDNA without any changes in the number of active rDNA genes. The inhibition of RNA polymerase I transcription by actinomycin D or by knocking down nucleolin, induces the recruitment of macroH2A1 on the rDNA and the relocalization of macroH2A1 in the nucleolus. Interestingly, the inhibition of rDNA transcription induced by nucleolin depletion is alleviated by the inactivation of macroH2A1. These results demonstrate that macroH2A1 is a new factor involved in the regulation of rDNA transcription.
Collapse
Affiliation(s)
- Rong Cong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Sadhan Das
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Julien Douet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Marcus Buschbeck
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fabien Mongelard
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Philippe Bouvet
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS USR 3010, Laboratoire Joliot-Curie, 69364 Lyon, France, The Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona, Barcelona, Spain and The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| |
Collapse
|
33
|
Karim MF, Yoshizawa T, Sato Y, Sawa T, Tomizawa K, Akaike T, Yamagata K. Inhibition of H3K18 deacetylation of Sirt7 by Myb-binding protein 1a (Mybbp1a). Biochem Biophys Res Commun 2013; 441:157-63. [DOI: 10.1016/j.bbrc.2013.10.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/07/2013] [Indexed: 11/29/2022]
|
34
|
Jakhesara SJ, Koringa PG, Bhatt VD, Shah TM, Vangipuram S, Shah S, Joshi CG. RNA-Seq reveals differentially expressed isoforms and novel splice variants in buccal mucosal cancer. Gene 2013; 516:24-32. [DOI: 10.1016/j.gene.2012.11.079] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/23/2012] [Accepted: 11/24/2012] [Indexed: 11/25/2022]
|