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Nagelberg AL, Sihota TS, Chuang YC, Shi R, Chow JLM, English J, MacAulay C, Lam S, Lam WL, Lockwood WW. Integrative genomics identifies SHPRH as a tumor suppressor gene in lung adenocarcinoma that regulates DNA damage response. Br J Cancer 2024; 131:534-550. [PMID: 38890444 PMCID: PMC11300780 DOI: 10.1038/s41416-024-02755-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: 09/20/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Identification of driver mutations and development of targeted therapies has considerably improved outcomes for lung cancer patients. However, significant limitations remain with the lack of identified drivers in a large subset of patients. Here, we aimed to assess the genomic landscape of lung adenocarcinomas (LUADs) from individuals without a history of tobacco use to reveal new genetic drivers of lung cancer. METHODS Integrative genomic analyses combining whole-exome sequencing, copy number, and mutational information for 83 LUAD tumors was performed and validated using external datasets to identify genetic variants with a predicted functional consequence and assess association with clinical outcomes. LUAD cell lines with alteration of identified candidates were used to functionally characterize tumor suppressive potential using a conditional expression system both in vitro and in vivo. RESULTS We identified 21 genes with evidence of positive selection, including 12 novel candidates that have yet to be characterized in LUAD. In particular, SNF2 Histone Linker PHD RING Helicase (SHPRH) was identified due to its frequency of biallelic disruption and location within the familial susceptibility locus on chromosome arm 6q. We found that low SHPRH mRNA expression is associated with poor survival outcomes in LUAD patients. Furthermore, we showed that re-expression of SHPRH in LUAD cell lines with inactivating alterations for SHPRH reduces their in vitro colony formation and tumor burden in vivo. Finally, we explored the biological pathways associated SHPRH inactivation and found an association with the tolerance of LUAD cells to DNA damage. CONCLUSIONS These data suggest that SHPRH is a tumor suppressor gene in LUAD, whereby its expression is associated with more favorable patient outcomes, reduced tumor and mutational burden, and may serve as a predictor of response to DNA damage. Thus, further exploration into the role of SHPRH in LUAD development may make it a valuable biomarker for predicting LUAD risk and prognosis.
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Affiliation(s)
- Amy L Nagelberg
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tianna S Sihota
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yu-Chi Chuang
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Justine L M Chow
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - John English
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Calum MacAulay
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada.
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
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Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
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3
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Chakraborty S, Nandi P, Mishra J, Niharika, Roy A, Manna S, Baral T, Mishra P, Mishra PK, Patra SK. Molecular mechanisms in regulation of autophagy and apoptosis in view of epigenetic regulation of genes and involvement of liquid-liquid phase separation. Cancer Lett 2024; 587:216779. [PMID: 38458592 DOI: 10.1016/j.canlet.2024.216779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Cellular physiology is critically regulated by multiple signaling nexuses, among which cell death mechanisms play crucial roles in controlling the homeostatic landscape at the tissue level within an organism. Apoptosis, also known as programmed cell death, can be induced by external and internal stimuli directing the cells to commit suicide in unfavourable conditions. In contrast, stress conditions like nutrient deprivation, infection and hypoxia trigger autophagy, which is lysosome-mediated processing of damaged cellular organelle for recycling of the degraded products, including amino acids. Apparently, apoptosis and autophagy both are catabolic and tumor-suppressive pathways; apoptosis is essential during development and cancer cell death, while autophagy promotes cell survival under stress. Moreover, autophagy plays dual role during cancer development and progression by facilitating the survival of cancer cells under stressed conditions and inducing death in extreme adversity. Despite having two different molecular mechanisms, both apoptosis and autophagy are interconnected by several crosslinking intermediates. Epigenetic modifications, such as DNA methylation, post-translational modification of histone tails, and miRNA play a pivotal role in regulating genes involved in both autophagy and apoptosis. Both autophagic and apoptotic genes can undergo various epigenetic modifications and promote or inhibit these processes under normal and cancerous conditions. Epigenetic modifiers are uniquely important in controlling the signaling pathways regulating autophagy and apoptosis. Therefore, these epigenetic modifiers of both autophagic and apoptotic genes can act as novel therapeutic targets against cancers. Additionally, liquid-liquid phase separation (LLPS) also modulates the aggregation of misfolded proteins and provokes autophagy in the cytosolic environment. This review deals with the molecular mechanisms of both autophagy and apoptosis including crosstalk between them; emphasizing epigenetic regulation, involvement of LLPS therein, and possible therapeutic approaches against cancers.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Prahallad Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bypass Road, Bhauri, Bhopal, 462 030, MP, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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Zhu W, Xie Z, Chu Z, Ding Y, Shi G, Chen W, Wei X, Yuan Y, Wei F, Tian B. The Chromatin Remodeling Factor BrCHR39 Targets DNA Methylation to Positively Regulate Apical Dominance in Brassica rapa. PLANTS (BASEL, SWITZERLAND) 2023; 12:1384. [PMID: 36987072 PMCID: PMC10051476 DOI: 10.3390/plants12061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa.
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Affiliation(s)
- Wei Zhu
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhengqing Xie
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenni Chu
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yakun Ding
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gongyao Shi
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Weiwei Chen
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaochun Wei
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Yuxiang Yuan
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou 450002, China
| | - Fang Wei
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Baoming Tian
- Henan International Joint Laboratory of Crop Gene Resource and Improvements, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
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Hou X, Xu M, Zhu C, Gao J, Li M, Chen X, Sun C, Nashan B, Zang J, Zhou Y, Guang S, Feng X. Systematic characterization of chromodomain proteins reveals an H3K9me1/2 reader regulating aging in C. elegans. Nat Commun 2023; 14:1254. [PMID: 36878913 PMCID: PMC9988841 DOI: 10.1038/s41467-023-36898-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: 09/14/2022] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
The chromatin organization modifier domain (chromodomain) is an evolutionally conserved motif across eukaryotic species. The chromodomain mainly functions as a histone methyl-lysine reader to modulate gene expression, chromatin spatial conformation and genome stability. Mutations or aberrant expression of chromodomain proteins can result in cancer and other human diseases. Here, we systematically tag chromodomain proteins with green fluorescent protein (GFP) using CRISPR/Cas9 technology in C. elegans. By combining ChIP-seq analysis and imaging, we delineate a comprehensive expression and functional map of chromodomain proteins. We then conduct a candidate-based RNAi screening and identify factors that regulate the expression and subcellular localization of the chromodomain proteins. Specifically, we reveal an H3K9me1/2 reader, CEC-5, both by in vitro biochemistry and in vivo ChIP assays. MET-2, an H3K9me1/2 writer, is required for CEC-5 association with heterochromatin. Both MET-2 and CEC-5 are required for the normal lifespan of C. elegans. Furthermore, a forward genetic screening identifies a conserved Arginine124 of CEC-5's chromodomain, which is essential for CEC-5's association with chromatin and life span regulation. Thus, our work will serve as a reference to explore chromodomain functions and regulation in C. elegans and allow potential applications in aging-related human diseases.
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Affiliation(s)
- Xinhao Hou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Mingjing Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Jianing Gao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Meili Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Cheng Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Björn Nashan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Jianye Zang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China
| | - Ying Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 230027, Hefei, Anhui, P. R. China.
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, 230027, Hefei, Anhui, China.
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6
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Mechanistic insights into the multiple activities of the Rad5 family of enzymes. J Mol Biol 2022; 434:167581. [DOI: 10.1016/j.jmb.2022.167581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 11/18/2022]
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7
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Abstract
Autophagy is an intracellular catabolic degradative process in which damaged cellular organelles, unwanted proteins and different cytoplasmic components get recycled to maintain cellular homeostasis or metabolic balance. During autophagy, a double membrane vesicle is formed to engulf these cytosolic materials and fuse to lysosomes wherein the entire cargo degrades to be used again. Because of this unique recycling ability of cells, autophagy is a universal stress response mechanism. Dysregulation of autophagy leads to several diseases, including cancer, neurodegeneration and microbial infection. Thus, autophagy machineries have become targets for therapeutics. This chapter provides an overview of the paradoxical role of autophagy in tumorigenesis in the perspective of metabolism.
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Affiliation(s)
- Sweta Sikder
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, India.
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Antagonising Chromatin Remodelling Activities in the Regulation of Mammalian Ribosomal Transcription. Genes (Basel) 2021; 12:genes12070961. [PMID: 34202617 PMCID: PMC8303148 DOI: 10.3390/genes12070961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 12/29/2022] Open
Abstract
Ribosomal transcription constitutes the major energy consuming process in cells and is regulated in response to proliferation, differentiation and metabolic conditions by several signalling pathways. These act on the transcription machinery but also on chromatin factors and ncRNA. The many ribosomal gene repeats are organised in a number of different chromatin states; active, poised, pseudosilent and repressed gene repeats. Some of these chromatin states are unique to the 47rRNA gene repeat and do not occur at other locations in the genome, such as the active state organised with the HMG protein UBF whereas other chromatin state are nucleosomal, harbouring both active and inactive histone marks. The number of repeats in a certain state varies on developmental stage and cell type; embryonic cells have more rRNA gene repeats organised in an open chromatin state, which is replaced by heterochromatin during differentiation, establishing different states depending on cell type. The 47S rRNA gene transcription is regulated in different ways depending on stimulus and chromatin state of individual gene repeats. This review will discuss the present knowledge about factors involved, such as chromatin remodelling factors NuRD, NoRC, CSB, B-WICH, histone modifying enzymes and histone chaperones, in altering gene expression and switching chromatin states in proliferation, differentiation, metabolic changes and stress responses.
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Shi Y, Shen HM, Gopalakrishnan V, Gordon N. Epigenetic Regulation of Autophagy Beyond the Cytoplasm: A Review. Front Cell Dev Biol 2021; 9:675599. [PMID: 34195194 PMCID: PMC8237754 DOI: 10.3389/fcell.2021.675599] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a highly conserved catabolic process induced under various stress conditions to protect the cell from harm and allow survival in the face of nutrient- or energy-deficient states. Regulation of autophagy is complex, as cells need to adapt to a continuously changing microenvironment. It is well recognized that the AMPK and mTOR signaling pathways are the main regulators of autophagy. However, various other signaling pathways have also been described to regulate the autophagic process. A better understanding of these complex autophagy regulatory mechanisms will allow the discovery of new potential therapeutic targets. Here, we present a brief overview of autophagy and its regulatory pathways with emphasis on the epigenetic control mechanisms.
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Affiliation(s)
- Yin Shi
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, China
| | - Han-Ming Shen
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Vidya Gopalakrishnan
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nancy Gordon
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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10
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Rolicka A, Guo Y, Gañez Zapater A, Tariq K, Quin J, Vintermist A, Sadeghifar F, Arsenian-Henriksson M, Östlund Farrants AK. The chromatin-remodeling complexes B-WICH and NuRD regulate ribosomal transcription in response to glucose. FASEB J 2020; 34:10818-10834. [PMID: 32598531 DOI: 10.1096/fj.202000411r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022]
Abstract
Regulation of ribosomal transcription is under tight control from environmental stimuli, and this control involves changes in the chromatin structure. The underlying mechanism of how chromatin changes in response to nutrient and energy supply in the cell is still unclear. The chromatin-remodeling complex B-WICH is involved in activating the ribosomal transcription, and we show here that knock down of the B-WICH component WSTF results in cells that do not respond to glucose. The promoter is less accessible, and RNA pol I and its transcription factors SL1/TIF-1B and RRN3/TIF-1A, as well as the proto-oncogene c-MYC and the activating deacetylase SIRT7 do not bind upon glucose stimulation. In contrast, the repressive chromatin state that forms after glucose deprivation is reversible, and RNA pol I factors are recruited. WSTF knock down results in an accumulation of the ATPase CHD4, a component of the NuRD chromatin remodeling complex, which is responsible for establishing a repressive poised state at the promoter. The TTF-1, which binds and affect the binding of the chromatin complexes, is important to control the association of activating chromatin component UBF. We suggest that B-WICH is required to allow for a shift to an active chromatin state upon environmental stimulation, by counteracting the repressive state induced by the NuRD complex.
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Affiliation(s)
- Anna Rolicka
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Antoni Gañez Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Kanwal Tariq
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Jaclyn Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Anna Vintermist
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Fatemeh Sadeghifar
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum B7, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Lab F4, Stockholm University, Stockholm, Sweden
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11
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Wang J, Zhu S, Meng N, He Y, Lu R, Yan GR. ncRNA-Encoded Peptides or Proteins and Cancer. Mol Ther 2019; 27:1718-1725. [PMID: 31526596 DOI: 10.1016/j.ymthe.2019.09.001] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/26/2019] [Accepted: 09/01/2019] [Indexed: 12/31/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are unique RNA transcripts that have been widely identified in the eukaryotic genome and have been shown to play key roles in the development of many cancers. However, the rapid development of genome-wide translation profiling and ribosome profiling has revealed that a small number of small open reading frames (sORFs) within ncRNAs actually have peptide- or protein-coding potential. The peptides or proteins encoded by ncRNA (HOXB-AS3, encoded by long ncRNA [lncRNA]; FBXW7-185aa, PINT-87aa, and SHPRH-146aa, encoded by circular RNA [circRNA]; and miPEP-200a and miPEP-200b, encoded by primary miRNAs) have been shown to be critical players in cancer development and progression, through effects upon the regulation of glucose metabolism, the epithelial-to-mesenchymal transition, and the ubiquitination pathway. In this review, we summarize the reported peptides or proteins encoded by ncRNAs in cancer and explore the application of these peptides or proteins in the development of anti-tumor drugs and the identification of relevant therapeutic targets and tumor biomarkers.
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Affiliation(s)
- Jizhong Wang
- Biomedicine Research Center, State Key Laboratory of Respiratory Disease, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Song Zhu
- Biomedicine Research Center, State Key Laboratory of Respiratory Disease, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Nan Meng
- Biomedicine Research Center, State Key Laboratory of Respiratory Disease, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yutian He
- Biomedicine Research Center, State Key Laboratory of Respiratory Disease, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Ruixun Lu
- Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou 511436, China
| | - Guang-Rong Yan
- Biomedicine Research Center, State Key Laboratory of Respiratory Disease, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou 511436, China.
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12
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Brühl J, Trautwein J, Schäfer A, Linne U, Bouazoune K. The DNA repair protein SHPRH is a nucleosome-stimulated ATPase and a nucleosome-E3 ubiquitin ligase. Epigenetics Chromatin 2019; 12:52. [PMID: 31434570 PMCID: PMC6702750 DOI: 10.1186/s13072-019-0294-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2019] [Indexed: 12/22/2022] Open
Abstract
Background Maintenance of genome integrity during DNA replication is crucial to the perpetuation of all organisms. In eukaryotes, the bypass of DNA lesions by the replication machinery prevents prolonged stalling of the replication fork, which could otherwise lead to greater damages such as gross chromosomal rearrangements. Bypassing DNA lesions and subsequent repair are accomplished by the activation of DNA damage tolerance pathways such as the template switching (TS) pathway. In yeast, the RAD5 (Radiation-sensitive 5) protein plays a crucial role in initiating the TS pathway by catalyzing the polyubiquitination of PCNA (Proliferation Cell Nuclear Antigen). Likewise, one of the mammalian RAD5-homologs, SHPRH (SNF2, histone linker, PHD, RING, helicase) mediates PCNA polyubiquitination. To date, the study of SHPRH enzymatic functions has been limited to this modification. It is therefore unclear how SHPRH carries out its function in DNA repair. Moreover, how this protein regulates gene transcription at the enzymatic level is also unknown. Results Given that SHPRH harbors domains found in chromatin remodeling proteins, we investigated its biochemical properties in the presence of nucleosomal substrates. We find that SHPRH binds equally well to double-stranded (ds) DNA and to nucleosome core particles, however, like ISWI and CHD-family remodelers, SHPRH shows a strong preference for nucleosomes presenting extranucleosomal DNA. Moreover, nucleosomes but not dsDNA strongly stimulate the ATPase activity of SHPRH. Intriguingly, unlike typically observed with SNF2-family enzymes, ATPase activity does not translate into conventional nucleosome remodeling, under standard assay conditions. To test whether SHPRH can act as a ubiquitin E3 ligase for nucleosomes, we performed a screen using 26 E2-conjugating enzymes. We uncover that SHPRH is a potent nucleosome E3-ubiquitin-ligase that can function with at least 7 different E2s. Mass spectrometry analyses of products generated in the presence of the UBE2D1-conjugating enzyme reveal that SHPRH can catalyze the formation of polyubiquitin linkages that are either branched or associated with the recruitment of DNA repair factors, as well as linkages involved in proteasomal degradation. Conclusions We propose that, in addition to polyubiquitinating PCNA, SHPRH promotes DNA repair or transcriptional regulation in part through chromatin ubiquitination. Our study sets a biochemical framework for studying other RAD5- and RAD16-related protein functions through the ubiquitination of nucleosomes. Electronic supplementary material The online version of this article (10.1186/s13072-019-0294-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joanna Brühl
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Jonathan Trautwein
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Agnes Schäfer
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Uwe Linne
- Fachbereich Chemie und Synmikro, Gerätezentrum Massenspektrometrie und Elementanalaytik, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany
| | - Karim Bouazoune
- Institut für Molekularbiologie und Tumorforschung (IMT), Biomedizinisches Forschungszentrum, Philipps-Universität Marburg, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany.
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13
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Kang HJ, Park H, Yoo EJ, Lee JH, Choi SY, Lee-Kwon W, Lee KY, Hur JH, Seo JK, Ra JS, Lee EA, Myung K, Kwon HM. TonEBP Regulates PCNA Polyubiquitination in Response to DNA Damage through Interaction with SHPRH and USP1. iScience 2019; 19:177-190. [PMID: 31376680 PMCID: PMC6677787 DOI: 10.1016/j.isci.2019.07.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/13/2019] [Accepted: 07/15/2019] [Indexed: 12/16/2022] Open
Abstract
Polyubiquitination of proliferating cell nuclear antigen (PCNA) regulates the error-free template-switching mechanism for the bypass of DNA lesions during DNA replication. PCNA polyubiquitination is critical for the maintenance of genomic integrity; however, the underlying mechanism is poorly understood. Here, we demonstrate that tonicity-responsive enhancer-binding protein (TonEBP) regulates PCNA polyubiquitination in response to DNA damage. TonEBP was recruited to DNA damage sites with bulky adducts and sequentially recruited E3 ubiquitin ligase SHPRH, followed by deubiquitinase USP1, to DNA damage sites, in correlation with the dynamics of PCNA polyubiquitination. Similarly, TonEBP was found to be required for replication fork protection in response to DNA damage. The Rel-homology domain of TonEBP, which encircles DNA, was essential for the interaction with SHPRH and USP1, PCNA polyubiquitination, and cell survival after DNA damage. The present findings suggest that TonEBP is an upstream regulator of PCNA polyubiquitination and of the DNA damage bypass pathway.
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Affiliation(s)
- Hyun Je Kang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyun Park
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Eun Jin Yoo
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jun Ho Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Soo Youn Choi
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Whaseon Lee-Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jin-Hoe Hur
- UNIST-Optical Biomed Imaging Center (UOBC), Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jeong Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eun-A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea.
| | - Hyug Moo Kwon
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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14
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Li F, Huang Q, Gong Z, Wang H, Chen J. Diagnostic and prognostic roles of circ-SHPRH for solid cancers: a meta-analysis. Onco Targets Ther 2019; 12:4351-4357. [PMID: 31213850 PMCID: PMC6549407 DOI: 10.2147/ott.s200755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/04/2019] [Indexed: 01/11/2023] Open
Abstract
Background: Circ-SHPRH is a novel circular RNA which was down-regulated in various cancer tissues. Several recent studies hinted that circ-SHPRH might function as a diagnostic and prognostic biomarker for solid cancers. This meta-analysis was performed to determine the diagnostic and prognostic roles of circ-SHPRH for these solid cancers. Methods: Publications were searched in PubMed, MEDLINE, Web of Science, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang database. Pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the summary receiver operating characteristic curve (SROC) (AUC) with 95% confidence interval (95% CI) were calculated to evaluate the diagnostic value of circ-SHPRH. Pooled hazard ratio (HR) with 95% CI was applied to assess the prognostic value of circ-SHPRH. Results: Nine eligible studies, including 4 for diagnosis and 5 for prognosis, were included in this meta-analysis. Pooled sensitivity, specificity, PLR, NLR, DOR, and AUC were 0.79 (95% CI: 0.73–0.84), 0.75 (95% CI: 0.69–0.81), 3.20 (95% CI: 2.53–4.06), 0.28 (95% CI: 0.22–0.36), 11.27 (95% CI: 7.57–16.79), and 0.84 (95% CI: 0.80–0.87), respectively. Pooled HR indicated that low circ-SHPRH expression was significantly associated with poor overall survival (OS) (low vs high, HR=2.22, 95% CI: 1.60–3.09). Conclusion: The results of this meta-analysis indicate that circ-SHPRH might be an important diagnostic and prognostic biomarker for various solid cancers.
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Affiliation(s)
- Feng Li
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Qilin Huang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Zhenyu Gong
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Hongxiang Wang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Juxiang Chen
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, People's Republic of China
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15
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Tonzi P, Huang TT. Role of Y-family translesion DNA polymerases in replication stress: Implications for new cancer therapeutic targets. DNA Repair (Amst) 2019; 78:20-26. [PMID: 30954011 DOI: 10.1016/j.dnarep.2019.03.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/18/2022]
Abstract
DNA replication stress, defined as the slowing or stalling of replication forks, is considered an emerging hallmark of cancer and a major contributor to genomic instability associated with tumorigenesis (Macheret and Halazonetis, 2015). Recent advances have been made in attempting to target DNA repair factors involved in alleviating replication stress to potentiate genotoxic treatments. Various inhibitors of ATR and Chk1, the two major kinases involved in the intra-S-phase checkpoint, are currently in Phase I and II clinical trials [2]. In addition, currently approved inhibitors of Poly-ADP Ribose Polymerase (PARP) show synthetic lethality in cells that lack double-strand break repair such as in BRCA1/2 deficient tumors [3]. These drugs have also been shown to exacerbate replication stress by creating a DNA-protein crosslink, termed PARP 'trapping', and this is now thought to contribute to the therapeutic efficacy. Translesion synthesis (TLS) is a mechanism whereby special repair DNA polymerases accommodate and tolerate various DNA lesions to allow for damage bypass and continuation of DNA replication (Yang and Gao, 2018). This class of proteins is best characterized by the Y-family, encompassing DNA polymerases (Pols) Kappa, Eta, Iota, and Rev1. While best studied for their ability to bypass physical lesions on the DNA, there is accumulating evidence for these proteins in coping with various natural replication fork barriers and alleviating replication stress. In this mini-review, we will highlight some of these recent advances, and discuss why targeting the TLS pathway may be a mechanism of enhancing cancer-associated replication stress. Exacerbation of replication stress can lead to increased genome instability, which can be toxic to cancer cells and represent a therapeutic vulnerability.
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Affiliation(s)
- Peter Tonzi
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tony T Huang
- Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.
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16
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Valvezan AJ, Manning BD. Molecular logic of mTORC1 signalling as a metabolic rheostat. Nat Metab 2019; 1:321-333. [PMID: 32694720 DOI: 10.1038/s42255-019-0038-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/24/2019] [Indexed: 02/05/2023]
Abstract
The protein kinase complex mechanistic target of rapamycin complex 1 (mTORC1) serves as a key conduit between growth signals and the metabolic processes underlying cell growth. The activation state of mTORC1 is controlled by intracellular nutrients and energy, as well as exogenous hormones and growth factors, thereby integrating local and systemic growth signals. Here we discuss the molecular logic of the mTORC1 signalling network and its importance in coupling growth signals to the control of cellular metabolism. After activation, mTORC1 promotes the conversion of available nutrients and energy into the major macromolecular species contributing to cellular mass, including proteins, nucleic acids and lipids, while suppressing the autophagic recycling of these macromolecules back into their nutrient constituents. Given that uncoupling of mTORC1 from its normal regulatory inputs contributes to many diseases-including cancer, genetic tumour syndromes, metabolic diseases, autoimmune diseases and neurological disorders-understanding the molecular logic of the mTORC1 network and how to modulate it may present therapeutic opportunities for treatment of a broad range of diseases and potentially even for the extension of lifespan.
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Affiliation(s)
- Alexander J Valvezan
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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17
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Abstract
Fanconi anemia (FA) is a disease of DNA repair characterized by bone marrow failure and a reduced ability to remove DNA interstrand cross-links. Here, we provide evidence that the FA protein FANCI also functions in ribosome biogenesis, the process of making ribosomes that initiates in the nucleolus. We show that FANCI localizes to the nucleolus and is functionally and physically tied to the transcription of pre-ribosomal RNA (pre-rRNA) and to large ribosomal subunit (LSU) pre-rRNA processing independent of FANCD2. While FANCI is known to be monoubiquitinated when activated for DNA repair, we find that it is predominantly in the deubiquitinated state in the nucleolus, requiring the nucleoplasmic deubiquitinase (DUB) USP1 and the nucleolar DUB USP36. Our model suggests a possible dual pathophysiology for FA that includes defects in DNA repair and in ribosome biogenesis.
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18
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Figueiredo VC, McCarthy JJ. Regulation of Ribosome Biogenesis in Skeletal Muscle Hypertrophy. Physiology (Bethesda) 2019; 34:30-42. [PMID: 30540235 PMCID: PMC6383632 DOI: 10.1152/physiol.00034.2018] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/11/2018] [Accepted: 09/13/2018] [Indexed: 01/22/2023] Open
Abstract
The ribosome is the enzymatic macromolecular machine responsible for protein synthesis. The rates of protein synthesis are primarily dependent on translational efficiency and capacity. Ribosome biogenesis has emerged as an important regulator of skeletal muscle growth and maintenance by altering the translational capacity of the cell. Here, we provide evidence to support a central role for ribosome biogenesis in skeletal muscle growth during postnatal development and in response to resistance exercise training. Furthermore, we discuss the cellular signaling pathways regulating ribosome biogenesis, discuss how myonuclear accretion affects translational capacity, and explore future areas of investigation within the field.
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Affiliation(s)
- Vandré Casagrande Figueiredo
- The Center for Muscle Biology, College of Health Sciences, University of Kentucky , Lexington, Kentucky
- Department of Rehabilitation Sciences, College of Medicine, University of Kentucky , Lexington, Kentucky
| | - John J McCarthy
- The Center for Muscle Biology, College of Health Sciences, University of Kentucky , Lexington, Kentucky
- Department of Physiology, University of Kentucky , Lexington, Kentucky
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19
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Laribee RN. Transcriptional and Epigenetic Regulation by the Mechanistic Target of Rapamycin Complex 1 Pathway. J Mol Biol 2018; 430:4874-4890. [PMID: 30359581 DOI: 10.1016/j.jmb.2018.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 11/28/2022]
Abstract
Nutrient availability impacts health such that nutrient excess states can dysregulate epigenetic and transcriptional pathways to cause many diseases. Increasing evidence implicates aberrant regulation of nutrient signaling cascades as one means of communicating nutrient information to the epigenetic and transcriptional regulatory machinery. One such signaling cascade, the mechanistic target of rapamycin complex 1 (mTORC1), is conserved from yeast to man, and it is deregulated in diverse disease states. The catalytic subunit of the mTORC1 kinase complex (Tor1 or Tor2 in budding yeast and mTor in mammals) phosphorylates several downstream effectors regulating transcriptional and translational responses controlling growth and proliferation. Delineating mechanisms of cytoplasmic nutrient mTORC1 activation continues to be a major research focus. However, Tor kinases not only localize to the cytoplasm but also are found in the nucleus where they selectively bind and regulate genes controlling cellular metabolism and anabolism. The nuclear mTORC1 functions are now beginning to be defined, and they suggest that mTORC1 has a critical role in regulating the complex transcriptional activities required for ribosomal biogenesis. The mTORC1 pathway also interacts with epigenetic regulators required for modifying chromatin structure and function to control gene expression. Because altered nutrient states exert both individual and transgenerational phenotypic changes, mTORC1 signaling to chromatin effectors may have a significant role in mediating the effects of diet and nutrients on the epigenome. This article will discuss the recent inroads into the function of nuclear mTORC1 and its role in epigenetic and transcriptional regulation.
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Affiliation(s)
- R Nicholas Laribee
- Department of Pathology and Laboratory Medicine, and Center for Cancer Research, University of Tennessee Health Science Center, 19 South Manassas, Cancer Research Building Rm 318, Memphis, TN 38163, USA.
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20
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Abstract
The nucleolus as site of ribosome biogenesis holds a pivotal role in cell metabolism. It is composed of ribosomal DNA (rDNA), which is present as tandem arrays located in nucleolus organizer regions (NORs). In interphase cells, rDNA can be found inside and adjacent to nucleoli and the location is indicative for transcriptional activity of ribosomal genes-inactive rDNA (outside) versus active one (inside). Moreover, the nucleolus itself acts as a spatial organizer of non-nucleolar chromatin. Microscopy-based approaches offer the possibility to explore the spatially distinct localization of the different DNA populations in relation to the nucleolar structure. Recent technical developments in microscopy and preparatory methods may further our understanding of the functional architecture of nucleoli. This review will attempt to summarize the current understanding of mammalian nucleolar chromatin organization as seen from a microscopist's perspective.
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Affiliation(s)
- Christian Schöfer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria.
| | - Klara Weipoltshammer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstr. 17, 1090, Vienna, Austria
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21
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Lee Y, Lee SJV, Min KJ. Meeting report: Asian Society for Aging Research Symposium 2018. TRANSLATIONAL MEDICINE OF AGING 2018. [DOI: 10.1016/j.tma.2018.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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22
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Lee D, Park JH, Kim S, Lee SG, Myung K. SHPRH as a new player in ribosomal RNA transcription and its potential role in homeostasis of ribosomal DNA repeats. Transcription 2017; 9:190-195. [PMID: 29139335 DOI: 10.1080/21541264.2017.1381795] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
There are hundreds of copies of rDNA repeats in mammalian chromosomes and the ratio of active, poised, or inactive rDNA is regulated in epigenetic manners. Recent studies demonstrated that a post-DNA replication repair enzyme, SHPRH affects rRNA transcription by recognizing epigenetic markers on rDNA promoters and unveiled potential links between DNA repair and ribosome biogenesis. This study suggests that SHPRH could be a link between mTOR-mediated epigenetic regulations and rRNA transcription, while concomitantly affecting genomic integrity.
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Affiliation(s)
- Deokjae Lee
- a Medytox Inc. 114 , Yeongtong-gu , Suwon-si , Gyeonggi-do , Korea
| | - Jun Hong Park
- b Center for Genomic Integrity , Institute for Basic Science , Ulsan , Korea
| | - Shinseog Kim
- b Center for Genomic Integrity , Institute for Basic Science , Ulsan , Korea
| | - Seon-Gyeong Lee
- b Center for Genomic Integrity , Institute for Basic Science , Ulsan , Korea.,c Department of Biological Sciences , School of Life Sciences , Ulsan National Institute of Science and Technology , Ulsan , Korea
| | - Kyungjae Myung
- b Center for Genomic Integrity , Institute for Basic Science , Ulsan , Korea.,c Department of Biological Sciences , School of Life Sciences , Ulsan National Institute of Science and Technology , Ulsan , Korea
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Kanao R, Masutani C. Regulation of DNA damage tolerance in mammalian cells by post-translational modifications of PCNA. Mutat Res 2017; 803-805:82-88. [PMID: 28666590 DOI: 10.1016/j.mrfmmm.2017.06.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 05/25/2017] [Accepted: 06/19/2017] [Indexed: 11/29/2022]
Abstract
DNA damage tolerance pathways, which include translesion DNA synthesis (TLS) and template switching, are crucial for prevention of DNA replication arrest and maintenance of genomic stability. However, these pathways utilize error-prone DNA polymerases or template exchange between sister DNA strands, and consequently have the potential to induce mutations or chromosomal rearrangements. Post-translational modifications of proliferating cell nuclear antigen (PCNA) play important roles in controlling these pathways. For example, TLS is mediated by mono-ubiquitination of PCNA at lysine 164, for which RAD6-RAD18 is the primary E2-E3 complex. Elaborate protein-protein interactions between mono-ubiquitinated PCNA and Y-family DNA polymerases constitute the core of the TLS regulatory system, and enhancers of PCNA mono-ubiquitination and de-ubiquitinating enzymes finely regulate TLS and suppress TLS-mediated mutagenesis. The template switching pathway is promoted by K63-linked poly-ubiquitination of PCNA at lysine 164. Poly-ubiquitination is achieved by a coupled reaction mediated by two sets of E2-E3 complexes, RAD6-RAD18 and MMS2-UBC13-HTLF/SHPRH. In addition to these mono- and poly-ubiquitinations, simultaneous mono-ubiquitinations on multiple units of the PCNA homotrimeric ring promote an unidentified damage tolerance mechanism that remains to be fully characterized. Furthermore, SUMOylation of PCNA in mammalian cells can negatively regulate recombination. Other modifications, including ISGylation, acetylation, methylation, or phosphorylation, may also play roles in DNA damage tolerance and control of genomic stability.
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Affiliation(s)
- Rie Kanao
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.
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