1
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Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024; 67:292-306. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [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: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
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Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
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2
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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3
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Liu W, He QY, Brunet MA. Editorial: Emerging Proteins and Polypeptides Expressed by "Non-Coding RNAs". Front Cell Dev Biol 2022; 10:862870. [PMID: 35265627 PMCID: PMC8899286 DOI: 10.3389/fcell.2022.862870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Wanting Liu
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Marie A Brunet
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, QC, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
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4
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Nwokwu CD, Xiao AY, Harrison L, Nestorova GG. Identification of microRNA-mRNA regulatory network associated with oxidative DNA damage in human astrocytes. ASN Neuro 2022; 14:17590914221101704. [PMID: 35570825 PMCID: PMC9118907 DOI: 10.1177/17590914221101704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/23/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
The high lipid content of the brain, coupled with its heavy oxygen dependence and relatively weak antioxidant system, makes it highly susceptible to oxidative DNA damage that contributes to neurodegeneration. This study is aimed at identifying specific ROS-responsive miRNAs that modulate the expression and activity of the DNA repair proteins in human astrocytes, which could serve as potential biomarkers and lead to the development of targeted therapeutic strategies for neurological diseases. Oxidative DNA damage was established after treatment of human astrocytes with 10μM sodium dichromate for 16 h. Comet assay analysis indicated a significant increase in oxidized guanine lesions. RT-qPCR and ELISA assays confirmed that sodium dichromate reduced the mRNA and protein expression levels of the human base-excision repair enzyme, 8-deoxyguanosine DNA glycosylase 1 (hOGG1). Small RNAseq data were generated on an Ion Torrent™ system and the differentially expressed miRNAs were identified using Partek Flow® software. The biologically significant miRNAs were selected using miRNet 2.0. Oxidative-stress-induced DNA damage was associated with a significant decrease in miRNA expression: 231 downregulated miRNAs and 2 upregulated miRNAs (p < 0.05; >2-fold). In addition to identifying multiple miRNA-mRNA pairs involved in DNA repair processes, this study uncovered a novel miRNA-mRNA pair interaction: miR-1248:OGG1. Inhibition of miR-1248 via the transfection of its inhibitor restored the expression levels of hOGG1. Therefore, targeting the identified microRNA candidates could ameliorate the nuclear DNA damage caused by the brain's exposure to mutagens, reduce the incidence and improve the treatment of cancer and neurodegenerative disorders.
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Affiliation(s)
| | - Adam Y. Xiao
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Lynn Harrison
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
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5
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Dorraki N, Ghale-Noie ZN, Ahmadi NS, Keyvani V, Bahadori RA, Nejad AS, Aschner M, Pourghadamyari H, Mollazadeh S, Mirzaei H. miRNA-148b and its role in various cancers. Epigenomics 2021; 13:1939-1960. [PMID: 34852637 DOI: 10.2217/epi-2021-0155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
miRNA-148b belongs to the family miR-148/-152, with significant differences in nonseed sequences, which can target diverse mRNA molecules. Reportedly, it may undergo deregulation in lung and ovarian cancers and downregulation in gastric, pancreatic and colon cancers. However, there is a need for further studies to better characterize its mechanism of action and in different types of cancer. In this review, we focus on the aberrant expression of miR-148b in different cancer types and highlight its main target genes and signaling pathways, as well as its pathophysiologic role and relevance to tumorigenesis in several types of cancer.
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Affiliation(s)
- Najmeh Dorraki
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nooshin Sadegh Ahmadi
- Department of Genetics, Faculty of Medicine, Tehran Medical Sciences Islamic Azad University, Tehran, Iran
| | - Vahideh Keyvani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Arash Salmani Nejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hossein Pourghadamyari
- Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Samaneh Mollazadeh
- Natural Products & Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry & Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.,Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
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6
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Dong X, Jin C, Chen D, Chen Y, Ye ZQ, Zhang X, Huang X, Zhang W, Gu DN. Genomic Instability-Related LncRNA Signature Predicts the Prognosis and Highlights LINC01614 Is a Tumor Microenvironment-Related Oncogenic lncRNA of Papillary Thyroid Carcinoma. Front Oncol 2021; 11:737867. [PMID: 34604079 PMCID: PMC8481916 DOI: 10.3389/fonc.2021.737867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/30/2021] [Indexed: 12/20/2022] Open
Abstract
Background Genomic instability (GI) is among the top ten characteristics of malignancy. Long non-coding RNAs (lncRNAs) are promising cancer biomarkers that are reportedly involved in GI. So far, the clinical value of GI-related lncRNAs (GIlncs) in papillary thyroid cancer (PTC) has not been clarified. Methods Integrative analysis of lncRNA expression and somatic mutation profiles was performed to identify GIlncs. Analysis of differentially expressed lncRNAs in the group with high- and low- cumulative number of somatic mutations revealed significant GIlncs in PTC. Univariate and multivariate Cox proportional hazard regression analyses were performed to identify hub-GIlncs. Results A computational model based on four lncRNAs (FOXD2-AS1, LINC01614, AC073257.2, and AC005082.1) was identified as a quantitative index using an in-silicon discovery cohort. GILS score was significantly associated with poor prognosis, as validated in the TCGA dataset and further tested in our local RNA-Seq cohort. Moreover, a combination of clinical characteristics and the composite GILS-clinical prognostic nomogram demonstrates satisfactory discrimination and calibration. Furthermore, the GILS score and FOXD2-AS1, LINC01614, AC073257.2, and AC005082.1 were also associated with driver mutations and multiple clinical-pathological variables, respectively. Moreover, RNA-Seq confirmed the expression patterns of FOXD2-AS1, LINC01614, AC073257.2, and AC005082.1 in PTC and normal thyroid tissues. Biological experiments demonstrated that downregulated or overexpressed LINC01614 affect PTC cell proliferation, migration, and invasion in vitro. Activation of the stromal and immune cell infiltration was also observed in the high LINC01614 group in the PTC microenvironment. Conclusion In summary, we identified a signature for clinical outcome prediction in PTC comprising four lncRNAs associated with GI. A better understanding of the GI providing an alternative evaluation of the progression risk of PTC. Our study also demonstrated LINC01614 as a novel oncogenic lncRNA and verified its phenotype in PTC.
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Affiliation(s)
- Xubin Dong
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cong Jin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Danxiang Chen
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yizuo Chen
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhi-Qiang Ye
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaohua Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoli Huang
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dian-Na Gu
- Department of Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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7
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Shaw A, Gullerova M. Home and Away: The Role of Non-Coding RNA in Intracellular and Intercellular DNA Damage Response. Genes (Basel) 2021; 12:1475. [PMID: 34680868 PMCID: PMC8535248 DOI: 10.3390/genes12101475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022] Open
Abstract
Non-coding RNA (ncRNA) has recently emerged as a vital component of the DNA damage response (DDR), which was previously believed to be solely regulated by proteins. Many species of ncRNA can directly or indirectly influence DDR and enhance DNA repair, particularly in response to double-strand DNA breaks, which may hold therapeutic potential in the context of cancer. These include long non-coding RNA (lncRNA), microRNA, damage-induced lncRNA, DNA damage response small RNA, and DNA:RNA hybrid structures, which can be categorised as cis or trans based on the location of their synthesis relative to DNA damage sites. Mechanisms of RNA-dependent DDR include the recruitment or scaffolding of repair factors at DNA break sites, the regulation of repair factor expression, and the stabilisation of repair intermediates. DDR can also be communicated intercellularly via exosomes, leading to bystander responses in healthy neighbour cells to generate a population-wide response to damage. Many microRNA species have been directly implicated in the propagation of bystander DNA damage, autophagy, and radioresistance, which may prove significant for enhancing cancer treatment via radiotherapy. Here, we review recent developments centred around ncRNA and their contributions to intracellular and intercellular DDR mechanisms.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK;
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8
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Maliszewska-Olejniczak K, Kaniowski D, Araszkiewicz M, Tymińska K, Korgul A. Molecular Mechanisms of Specific Cellular DNA Damage Response and Repair Induced by the Mixed Radiation Field During Boron Neutron Capture Therapy. Front Oncol 2021; 11:676575. [PMID: 34094980 PMCID: PMC8170402 DOI: 10.3389/fonc.2021.676575] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/28/2021] [Indexed: 01/04/2023] Open
Abstract
The impact of a mixed neutron-gamma beam on the activation of DNA damage response (DDR) proteins and non-coding RNAs (ncRNAs) is poorly understood. Ionizing radiation is characterized by its biological effectiveness and is related to linear energy transfer (LET). Neutron-gamma mixed beam used in boron neutron capture therapy (BNCT) can induce another type of DNA damage such as clustered DNA or multiple damaged sites, as indicated for high LET particles, such as alpha particles, carbon ions, and protons. We speculate that after exposure to a mixed radiation field, the repair capacity might reduce, leading to unrepaired complex DNA damage for a long period and may promote genome instability and cell death. This review will focus on the poorly studied impact of neutron-gamma mixed beams with an emphasis on DNA damage and molecular mechanisms of repair. In case of BNCT, it is not clear which repair pathway is involved, and recent experimental work will be presented. Further understanding of BNCT-induced DDR mechanisms may lead to improved therapeutic efficiency against different tumors.
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Affiliation(s)
| | - Damian Kaniowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Martyna Araszkiewicz
- Faculty of Physics, University of Warsaw, Warsaw, Poland.,Nuclear Facilities Operations Department, National Centre for Nuclear Research, Otwock, Poland
| | - Katarzyna Tymińska
- Nuclear Facilities Operations Department, National Centre for Nuclear Research, Otwock, Poland
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9
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Klaric JA, Wüst S, Panier S. New Faces of old Friends: Emerging new Roles of RNA-Binding Proteins in the DNA Double-Strand Break Response. Front Mol Biosci 2021; 8:668821. [PMID: 34026839 PMCID: PMC8138124 DOI: 10.3389/fmolb.2021.668821] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. To protect genomic stability and ensure cell homeostasis, cells mount a complex signaling-based response that not only coordinates the repair of the broken DNA strand but also activates cell cycle checkpoints and, if necessary, induces cell death. The last decade has seen a flurry of studies that have identified RNA-binding proteins (RBPs) as novel regulators of the DSB response. While many of these RBPs have well-characterized roles in gene expression, it is becoming increasingly clear that they also have non-canonical functions in the DSB response that go well beyond transcription, splicing and mRNA processing. Here, we review the current understanding of how RBPs are integrated into the cellular response to DSBs and describe how these proteins directly participate in signal transduction, amplification and repair at damaged chromatin. In addition, we discuss the implications of an RBP-mediated DSB response for genome instability and age-associated diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Julie A Klaric
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stas Wüst
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stephanie Panier
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Cologne, Germany
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10
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Nakaoka A, Nakahana M, Inubushi S, Akasaka H, Salah M, Fujita Y, Kubota H, Hassan M, Nishikawa R, Mukumoto N, Ishihara T, Miyawaki D, Sasayama T, Sasaki R. Exosome-mediated radiosensitizing effect on neighboring cancer cells via increase in intracellular levels of reactive oxygen species. Oncol Rep 2021; 45:13. [PMID: 33649776 PMCID: PMC7877005 DOI: 10.3892/or.2021.7964] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
The precise mechanism of intercellular communication between cancer cells following radiation exposure is unclear. Exosomes are membrane‑enclosed small vesicles comprising lipid bilayers and are mediators of intercellular communication that transport a variety of intracellular components, including microRNAs (miRNAs or miRs). The present study aimed to identify novel roles of exosomes released from irradiated cells to neighboring cancer cells. In order to confirm the presence of exosomes in the human pancreatic cancer cell line MIAPaCa‑2, ultracentrifugation was performed followed by transmission electron microscopy and nanoparticle tracking analysis (NanoSight) using the exosome‑specific surface markers CD9 and CD63. Subsequent endocytosis of exosomes was confirmed by fluorescent microscopy. Cell survival following irradiation and the addition of exosomes was evaluated by colony forming assay. Expression levels of miRNAs in exosomes were then quantified by microarray analysis, while protein expression levels of Cu/Zn‑ and Mn‑superoxide dismutase (SOD1 and 2, respectively) enzymes in MIAPaCa‑2 cells were evaluated by western blotting. Results showed that the uptake of irradiated exosomes was significantly higher than that of non‑irradiated exosomes. Notably, irradiated exosomes induced higher intracellular levels of reactive oxygen species (ROS) and a higher frequency of DNA damage in MIAPaCa‑2 cells, as determined by fluorescent microscopy and immunocytochemistry, respectively. Moreover, six up‑ and five downregulated miRNAs were identified in 5 and 8 Gy‑irradiated cells using miRNA microarray analyses. Further analysis using miRNA mimics and reverse transcription‑quantitative PCR identified miR‑6823‑5p as a potential candidate to inhibit SOD1, leading to increased intracellular ROS levels and DNA damage. To the best of our knowledge, the present study is the first to demonstrate that irradiated exosomes enhance the radiation effect via increasing intracellular ROS levels in cancer cells. This contributes to improved understanding of the bystander effect of neighboring cancer cells.
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Affiliation(s)
- Ai Nakaoka
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Makiko Nakahana
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Sachiko Inubushi
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Hiroaki Akasaka
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Mohammed Salah
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
- Department of Biochemistry, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Yoshiko Fujita
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Hikaru Kubota
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Mennaallah Hassan
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
- Department of Clinical Oncology, Faculty of Medicine, Sohag University, Sohag 82524, Egypt
| | - Ryo Nishikawa
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Naritoshi Mukumoto
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Takeaki Ishihara
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Daisuke Miyawaki
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Takashi Sasayama
- Department of Neurosurgery, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Ryohei Sasaki
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
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11
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BRCA1 and RNAi factors promote repair mediated by small RNAs and PALB2-RAD52. Nature 2021; 591:665-670. [PMID: 33536619 PMCID: PMC8245199 DOI: 10.1038/s41586-020-03150-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Strong connections exist between R-loops (three-stranded structures harbouring an RNA:DNA hybrid and a displaced single-strand DNA), genome instability and human disease1-5. Indeed, R-loops are favoured in relevant genomic regions as regulators of certain physiological processes through which homeostasis is typically maintained. For example, transcription termination pause sites regulated by R-loops can induce the synthesis of antisense transcripts that enable the formation of local, RNA interference (RNAi)-driven heterochromation6. Pause sites are also protected against endogenous single-stranded DNA breaks by BRCA17. Hypotheses about how DNA repair is enacted at pause sites include a role for RNA, which is emerging as a normal, albeit unexplained, regulator of genome integrity8. Here we report that a species of single-stranded, DNA-damage-associated small RNA (sdRNA) is generated by a BRCA1-RNAi protein complex. sdRNAs promote DNA repair driven by the PALB2-RAD52 complex at transcriptional termination pause sites that form R-loops and are rich in single-stranded DNA breaks. sdRNA repair operates in both quiescent (G0) and proliferating cells. Thus, sdRNA repair can occur in intact tissue and/or stem cells, and may contribute to tumour suppression mediated by BRCA1.
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12
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Hydrogen peroxide and Helicobacter pylori extract treatment combined with APE1 knockdown induce DNA damage, G2/M arrest and cell death in gastric cancer cell line. DNA Repair (Amst) 2020; 96:102976. [DOI: 10.1016/j.dnarep.2020.102976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/28/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
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13
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Ketley RF, Gullerova M. Jack of all trades? The versatility of RNA in DNA double-strand break repair. Essays Biochem 2020; 64:721-735. [PMID: 32618336 PMCID: PMC7592198 DOI: 10.1042/ebc20200008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022]
Abstract
The mechanisms by which RNA acts in the DNA damage response (DDR), specifically in the repair of DNA double-strand breaks (DSBs), are emerging as multifaceted and complex. Different RNA species, including but not limited to; microRNA (miRNA), long non-coding RNA (lncRNA), RNA:DNA hybrid structures, the recently identified damage-induced lncRNA (dilncRNA), damage-responsive transcripts (DARTs), and DNA damage-dependent small RNAs (DDRNAs), have been shown to play integral roles in the DSB response. The diverse properties of these RNAs, such as sequence, structure, and binding partners, enable them to fulfil a variety of functions in different cellular contexts. Additionally, RNA can be modified post-transcriptionally, a process which is regulated in response to cellular stressors such as DNA damage. Many of these mechanisms are not yet understood and the literature contradictory, reflecting the complexity and expansive nature of the roles of RNA in the DDR. However, it is clear that RNA is pivotal in ensuring the maintenance of genome integrity. In this review, we will discuss and summarise recent evidence which highlights the roles of these various RNAs in preserving genomic integrity, with a particular focus on the emerging role of RNA in the DSB repair response.
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Affiliation(s)
- Ruth F Ketley
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom
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14
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Shadrina O, Garanina I, Korolev S, Zatsepin T, Van Assche J, Daouad F, Wallet C, Rohr O, Gottikh M. Analysis of RNA binding properties of human Ku protein reveals its interactions with 7SK snRNA and protein components of 7SK snRNP complex. Biochimie 2020; 171-172:110-123. [PMID: 32105815 DOI: 10.1016/j.biochi.2020.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/21/2020] [Indexed: 12/21/2022]
Abstract
Human Ku heterodimeric protein composed of Ku70 and Ku80 subunits plays an important role in the non-homologous end-joining DNA repair pathway as a sensor of double strand DNA breaks. Ku is also involved in numerous cellular processes, and in some of them it acts in an RNA-dependent manner. However, RNA binding properties of the human Ku have not been well studied. Here we have analyzed interactions of a recombinant Ku heterodimer with a set of RNAs of various structure as well as eCLIP (enhanced crosslinking and immunoprecipitation) data for human Ku70. As a result, we have proposed a consensus RNA structure preferable for the Ku binding that is a hairpin possessing a bulge just near GpG sequence-containing terminal loop. 7SK snRNA is a scaffold for a ribonucleoprotein complex (7SK snRNP), which is known to participate in transcription regulation. We have shown that the recombinant Ku specifically binds a G-rich loop of hairpin 1 within 7SK snRNA. Moreover, Ku protein has been co-precipitated from HEK 293T cells with endogenous 7SK snRNA and such proteins included in 7SK snRNP as HEXIM1, Cdk9 and CTIP2. Ku and Cdk9 binding is found to be RNA-independent, meanwhile HEXIM1 and Ku co-precipitation depended on the presence of intact 7SK snRNA. The latter result has been confirmed using recombinant HEXIM1 and Ku proteins. Colocalization of Ku and CTIP2 was additionally confirmed by confocal microscopy. These results allow us to propose human Ku as a new component of the 7SK snRNP complex.
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Affiliation(s)
- Olga Shadrina
- Chemistry Department, Lomonosov Moscow State University, Moscow, 199991, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.
| | - Irina Garanina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Sergey Korolev
- Chemistry Department, Lomonosov Moscow State University, Moscow, 199991, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Timofei Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Moscow, 199991, Russia; Skolkovo Institute of Science and Technology, Skolkovo, 121205, Russia
| | - Jeanne Van Assche
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Fadoua Daouad
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Clementine Wallet
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Olivier Rohr
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Marina Gottikh
- Chemistry Department, Lomonosov Moscow State University, Moscow, 199991, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
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15
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Durut N, Mittelsten Scheid O. The Role of Noncoding RNAs in Double-Strand Break Repair. FRONTIERS IN PLANT SCIENCE 2019; 10:1155. [PMID: 31611891 PMCID: PMC6776598 DOI: 10.3389/fpls.2019.01155] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Genome stability is constantly threatened by DNA lesions generated by different environmental factors as well as endogenous processes. If not properly and timely repaired, damaged DNA can lead to mutations or chromosomal rearrangements, well-known reasons for genetic diseases or cancer in mammals, or growth abnormalities and/or sterility in plants. To prevent deleterious consequences of DNA damage, a sophisticated system termed DNA damage response (DDR) detects DNA lesions and initiates DNA repair processes. In addition to many well-studied canonical proteins involved in this process, noncoding RNA (ncRNA) molecules have recently been discovered as important regulators of the DDR pathway, extending the broad functional repertoire of ncRNAs to the maintenance of genome stability. These ncRNAs are mainly connected with double-strand breaks (DSBs), the most dangerous type of DNA lesions. The possibility to intentionally generate site-specific DSBs in the genome with endonucleases constitutes a powerful tool to study, in vivo, how DSBs are processed and how ncRNAs participate in this crucial event. In this review, we will summarize studies reporting the different roles of ncRNAs in DSB repair and discuss how genome editing approaches, especially CRISPR/Cas systems, can assist DNA repair studies. We will summarize knowledge concerning the functional significance of ncRNAs in DNA repair and their contribution to genome stability and integrity, with a focus on plants.
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16
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Kim JH. Chromatin Remodeling and Epigenetic Regulation in Plant DNA Damage Repair. Int J Mol Sci 2019; 20:ijms20174093. [PMID: 31443358 PMCID: PMC6747262 DOI: 10.3390/ijms20174093] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
DNA damage response (DDR) in eukaryotic cells is initiated in the chromatin context. DNA damage and repair depend on or have influence on the chromatin dynamics associated with genome stability. Epigenetic modifiers, such as chromatin remodelers, histone modifiers, DNA (de-)methylation enzymes, and noncoding RNAs regulate DDR signaling and DNA repair by affecting chromatin dynamics. In recent years, significant progress has been made in the understanding of plant DDR and DNA repair. SUPPRESSOR OF GAMMA RESPONSE1, RETINOBLASTOMA RELATED1 (RBR1)/E2FA, and NAC103 have been proven to be key players in the mediation of DDR signaling in plants, while plant-specific chromatin remodelers, such as DECREASED DNA METHYLATION1, contribute to chromatin dynamics for DNA repair. There is accumulating evidence that plant epigenetic modifiers are involved in DDR and DNA repair. In this review, I examine how DDR and DNA repair machineries are concertedly regulated in Arabidopsis thaliana by a variety of epigenetic modifiers directing chromatin remodeling and epigenetic modification. This review will aid in updating our knowledge on DDR and DNA repair in plants.
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Affiliation(s)
- Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do 56212, Korea.
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17
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Burger K, Ketley RF, Gullerova M. Beyond the Trinity of ATM, ATR, and DNA-PK: Multiple Kinases Shape the DNA Damage Response in Concert With RNA Metabolism. Front Mol Biosci 2019; 6:61. [PMID: 31428617 PMCID: PMC6688092 DOI: 10.3389/fmolb.2019.00061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/22/2022] Open
Abstract
Our genome is constantly exposed to endogenous and exogenous sources of DNA damage resulting in various alterations of the genetic code. DNA double-strand breaks (DSBs) are considered one of the most cytotoxic lesions. Several types of repair pathways act to repair DNA damage and maintain genome stability. In the canonical DNA damage response (DDR) DSBs are recognized by the sensing kinases Ataxia-telangiectasia mutated (ATM), Ataxia-telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK), which initiate a cascade of kinase-dependent amplification steps known as DSB signaling. Recent evidence suggests that efficient recognition and repair of DSBs relies on the transcription and processing of non-coding (nc)RNA molecules by RNA polymerase II (RNAPII) and the RNA interference (RNAi) factors Drosha and Dicer. Multiple kinases influence the phosphorylation status of both the RNAPII carboxy-terminal domain (CTD) and Dicer in order to regulate RNA-dependent DSBs repair. The importance of kinase signaling and RNA processing in the DDR is highlighted by the regulation of p53-binding protein (53BP1), a key regulator of DSB repair pathway choice between homologous recombination (HR) and non-homologous end joining (NHEJ). Additionally, emerging evidence suggests that RNA metabolic enzymes also play a role in the repair of other types of DNA damage, including the DDR to ultraviolet radiation (UVR). RNAi factors are also substrates for mitogen-activated protein kinase (MAPK) signaling and mediate the turnover of ncRNA during nucleotide excision repair (NER) in response to UVR. Here, we review kinase-dependent phosphorylation events on RNAPII, Drosha and Dicer, and 53BP1 that modulate the key steps of the DDR to DSBs and UVR, suggesting an intimate link between the DDR and RNA metabolism.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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18
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Huang C, Leng D, Lei KC, Sun S, Zhang XD. Transcriptome analysis reveals lncRNA-mediated complex regulatory network response to DNA damage in the liver tissue of Rattus norvegicus. J Cell Physiol 2019; 234:23216-23231. [PMID: 31140619 DOI: 10.1002/jcp.28889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/14/2022]
Abstract
DNA is prone to damages, which would result in genetic disorders and enhance risk of tumorigenesis. Hence, understanding the molecular mechanisms of DNA damage and repair will provide deep insights into tumorigenesis, carcinogenesis as well as the corresponding treatments. Aiming at investigating potential long noncoding RNAs (lncRNAs) response against DNA damage, we performed a comprehensive transcriptomic analysis based on RNA sequencing data of the liver tissue from Rattus norvegicus, in which DNA damage was induced using aflatoxin B1, ifosfamide and N-nitrosodimethylamine. Through our analyses, numerous novel lncRNAs are identified for the first time, and differential network analysis discloses lncRNA-mediated regulatory networks related to DNA-damage response. The result shows that these DNA-damage-inducing chemicals might disrupt many lncRNA-mediated interactions involved in diverse biological processes and pathways, for example, immune function and cell adhesion. In contrast, the host might also activate a few RNA interactions in response to DNA damage, involving response to drug and regulation of cell cycle.
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Affiliation(s)
- Chen Huang
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Dongliang Leng
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
| | - Shixue Sun
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China
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19
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Manoel-Caetano FS, Rossi AFT, Calvet de Morais G, Severino FE, Silva AE. Upregulation of the APE1 and H2AX genes and miRNAs involved in DNA damage response and repair in gastric cancer. Genes Dis 2019; 6:176-184. [PMID: 31194025 PMCID: PMC6545450 DOI: 10.1016/j.gendis.2019.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/28/2019] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer remains one of the leading causes of cancer-related death worldwide, and most of the cases are associated with Helicobacter pylori infection. This bacterium promotes the production of reactive oxygen species (ROS), which cause DNA damage in gastric epithelial cells. In this study, we evaluated the expression of important genes involved in the recognition of DNA damage (ATM, ATR, and H2AX) and ROS-induced damage repair (APE1) and the expression of some miRNAs (miR-15a, miR-21, miR-24, miR-421 and miR-605) that target genes involved in the DNA damage response (DDR) in 31 fresh tissues of gastric cancer. Cytoscape v3.1.1 was used to construct the postulated miRNA:mRNA interaction network. Analysis performed by real-time quantitative PCR exhibited significantly increased levels of the APE1 (RQ = 2.55, p < 0.0001) and H2AX (RQ = 2.88, p = 0.0002) genes beyond the miR-421 and miR-605 in the gastric cancer samples. In addition, significantly elevated levels of miR-21, miR-24 and miR-421 were observed in diffuse-type gastric cancer. Correlation analysis reinforced some of the gene:gene (ATM/ATR/H2AX) and miRNA:mRNA relationships obtained also with the interaction network. Thus, our findings show that tumor cells from gastric cancer presents deregulation of genes and miRNAs that participate in the recognition and repair of DNA damage, which could confer an advantage to cell survival and proliferation in the tumor microenvironment.
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Affiliation(s)
- Fernanda S Manoel-Caetano
- Department of Biology, UNESP, São Paulo State University, Campus of São José do Rio Preto, Rua Cristóvão Colombo, 2265, 15.054-000, São José do Rio Preto, São Paulo, Brazil
| | - Ana Flávia T Rossi
- Department of Biology, UNESP, São Paulo State University, Campus of São José do Rio Preto, Rua Cristóvão Colombo, 2265, 15.054-000, São José do Rio Preto, São Paulo, Brazil
| | - Gabriela Calvet de Morais
- Department of Biology, UNESP, São Paulo State University, Campus of São José do Rio Preto, Rua Cristóvão Colombo, 2265, 15.054-000, São José do Rio Preto, São Paulo, Brazil
| | - Fábio Eduardo Severino
- Department of Surgery and Orthopedics, Faculty of Medicine, UNESP, São Paulo State University, Campus of Botucatu, Av. Prof. Mário Rubens Guimarães Montenegro, s/n, 18.618-687, Botucatu, São Paulo, Brazil
| | - Ana Elizabete Silva
- Department of Biology, UNESP, São Paulo State University, Campus of São José do Rio Preto, Rua Cristóvão Colombo, 2265, 15.054-000, São José do Rio Preto, São Paulo, Brazil
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20
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Small Non-Coding RNAs Derived From Eukaryotic Ribosomal RNA. Noncoding RNA 2019; 5:ncrna5010016. [PMID: 30720712 PMCID: PMC6468398 DOI: 10.3390/ncrna5010016] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/24/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will present a nonexhaustive list of referenced small non-coding RNAs (ncRNAs) derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs). We will focus on the rRFs that are experimentally verified, and discuss their origin, length, structure, biogenesis, association with known regulatory proteins, and potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences-because of their overabundance-from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because no one could believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.
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21
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Barman P, Reddy D, Bhaumik SR. Mechanisms of Antisense Transcription Initiation with Implications in Gene Expression, Genomic Integrity and Disease Pathogenesis. Noncoding RNA 2019; 5:ncrna5010011. [PMID: 30669611 PMCID: PMC6468509 DOI: 10.3390/ncrna5010011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/01/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Non-coding antisense transcripts arise from the strand opposite the sense strand. Over 70% of the human genome generates non-coding antisense transcripts while less than 2% of the genome codes for proteins. Antisense transcripts and/or the act of antisense transcription regulate gene expression and genome integrity by interfering with sense transcription and modulating histone modifications or DNA methylation. Hence, they have significant pathological and physiological relevance. Indeed, antisense transcripts were found to be associated with various diseases including cancer, diabetes, cardiac and neurodegenerative disorders, and, thus, have promising potentials for prognostic and diagnostic markers and therapeutic development. However, it is not clearly understood how antisense transcription is initiated and epigenetically regulated. Such knowledge would provide new insights into the regulation of antisense transcription, and hence disease pathogenesis with therapeutic development. The recent studies on antisense transcription initiation and its epigenetic regulation, which are limited, are discussed here. Furthermore, we concisely describe how antisense transcription/transcripts regulate gene expression and genome integrity with implications in disease pathogenesis and therapeutic development.
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Affiliation(s)
- Priyanka Barman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Divya Reddy
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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22
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Zhang W, Hu T, Song X. The function of lncRNAs in aging-related diseases and 3D genome. TRANSLATIONAL MEDICINE OF AGING 2019. [DOI: 10.1016/j.tma.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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23
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Aryankalayil MJ, Chopra S, Makinde A, Eke I, Levin J, Shankavaram U, MacMillan L, Vanpouille-Box C, Demaria S, Coleman CN. Microarray analysis of miRNA expression profiles following whole body irradiation in a mouse model. Biomarkers 2018; 23:689-703. [PMID: 29799276 PMCID: PMC6982201 DOI: 10.1080/1354750x.2018.1479771] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/08/2018] [Accepted: 05/12/2018] [Indexed: 12/13/2022]
Abstract
CONTEXT Accidental exposure to life-threatening radiation in a nuclear event is a major concern; there is an enormous need for identifying biomarkers for radiation biodosimetry to triage populations and treat critically exposed individuals. OBJECTIVE To identify dose-differentiating miRNA signatures from whole blood samples of whole body irradiated mice. METHODS Mice were whole body irradiated with X-rays (2 Gy-15 Gy); blood was collected at various time-points post-exposure; total RNA was isolated; miRNA microarrays were performed; miRNAs differentially expressed in irradiated vs. unirradiated controls were identified; feature extraction and classification models were applied to predict dose-differentiating miRNA signature. RESULTS We observed a time and dose responsive alteration in the expression levels of miRNAs. Maximum number of miRNAs were altered at 24-h and 48-h time-points post-irradiation. A 23-miRNA signature was identified using feature selection algorithms and classifier models. An inverse correlation in the expression level changes of miR-17 members, and their targets were observed in whole body irradiated mice and non-human primates. CONCLUSION Whole blood-based miRNA expression signatures might be used for predicting radiation exposures in a mass casualty nuclear incident.
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Affiliation(s)
- Molykutty J Aryankalayil
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
| | - Sunita Chopra
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
| | - Adeola Makinde
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
| | - Iris Eke
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
| | - Joel Levin
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
| | - Uma Shankavaram
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
| | | | | | - Sandra Demaria
- c Department of Radiation Oncology , Weill Cornell Medicine , New York , NY , USA
| | - C Norman Coleman
- a Radiation Oncology Branch, Center for Cancer Research , National Cancer Institute , Bethesda , MD , USA
- d Radiation Research Program, National Cancer Institute , National Institutes of Health , Rockville , MD , USA
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24
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Thapar R. Regulation of DNA Double-Strand Break Repair by Non-Coding RNAs. Molecules 2018; 23:molecules23112789. [PMID: 30373256 PMCID: PMC6278438 DOI: 10.3390/molecules23112789] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
DNA double-strand breaks (DSBs) are deleterious lesions that are generated in response to ionizing radiation or replication fork collapse that can lead to genomic instability and cancer. Eukaryotes have evolved two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ) to repair DSBs. Whereas the roles of protein-DNA interactions in HR and NHEJ have been fairly well defined, the functions of small and long non-coding RNAs and RNA-DNA hybrids in the DNA damage response is just beginning to be elucidated. This review summarizes recent discoveries on the identification of non-coding RNAs and RNA-mediated regulation of DSB repair.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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25
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Hahne JC, Valeri N. Non-Coding RNAs and Resistance to Anticancer Drugs in Gastrointestinal Tumors. Front Oncol 2018; 8:226. [PMID: 29967761 PMCID: PMC6015885 DOI: 10.3389/fonc.2018.00226] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/31/2018] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs are important regulators of gene expression and transcription. It is well established that impaired non-coding RNA expression especially the one of long non-coding RNAs and microRNAs is involved in a number of pathological conditions including cancer. Non-coding RNAs are responsible for the development of resistance to anticancer treatments as they regulate drug resistance-related genes, affect intracellular drug concentrations, induce alternative signaling pathways, alter drug efficiency via blocking cell cycle regulation, and DNA damage response. Furthermore, they can prevent therapeutic-induced cell death and promote epithelial-mesenchymal transition (EMT) and elicit non-cell autonomous mechanisms of resistance. In this review, we summarize the role of non-coding RNAs for different mechanisms resulting in drug resistance (e.g., drug transport, drug metabolism, cell cycle regulation, regulation of apoptotic pathways, cancer stem cells, and EMT) in the context of gastrointestinal cancers.
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Affiliation(s)
- Jens C. Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Department of Medicine, The Royal Marsden NHS Trust, London, United Kingdom
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26
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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27
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Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks. Nat Cell Biol 2017; 19:1400-1411. [PMID: 29180822 PMCID: PMC5714282 DOI: 10.1038/ncb3643] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 10/13/2017] [Indexed: 12/13/2022]
Abstract
The DNA damage response (DDR) preserves genomic integrity. Small non-coding RNAs termed DDRNAs are generated at DNA double-strand breaks (DSBs) and are critical for DDR activation. Here we show that active DDRNAs specifically localize to their damaged homologous genomic sites in a transcription-dependent manner. Following DNA damage, RNA polymerase II (RNAPII) binds to the MRE11-RAD50-NBS1 complex, is recruited to DSBs and synthesizes damage-induced long non-coding RNAs (dilncRNAs) from and towards DNA ends. DilncRNAs act both as DDRNA precursors and by recruiting DDRNAs through RNA-RNA pairing. Together, dilncRNAs and DDRNAs fuel DDR focus formation and associate with 53BP1. Accordingly, inhibition of RNAPII prevents DDRNA recruitment, DDR activation and DNA repair. Antisense oligonucleotides matching dilncRNAs and DDRNAs impair site-specific DDR focus formation and DNA repair. We propose that DDR signalling sites, in addition to sharing a common pool of proteins, individually host a unique set of site-specific RNAs necessary for DDR activation.
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D'Alessandro G, d'Adda di Fagagna F. Transcription and DNA Damage: Holding Hands or Crossing Swords? J Mol Biol 2017; 429:3215-3229. [DOI: 10.1016/j.jmb.2016.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/12/2023]
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Brandão BB, Guerra BA, Mori MA. Shortcuts to a functional adipose tissue: The role of small non-coding RNAs. Redox Biol 2017; 12:82-102. [PMID: 28214707 PMCID: PMC5312655 DOI: 10.1016/j.redox.2017.01.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 01/30/2017] [Indexed: 12/20/2022] Open
Abstract
Metabolic diseases such as type 2 diabetes are a major public health issue worldwide. These diseases are often linked to a dysfunctional adipose tissue. Fat is a large, heterogenic, pleiotropic and rather complex tissue. It is found in virtually all cavities of the human body, shows unique plasticity among tissues, and harbors many cell types in addition to its main functional unit - the adipocyte. Adipose tissue function varies depending on the localization of the fat depot, the cell composition of the tissue and the energy status of the organism. While the white adipose tissue (WAT) serves as the main site for triglyceride storage and acts as an important endocrine organ, the brown adipose tissue (BAT) is responsible for thermogenesis. Beige adipocytes can also appear in WAT depots to sustain heat production upon certain conditions, and it is becoming clear that adipose tissue depots can switch phenotypes depending on cell autonomous and non-autonomous stimuli. To maintain such degree of plasticity and respond adequately to changes in the energy balance, three basic processes need to be properly functioning in the adipose tissue: i) adipogenesis and adipocyte turnover, ii) metabolism, and iii) signaling. Here we review the fundamental role of small non-coding RNAs (sncRNAs) in these processes, with focus on microRNAs, and demonstrate their importance in adipose tissue function and whole body metabolic control in mammals.
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Affiliation(s)
- Bruna B Brandão
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Beatriz A Guerra
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Marcelo A Mori
- Program in Molecular Biology, Universidade Federal de São Paulo, São Paulo, Brazil; Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas, Campinas, Brazil; Program in Genetics and Molecular Biology, Universidade Estadual de Campinas, Campinas, Brazil.
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Patne K, Rakesh R, Arya V, Chanana UB, Sethy R, Swer PB, Muthuswami R. BRG1 and SMARCAL1 transcriptionally co-regulate DROSHA, DGCR8 and DICER in response to doxorubicin-induced DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:936-951. [PMID: 28716689 DOI: 10.1016/j.bbagrm.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/13/2017] [Accepted: 07/13/2017] [Indexed: 12/19/2022]
Abstract
Recent investigations have emphasized the role of miRNA biogenesis proteins in the synthesis of non-coding RNA when double-strand DNA breaks are induced by ionizing radiations. However, the role of these non-coding RNA and their regulation in response to doxorubicin-induced DNA damage is not known. In this paper, BRG1 and SMARCAL1, members of the ATP-dependent chromatin remodelling family, are shown to co-regulate the transcription of DROSHA, DGCR8, and DICER in response to double-strand DNA breaks induced by doxorubicin. Both BRG1 and SMARCAL1 are needed for the upregulation of the three miRNA biogenesis genes as absence of BRG1 results in downregulation of DGCR8 and DICER while absence of SMARCAL1 results in downregulation of DROSHA. These two proteins act in coordination to upregulate expression of DROSHA, DGCR8, and DICER when cells are treated with doxorubicin. This transcriptional regulation of the miRNA biogenesis proteins is needed for the formation of 53BP1 foci as downregulation of either BRG1 or SMARCAL1 reduced the number of 53BP1 foci in DNA damaged cells. The foci formation was restored when the downregulated cells were treated with ncRNA purified from doxorubicin treated HeLa cells. From the results obtained, we conclude that the regulation of miRNA biogenesis proteins by SMARCAL1 and BRG1 is needed for the formation of non-coding RNA and thus, 53BP1 foci in response to doxorubicin-induced DNA damage.
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Affiliation(s)
- Ketki Patne
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India
| | - Radhakrishnan Rakesh
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India
| | - Vijendra Arya
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India
| | - Upasana Bedi Chanana
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India
| | - Ramesh Sethy
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India
| | - Pynskhem Bok Swer
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India
| | - Rohini Muthuswami
- Chromatin Remodelling Laboratory, School of Life Sciences, JNU, New Delhi, 110067, India.
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Variations within 3'-UTR of MDM4 gene contribute to clinical outcomes of advanced non-small cell lung cancer patients following platinum-based chemotherapy. Oncotarget 2017; 8:16313-16324. [PMID: 27462918 PMCID: PMC5369965 DOI: 10.18632/oncotarget.10771] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/17/2016] [Indexed: 01/22/2023] Open
Abstract
Single-nucleotide polymorphism (SNPs) in microRNA (miRNA)-binding sites may modulate the posttranscriptional regulation of gene expression and explain individual sensitivity to platinum agents. This study aimed to investigate the impact of SNPs located at 3′-untranslated region (UTR) of MDM4 gene, on clinical outcomes of advanced non-small cell lung cancer (NSCLC) patients. Four SNPs were genotyped by using DNA from blood samples of advanced NSCLC patients (642 in the Discovery set and 330 in the Replication set) and were analyzed the relationships with clinical outcomes. Carriers with rs10900598 CC genotype and rs4245739 AC genotype showed increased overall survival (OS) than those with AA genotype (P = 0.017 and P = 0.037, respectively) in the Discovery set and after pooling results from the Replication set. A combined effect on survival of variant alleles was also concluded and validated. Stratification analysis revealed that the effect of MDM4 SNPs was more pronounced in lung adenocarcinoma (LAC) subgroups. A reduced expression of the reporter gene for the C allele of rs4245739 was observed in NSCLC cells using luciferase reporter gene assays. Taken together, our results demonstrate that genetic variations in 3′-UTR of MDM4 gene may influence outcomes of advanced NSCLC by miRNAs-mediated regulation.
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Abstract
Bacteria and viruses possess circular DNA, whereas eukaryotes with typically very large DNA molecules have had to evolve into linear chromosomes to circumvent the problem of supercoiling circular DNA of that size. Consequently, such organisms possess telomeres to cap chromosome ends. Telomeres are essentially tandem repeats of any DNA sequence that are present at the ends of chromosomes. Their biology has been an enigmatic one, involving various molecules interacting dynamically in an evolutionarily well-trimmed fashion. Telomeres range from canonical hexameric repeats in most eukaryotes to unimaginably random retrotransposons, which attach to chromosome ends and reverse-transcribe to DNA in some plants and insects. Telomeres invariably associate with specialised protein complexes that envelop it, also regulating access of the ends to legitimate enzymes involved in telomere metabolism. They also transcribe into repetitive RNA which also seems to be playing significant roles in telomere maintenance. Telomeres thus form the intersection of DNA, protein, and RNA molecules acting in concert to maintain chromosome integrity. Telomere biology is emerging to appear ever more complex than previously envisaged, with the continual discovery of more molecules and interplays at the telomeres. This review also includes a section dedicated to the history of telomere biology, and intends to target the scientific audience new to the field by rendering an understanding of the phenomenon of chromosome end protection at large, with more emphasis on the biology of human telomeres. The review provides an update on the field and mentions the questions that need to be addressed.
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Affiliation(s)
- Shriram Venkatesan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore.
| | - Aik Kia Khaw
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore.
- Clinical Research Unit, Khoo Teck Puat Hospital, 768828 Singapore, Singapore.
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597 Singapore, Singapore.
- Tembusu College, National University of Singapore, 138598 Singapore, Singapore.
- VIT University, Vellore 632014, India.
- Mangalore University, Mangalore 574199, India.
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Abu-Zhayia ER, Khoury-Haddad H, Guttmann-Raviv N, Serruya R, Jarrous N, Ayoub N. A role of human RNase P subunits, Rpp29 and Rpp21, in homology directed-repair of double-strand breaks. Sci Rep 2017; 7:1002. [PMID: 28432356 PMCID: PMC5430778 DOI: 10.1038/s41598-017-01185-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/22/2017] [Indexed: 12/21/2022] Open
Abstract
DNA damage response (DDR) is needed to repair damaged DNA for genomic integrity preservation. Defective DDR causes accumulation of deleterious mutations and DNA lesions that can lead to genomic instabilities and carcinogenesis. Identifying new players in the DDR, therefore, is essential to advance the understanding of the molecular mechanisms by which cells keep their genetic material intact. Here, we show that the core protein subunits Rpp29 and Rpp21 of human RNase P complex are implicated in DDR. We demonstrate that Rpp29 and Rpp21 depletion impairs double-strand break (DSB) repair by homology-directed repair (HDR), but has no deleterious effect on the integrity of non-homologous end joining. We also demonstrate that Rpp29 and Rpp21, but not Rpp14, Rpp25 and Rpp38, are rapidly and transiently recruited to laser-microirradiated sites. Rpp29 and Rpp21 bind poly ADP-ribose moieties and are recruited to DNA damage sites in a PARP1-dependent manner. Remarkably, depletion of the catalytic H1 RNA subunit diminishes their recruitment to laser-microirradiated regions. Moreover, RNase P activity is augmented after DNA damage in a PARP1-dependent manner. Altogether, our results describe a previously unrecognized function of the RNase P subunits, Rpp29 and Rpp21, in fine-tuning HDR of DSBs.
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Affiliation(s)
- Enas R Abu-Zhayia
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Hanan Khoury-Haddad
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Noga Guttmann-Raviv
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Raphael Serruya
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel
| | - Nayef Jarrous
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, 91120, Jerusalem, Israel.
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel.
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Rossiello F, Aguado J, Sepe S, Iannelli F, Nguyen Q, Pitchiaya S, Carninci P, d'Adda di Fagagna F. DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs. Nat Commun 2017; 8:13980. [PMID: 28239143 PMCID: PMC5473644 DOI: 10.1038/ncomms13980] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/17/2016] [Indexed: 12/23/2022] Open
Abstract
The DNA damage response (DDR) is a set of cellular events that follows the generation of DNA damage. Recently, site-specific small non-coding RNAs, also termed DNA damage response RNAs (DDRNAs), have been shown to play a role in DDR signalling and DNA repair. Dysfunctional telomeres activate DDR in ageing, cancer and an increasing number of identified pathological conditions. Here we show that, in mammals, telomere dysfunction induces the transcription of telomeric DDRNAs (tDDRNAs) and their longer precursors from both DNA strands. DDR activation and maintenance at telomeres depend on the biogenesis and functions of tDDRNAs. Their functional inhibition by sequence-specific antisense oligonucleotides allows the unprecedented telomere-specific DDR inactivation in cultured cells and in vivo in mouse tissues. In summary, these results demonstrate that tDDRNAs are induced at dysfunctional telomeres and are necessary for DDR activation and they validate the viability of locus-specific DDR inhibition by targeting DDRNAs.
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Affiliation(s)
- Francesca Rossiello
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Julio Aguado
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Sara Sepe
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Fabio Iannelli
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Quan Nguyen
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fabrizio d'Adda di Fagagna
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
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35
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Dianatpour A, Ghafouri-Fard S. The Role of Long Non Coding RNAs in the Repair of DNA Double Strand Breaks. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2017; 6:1-12. [PMID: 28868264 PMCID: PMC5568187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/09/2017] [Indexed: 11/22/2022]
Abstract
DNA double strand breaks (DSBs) are abrasions caused in both strands of the DNA duplex following exposure to both exogenous and endogenous conditions. Such abrasions have deleterious effect in cells leading to genome rearrangements and cell death. A number of repair systems including homologous recombination (HR) and non-homologous end-joining (NHEJ) have been evolved to minimize the fatal effects of these lesions in cell. The role of protein coding genes in regulation of these pathways has been assessed previously. However, a number of recent studies have focused on evaluation of non-coding RNAs participation in DNA repair. We performed a computerized search of the Medline/ Pubmed databases with key words: DNA repair, homologous recombination, non-homologues end joining and long non-coding RNA (LncRNA). The existing data highlight the role of long non-coding RNAs in DSB repair as well as dysregulation in their expression which would lead to pathological conditions such as cancer. The specific mechanism of their contribution in DNA repair pathways has been elucidated for a few of them. LncRNAs participate in several steps of DNA repair pathways and regulate the expression of key components of these pathways including p53 tumor suppressor gene.
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Affiliation(s)
| | - Soudeh Ghafouri-Fard
- Corresponding author: Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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36
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Fang Y, Zhang L, Li Z, Li Y, Huang C, Lu X. MicroRNAs in DNA Damage Response, Carcinogenesis, and Chemoresistance. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 333:1-49. [DOI: 10.1016/bs.ircmb.2017.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Majidinia M, Yousefi B. DNA damage response regulation by microRNAs as a therapeutic target in cancer. DNA Repair (Amst) 2016; 47:1-11. [DOI: 10.1016/j.dnarep.2016.09.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
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38
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Vohhodina J, Harkin DP, Savage KI. Dual roles of DNA repair enzymes in RNA biology/post-transcriptional control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:604-19. [PMID: 27126972 DOI: 10.1002/wrna.1353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022]
Abstract
Despite consistent research into the molecular principles of the DNA damage repair pathway for almost two decades, it has only recently been found that RNA metabolism is very tightly related to this pathway, and the two ancient biochemical mechanisms act in alliance to maintain cellular genomic integrity. The close links between these pathways are well exemplified by examining the base excision repair pathway, which is now well known for dual roles of many of its members in DNA repair and RNA surveillance, including APE1, SMUG1, and PARP1. With additional links between these pathways steadily emerging, this review aims to provide a summary of the emerging roles for DNA repair proteins in the post-transcriptional regulation of RNAs. WIREs RNA 2016, 7:604-619. doi: 10.1002/wrna.1353 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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39
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Naccarati A, Rosa F, Vymetalkova V, Barone E, Jiraskova K, Di Gaetano C, Novotny J, Levy M, Vodickova L, Gemignani F, Buchler T, Landi S, Vodicka P, Pardini B. Double-strand break repair and colorectal cancer: gene variants within 3' UTRs and microRNAs binding as modulators of cancer risk and clinical outcome. Oncotarget 2016; 7:23156-69. [PMID: 26735576 PMCID: PMC5029617 DOI: 10.18632/oncotarget.6804] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/09/2015] [Indexed: 12/25/2022] Open
Abstract
Genetic variations in 3' untranslated regions of target genes may affect microRNA binding, resulting in differential protein expression. microRNAs regulate DNA repair, and single-nucleotide polymorphisms in miRNA binding sites (miRSNPs) may account for interindividual differences in the DNA repair capacity. Our hypothesis is that miRSNPs in relevant DNA repair genes may ultimately affect cancer susceptibility and impact prognosis.In the present study, we analysed the association of polymorphisms in predicted microRNA target sites of double-strand breaks (DSBs) repair genes with colorectal cancer (CRC) risk and clinical outcome. Twenty-one miRSNPs in non-homologous end-joining and homologous recombination pathways were assessed in 1111 cases and 1469 controls. The variant CC genotype of rs2155209 in MRE11A was strongly associated with decreased cancer risk when compared with the other genotypes (OR 0.54, 95% CI 0.38-0.76, p = 0.0004). A reduced expression of the reporter gene was observed for the C allele of this polymorphism by in vitro assay, suggesting a more efficient interaction with potentially binding miRNAs. In colon cancer patients, the rs2155209 CC genotype was associated with shorter survival while the TT genotype of RAD52 rs11226 with longer survival when both compared with their respective more frequent genotypes (HR 1.63, 95% CI 1.06-2.51, p = 0.03 HR 0.60, 95% CI 0.41-0.89, p = 0.01, respectively).miRSNPs in DSB repair genes involved in the maintenance of genomic stability may have a role on CRC susceptibility and clinical outcome.
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Affiliation(s)
- Alessio Naccarati
- Molecular and Genetic Epidemiology Research Unit, Human Genetics Foundation, Turin, Italy
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
| | - Fabio Rosa
- Genomic Variation in Human Populations and Complex Diseases Research Unit, Human Genetics Foundation, Turin, Italy
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elisa Barone
- Department of Biology, University of Pisa, Pisa, Italy
| | - Katerina Jiraskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Cornelia Di Gaetano
- Genomic Variation in Human Populations and Complex Diseases Research Unit, Human Genetics Foundation, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jan Novotny
- Department of Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Faculty of Medicine, Charles University and Thomayer University Hospital, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Tomas Buchler
- Department of Oncology, Thomayer Hospital and First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbara Pardini
- Genomic Variation in Human Populations and Complex Diseases Research Unit, Human Genetics Foundation, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
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40
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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.
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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
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41
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Giono LE, Nieto Moreno N, Cambindo Botto AE, Dujardin G, Muñoz MJ, Kornblihtt AR. The RNA Response to DNA Damage. J Mol Biol 2016; 428:2636-2651. [PMID: 26979557 DOI: 10.1016/j.jmb.2016.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 02/01/2023]
Abstract
Multicellular organisms must ensure genome integrity to prevent accumulation of mutations, cell death, and cancer. The DNA damage response (DDR) is a complex network that senses, signals, and executes multiple programs including DNA repair, cell cycle arrest, senescence, and apoptosis. This entails regulation of a variety of cellular processes: DNA replication and transcription, RNA processing, mRNA translation and turnover, and post-translational modification, degradation, and relocalization of proteins. Accumulated evidence over the past decades has shown that RNAs and RNA metabolism are both regulators and regulated actors of the DDR. This review aims to present a comprehensive overview of the current knowledge on the many interactions between the DNA damage and RNA fields.
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Affiliation(s)
- Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Nicolás Nieto Moreno
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Adrián E Cambindo Botto
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Gwendal Dujardin
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Centre for Genomic Regulation, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Manuel J Muñoz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Buenos Aires, Argentina.
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42
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Abstract
It is emerging that the pathways that process newly transcribed RNA molecules also regulate the response to DNA damage at multiple levels. Here, we discuss recent insights into how RNA processing pathways participate in DNA damage recognition, signaling, and repair, selectively influence the expression of genome-stabilizing proteins, and resolve deleterious DNA/RNA hybrids (R-loops) formed during transcription and RNA processing. The importance of these pathways for the DNA damage response (DDR) is underscored by the growing appreciation that defects in these regulatory connections may be connected to the genome instability involved in several human diseases, including cancer.
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Affiliation(s)
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
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43
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Li Y, Hu G, Li P, Tang S, Zhang J, Jia G. miR-3940-5p enhances homologous recombination after DSB in Cr(VI) exposed 16HBE cell. Toxicology 2016; 344-346:1-6. [DOI: 10.1016/j.tox.2016.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/11/2022]
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44
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Activation of the DNA Damage Response by RNA Viruses. Biomolecules 2016; 6:2. [PMID: 26751489 PMCID: PMC4808796 DOI: 10.3390/biom6010002] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/17/2015] [Accepted: 11/24/2015] [Indexed: 12/11/2022] Open
Abstract
RNA viruses are a genetically diverse group of pathogens that are responsible for some of the most prevalent and lethal human diseases. Numerous viruses introduce DNA damage and genetic instability in host cells during their lifecycles and some species also manipulate components of the DNA damage response (DDR), a complex and sophisticated series of cellular pathways that have evolved to detect and repair DNA lesions. Activation and manipulation of the DDR by DNA viruses has been extensively studied. It is apparent, however, that many RNA viruses can also induce significant DNA damage, even in cases where viral replication takes place exclusively in the cytoplasm. DNA damage can contribute to the pathogenesis of RNA viruses through the triggering of apoptosis, stimulation of inflammatory immune responses and the introduction of deleterious mutations that can increase the risk of tumorigenesis. In addition, activation of DDR pathways can contribute positively to replication of viral RNA genomes. Elucidation of the interactions between RNA viruses and the DDR has provided important insights into modulation of host cell functions by these pathogens. This review summarises the current literature regarding activation and manipulation of the DDR by several medically important RNA viruses.
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45
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Liu C, Srihari S, Lal S, Gautier B, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. Mol Oncol 2016; 10:179-93. [PMID: 26456802 PMCID: PMC5528935 DOI: 10.1016/j.molonc.2015.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/19/2015] [Accepted: 09/04/2015] [Indexed: 01/05/2023] Open
Abstract
The Homologous Recombination (HR) pathway is crucial for the repair of DNA double-strand breaks (DSBs) generated during DNA replication. Defects in HR repair have been linked to the initiation and development of a wide variety of human malignancies, and exploited in chemical, radiological and targeted therapies. In this study, we performed a personalised pathway analysis independently for four large sporadic breast cancer cohorts to investigate the status of HR pathway dysregulation in individual sporadic breast tumours, its association with HR repair deficiency and its impact on tumour characteristics. Specifically, we first manually curated a list of HR genes according to our recent review on this pathway (Liu et al., 2014), and then applied a personalised pathway analysis method named Pathifier (Drier et al., 2013) on the expression levels of the curated genes to obtain an HR score quantifying HR pathway dysregulation in individual tumours. Based on the score, we observed a great diversity in HR dysregulation between and within gene expression-based breast cancer subtypes, and by using two published HR-defect signatures, we found HR pathway dysregulation reflects HR repair deficiency. Furthermore, we identified a novel association between HR pathway dysregulation and chromosomal instability (CIN) in sporadic breast cancer. Although CIN has long been considered as a hallmark of most solid tumours, with recent extensive studies highlighting its importance in tumour evolution and drug resistance, the molecular basis of CIN in sporadic cancers remains poorly understood. Our results imply that HR pathway dysregulation might contribute to CIN in sporadic breast cancer.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Samir Lal
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD 4029, Australia
| | - Benoît Gautier
- University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Peter T Simpson
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD 4029, Australia; School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Kum Kum Khanna
- QIMR-Berghofer Medical Research Institute, Herston, Brisbane, QLD 4029, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia.
| | - Kim-Anh Lê Cao
- University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD 4102, Australia.
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46
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Abstract
The discovery of small regulatory noncoding RNAs revolutionized our thinking on gene regulation. The class of microRNAs (miRs), a group of small noncoding RNAs (20-22 nt in length) that bind imperfectly to the 3'-untranslated region of target mRNA, has been insistently implicated in several pathological conditions including cancer. Indeed, major hallmarks of cancer, such as cell differentiation, cell proliferation, cell cycle, cell survival, and cell invasion, has been described as being regulated by miRs. Recent studies have also implicated miRs in cancer drug resistance. Regardless of the several studies done until now, drug resistance still is a burden for cancer therapy and patients' outcome, often resulting in more aggressive tumors that tend to metastasize to distant organs. Hence, with this review, we aim to summarize the miRs that influence molecular pathways that are involved in cancer drug resistance, such as drug metabolism, drug influx/efflux, DNA damage response (DDR), epithelial-to-mesenchymal transition (EMT), and cancer stem cells.
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Affiliation(s)
- Bruno Costa Gomes
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana 6, Edificio CEDOC II, Room 2.22-2.23, Lisbon, 1150-008, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana 6, Edificio CEDOC II, Room 2.22-2.23, Lisbon, 1150-008, Portugal
| | - António Sebastião Rodrigues
- Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Rua Câmara Pestana 6, Edificio CEDOC II, Room 2.22-2.23, Lisbon, 1150-008, Portugal.
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47
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Swahari V, Nakamura A, Baran-Gale J, Garcia I, Crowther AJ, Sons R, Gershon TR, Hammond S, Sethupathy P, Deshmukh M. Essential Function of Dicer in Resolving DNA Damage in the Rapidly Dividing Cells of the Developing and Malignant Cerebellum. Cell Rep 2015; 14:216-24. [PMID: 26748703 DOI: 10.1016/j.celrep.2015.12.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 10/23/2015] [Accepted: 12/06/2015] [Indexed: 01/09/2023] Open
Abstract
Maintenance of genomic integrity is critical during neurodevelopment, particularly in rapidly dividing cerebellar granule neuronal precursors that experience constitutive replication-associated DNA damage. As Dicer was recently recognized to have an unexpected function in the DNA damage response, we examined whether Dicer was important for preserving genomic integrity in the developing brain. We report that deletion of Dicer in the developing mouse cerebellum resulted in the accumulation of DNA damage leading to cerebellar progenitor degeneration, which was rescued with p53 deficiency; deletion of DGCR8 also resulted in similar DNA damage and cerebellar degeneration. Dicer deficiency also resulted in DNA damage and death in other rapidly dividing cells including embryonic stem cells and the malignant cerebellar progenitors in a mouse model of medulloblastoma. Together, these results identify an essential function of Dicer in resolving the spontaneous DNA damage that occurs during the rapid proliferation of developmental progenitors and malignant cells.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jeanette Baran-Gale
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Idoia Garcia
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Neurology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrew J Crowther
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Neurology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert Sons
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy R Gershon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Neurology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Scott Hammond
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Praveen Sethupathy
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
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48
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Affiliation(s)
- Michal Goldberg
- a Department of Genetics ; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem ; Jerusalem , Israel
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49
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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50
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Sharma V, Khurana S, Kubben N, Abdelmohsen K, Oberdoerffer P, Gorospe M, Misteli T. A BRCA1-interacting lncRNA regulates homologous recombination. EMBO Rep 2015; 16:1520-34. [PMID: 26412854 DOI: 10.15252/embr.201540437] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/25/2015] [Indexed: 12/17/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are important players in diverse biological processes. Upon DNA damage, cells activate a complex signaling cascade referred to as the DNA damage response (DDR). Using a microarray screen, we identify here a novel lncRNA, DDSR1 (DNA damage-sensitive RNA1), which is induced upon DNA damage. DDSR1 induction is triggered in an ATM-NF-κB pathway-dependent manner by several DNA double-strand break (DSB) agents. Loss of DDSR1 impairs cell proliferation and DDR signaling and reduces DNA repair capacity by homologous recombination (HR). The HR defect in the absence of DDSR1 is marked by aberrant accumulation of BRCA1 and RAP80 at DSB sites. In line with a role in regulating HR, DDSR1 interacts with BRCA1 and hnRNPUL1, an RNA-binding protein involved in DNA end resection. Our results suggest a role for the lncRNA DDSR1 in modulating DNA repair by HR.
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Affiliation(s)
- Vivek Sharma
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Nard Kubben
- National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
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