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Podralska M, Sajek MP, Bielicka A, Żurawek M, Ziółkowska-Suchanek I, Iżykowska K, Kolenda T, Kazimierska M, Kasprzyk ME, Sura W, Pietrucha B, Cukrowska B, Rozwadowska N, Dzikiewicz-Krawczyk A. Identification of ATM-dependent long non-coding RNAs induced in response to DNA damage. DNA Repair (Amst) 2024; 135:103648. [PMID: 38382170 DOI: 10.1016/j.dnarep.2024.103648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/23/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
DNA damage response (DDR) is a complex process, essential for cell survival. Especially deleterious type of DNA damage are DNA double-strand breaks (DSB), which can lead to genomic instability and malignant transformation if not repaired correctly. The central player in DSB detection and repair is the ATM kinase which orchestrates the action of several downstream factors. Recent studies have suggested that long non-coding RNAs (lncRNAs) are involved in DDR. Here, we aimed to identify lncRNAs induced upon DNA damage in an ATM-dependent manner. DNA damage was induced by ionizing radiation (IR) in immortalized lymphoblastoid cell lines derived from 4 patients with ataxia-telangiectasia (AT) and 4 healthy donors. RNA-seq revealed 10 lncRNAs significantly induced 1 h after IR in healthy donors, whereas none in AT patients. 149 lncRNAs were induced 8 h after IR in the control group, while only three in AT patients. Among IR-induced mRNAs, we found several genes with well-known functions in DDR. Gene Set Enrichment Analysis and Gene Ontology revealed delayed induction of key DDR pathways in AT patients compared to controls. The induction and dynamics of selected 9 lncRNAs were confirmed by RT-qPCR. Moreover, using a specific ATM inhibitor we proved that the induction of those lncRNAs is dependent on ATM. Some of the detected lncRNA genes are localized next to protein-coding genes involved in DDR. We observed that induction of lncRNAs after IR preceded changes in expression of adjacent genes. This indicates that IR-induced lncRNAs may regulate the transcription of nearby genes. Subcellular fractionation into chromatin, nuclear, and cytoplasmic fractions revealed that the majority of studied lncRNAs are localized in chromatin. In summary, our study revealed several lncRNAs induced by IR in an ATM-dependent manner. Their genomic co-localization and co-expression with genes involved in DDR suggest that those lncRNAs may be important players in cellular response to DNA damage.
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Affiliation(s)
- Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marcin Piotr Sajek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Antonina Bielicka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | | | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Weronika Sura
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Pietrucha
- Children's Memorial Health Institute, Department of Immunology, Warsaw, Poland
| | - Bożena Cukrowska
- Children's Memorial Health Institute, Department of Pathomorphology, Immunology Laboratorium, Warsaw, Poland
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Serafim RB, Cardoso C, Storti CB, da Silva P, Qi H, Parasuram R, Navegante G, Peron JPS, Silva WA, Espreafico EM, Paçó-Larson ML, Price BD, Valente V. HJURP is recruited to double-strand break sites and facilitates DNA repair by promoting chromatin reorganization. Oncogene 2024; 43:804-820. [PMID: 38279062 DOI: 10.1038/s41388-024-02937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
HJURP is overexpressed in several cancer types and strongly correlates with patient survival. However, the mechanistic basis underlying the association of HJURP with cancer aggressiveness is not well understood. HJURP promotes the loading of the histone H3 variant, CENP-A, at the centromeric chromatin, epigenetically defining the centromeres and supporting proper chromosome segregation. In addition, HJURP is associated with DNA repair but its function in this process is still scarcely explored. Here, we demonstrate that HJURP is recruited to DSBs through a mechanism requiring chromatin PARylation and promotes epigenetic alterations that favor the execution of DNA repair. Incorporation of HJURP at DSBs promotes turnover of H3K9me3 and HP1, facilitating DNA damage signaling and DSB repair. Moreover, HJURP overexpression in glioma cell lines also affected global structure of heterochromatin independently of DNA damage induction, promoting genome-wide reorganization and assisting DNA damage response. HJURP overexpression therefore extensively alters DNA damage signaling and DSB repair, and also increases radioresistance of glioma cells. Importantly, HJURP expression levels in tumors are also associated with poor response of patients to radiation. Thus, our results enlarge the understanding of HJURP involvement in DNA repair and highlight it as a promising target for the development of adjuvant therapies that sensitize tumor cells to irradiation.
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Affiliation(s)
- Rodolfo B Serafim
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
| | - Cibele Cardoso
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Camila B Storti
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Patrick da Silva
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Hongyun Qi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ramya Parasuram
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Geovana Navegante
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil
| | - Jean Pierre S Peron
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Wilson A Silva
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Enilza M Espreafico
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Maria L Paçó-Larson
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Valeria Valente
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil.
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil.
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil.
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Feoktistov AV, Georgieva SG, Soshnikova NV. Chromatin Remodeling Complex PBAF Activates and Represses Inflammatory Genes. DOKL BIOCHEM BIOPHYS 2023; 513:332-336. [PMID: 38066320 DOI: 10.1134/s1607672923700539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 01/26/2024]
Abstract
The PBAF chromatin remodeling complex regulates chromatin state and gene transcription in higher eukaryotes. In this work, we studied the role of PBAF in the regulation of NF-κB-and JAK/STAT-dependent activation of inflammatory genes. We performed knockdown of specific module subunit BAF200, which resulted in destruction of the entire PBAF specific module and changed the level of the genes transcription of both pathways. PBAF can be both an activator and a repressor of inflammatory genes. Thus, PBAF is an important regulator of inflammatory gene expression.
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Affiliation(s)
- A V Feoktistov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - S G Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - N V Soshnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Schaffer ED, Beerman I, de Cabo R, Brosh RM. Frontiers in aging special issue: DNA repair and interventions in aging perspective on "loss of epigenetic information as a cause of mammalian aging". FRONTIERS IN AGING 2023; 4:1199596. [PMID: 37475956 PMCID: PMC10354253 DOI: 10.3389/fragi.2023.1199596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The recently published article in Cell by the Sinclair lab and collaborators entitled "Loss of Epigenetic Information as a Cause of Mammalian Aging" [1] implicates heritable changes in gene expression as the basis for aging, a postulate consistent with the emerging information theory of aging. Sinclair's group and colleagues induced epigenetic changes, i.e., DNA and histone modifications, via double-strand breaks (DSBs) catalyzed by the I-Pol endonuclease at specific genomic loci. The genomic DNA breaks, introduced without inducing insertion or deletion mutations (indels) in a mouse model, were targeted to 19 non-coding regions and one region in ribosomal DNA (rDNA), the latter shown to not have a significant effect on the function or transcription of rDNA [1]. With that experimental model in place, the authors present experimental evidence supporting a model that epigenetic changes drive aging via this inducible DNA break mechanism. After demonstrating the phenotypic alterations of this accelerated aging, they attempt to reverse selective phenotypes by resetting the altered epigenetic landscape. Establishing a causal relationship between epigenetic changes and aging, and how this connection might be manipulated to overturn cellular features of aging, is provocative and merits further study.
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Lu H, Yang M, Zhou Q. Reprogramming transcription after DNA damage: recognition, response, repair, and restart. Trends Cell Biol 2022:S0962-8924(22)00261-6. [PMID: 36513571 DOI: 10.1016/j.tcb.2022.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Genome integrity is constantly challenged by endogenous and exogenous insults that cause DNA damage. To cope with these threats, cells have a surveillance mechanism, known as the DNA damage response (DDR), to repair any lesions. Although transcription has long been implicated in DNA repair, how transcriptional reprogramming is coordinated with the DDR is just beginning to be understood. In this review, we highlight recent advances in elucidating the molecular mechanisms underlying major transcriptional events, including RNA polymerase (Pol) II stalling and transcriptional silencing and recovery, which occur in response to DNA damage. Furthermore, we discuss how such transcriptional adaptation contributes to sensing and eliminating damaged DNA and how it can jeopardize genome integrity when it goes awry.
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Affiliation(s)
- Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Min Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiang Zhou
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong.
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