51
|
Yasuhara T, Kato R, Yamauchi M, Uchihara Y, Zou L, Miyagawa K, Shibata A. RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair. Cell Rep 2022; 38:110335. [PMID: 35108530 DOI: 10.1016/j.celrep.2022.110335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/08/2021] [Accepted: 01/12/2022] [Indexed: 01/15/2023] Open
Abstract
Single-stranded DNA (ssDNA) arising as an intermediate of cellular processes on DNA is a potential vulnerability of the genome unless it is appropriately protected. Recent evidence suggests that R-loops, consisting of ssDNA and DNA-RNA hybrids, can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. However, how the vulnerability of ssDNA in R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops, chromosome translocations, and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end joining dependent on BRCA1, Polθ, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.
Collapse
Affiliation(s)
- Takaaki Yasuhara
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
| | - Reona Kato
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Motohiro Yamauchi
- Hospital Campus Laboratory, Radioisotope Center, Central Institute of Radioisotope Science and Safety Management, Kyushu University, Fukuoka, Japan
| | - Yuki Uchihara
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Atsushi Shibata
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan.
| |
Collapse
|
52
|
Rasheed M, Asghar R, Firdoos S, Ahmad N, Nazir A, Ullah KM, Li N, Zhuang F, Chen Z, Deng Y. A Systematic Review of Circulatory microRNAs in Major Depressive Disorder: Potential Biomarkers for Disease Prognosis. Int J Mol Sci 2022; 23:1294. [PMID: 35163214 PMCID: PMC8835958 DOI: 10.3390/ijms23031294] [Citation(s) in RCA: 8] [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: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Major depressive disorder (MDD) is a neuropsychiatric disorder, which remains challenging to diagnose and manage due to its complex endophenotype. In this aspect, circulatory microRNAs (cimiRNAs) offer great potential as biomarkers and may provide new insights for MDD diagnosis. Therefore, we systemically reviewed the literature to explore various cimiRNAs contributing to MDD diagnosis and underlying molecular pathways. A comprehensive literature survey was conducted, employing four databases from 2012 to January 2021. Out of 1004 records, 157 reports were accessed for eligibility criteria, and 32 reports meeting our inclusion criteria were considered for in-silico analysis. This study identified 99 dysregulated cimiRNAs in MDD patients, out of which 20 cimiRNAs found in multiple reports were selected for in-silico analysis. KEGG pathway analysis indicated activation of ALS, MAPK, p53, and P13K-Akt signaling pathways, while gene ontology analysis demonstrated that most protein targets were associated with transcription. In addition, chromosomal location analysis showed clustering of dysregulated cimiRNAs at proximity 3p22-p21, 9q22.32, and 17q11.2, proposing their coregulation with specific transcription factors primarily involved in MDD physiology. Further analysis of transcription factor sites revealed the existence of HIF-1, REST, and TAL1 in most cimiRNAs. These transcription factors are proposed to target genes linked with MDD, hypothesizing that first-wave cimiRNA dysregulation may trigger the second wave of transcription-wide changes, altering the protein expressions of MDD-affected cells. Overall, this systematic review presented a list of dysregulated cimiRNAs in MDD, notably miR-24-3p, let 7a-5p, miR-26a-5p, miR135a, miR-425-3p, miR-132, miR-124 and miR-16-5p as the most prominent cimiRNAs. However, various constraints did not permit us to make firm conclusions on the clinical significance of these cimiRNAs, suggesting the need for more research on single blood compartment to identify the biomarker potential of consistently dysregulated cimiRNAs in MDD, as well as the therapeutic implications of these in-silico insights.
Collapse
Affiliation(s)
- Madiha Rasheed
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| | - Rabia Asghar
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| | - Sundas Firdoos
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| | - Nadeem Ahmad
- Department of Pharmacy, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan;
| | - Amina Nazir
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan Industry North Road 202, Jinan 250100, China;
| | - Kakar Mohib Ullah
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| | - Noumin Li
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| | - Fengyuan Zhuang
- School of Biology and Medical Engineering, Beihang University, Beijing 100191, China;
| | - Zixuan Chen
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| | - Yulin Deng
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (R.A.); (S.F.); (K.M.U.); (N.L.)
| |
Collapse
|
53
|
Alagia A, Ketley RF, Gullerova M. Proximity Ligation Assay for Detection of R-Loop Complexes upon DNA Damage. Methods Mol Biol 2022; 2528:289-303. [PMID: 35704199 DOI: 10.1007/978-1-0716-2477-7_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In situ Proximity Ligation Assay (PLA ) can be used to detect the close proximity (less than ~40 nm) of two biological molecules of interest in cells. Here we report the application of this method for the specific detection of R-loop interacting proteins and RNA modifications in close proximity to R-loops in non-damage and ionizing radiation (IR) induced DNA damage conditions.
Collapse
Affiliation(s)
- Adele Alagia
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ruth F Ketley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
54
|
Betlej G, Lewińska A, Adamczyk-Grochala J, Błoniarz D, Rzeszutek I, Wnuk M. Deficiency of TRDMT1 impairs exogenous RNA-based response and promotes retrotransposon activity during long-term culture of osteosarcoma cells. Toxicol In Vitro 2022; 80:105323. [DOI: 10.1016/j.tiv.2022.105323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 01/11/2023]
|
55
|
Haluck-Kangas A, Patel M, Paudel B, Vaidyanathan A, Murmann AE, Peter ME. DISE/6mer seed toxicity-a powerful anti-cancer mechanism with implications for other diseases. J Exp Clin Cancer Res 2021; 40:389. [PMID: 34893072 PMCID: PMC8662895 DOI: 10.1186/s13046-021-02177-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023] Open
Abstract
micro(mi)RNAs are short noncoding RNAs that through their seed sequence (pos. 2-7/8 of the guide strand) regulate cell function by targeting complementary sequences (seed matches) located mostly in the 3' untranslated region (3' UTR) of mRNAs. Any short RNA that enters the RNA induced silencing complex (RISC) can kill cells through miRNA-like RNA interference when its 6mer seed sequence (pos. 2-7 of the guide strand) has a G-rich nucleotide composition. G-rich seeds mediate 6mer Seed Toxicity by targeting C-rich seed matches in the 3' UTR of genes critical for cell survival. The resulting Death Induced by Survival gene Elimination (DISE) predominantly affects cancer cells but may contribute to cell death in other disease contexts. This review summarizes recent findings on the role of DISE/6mer Seed Tox in cancer; its therapeutic potential; its contribution to therapy resistance; its selectivity, and why normal cells are protected. In addition, we explore the connection between 6mer Seed Toxicity and aging in relation to cancer and certain neurodegenerative diseases.
Collapse
Affiliation(s)
- Ashley Haluck-Kangas
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Monal Patel
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Bidur Paudel
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Aparajitha Vaidyanathan
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Andrea E. Murmann
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Marcus E. Peter
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| |
Collapse
|
56
|
RNA-DNA hybrids regulate meiotic recombination. Cell Rep 2021; 37:110097. [PMID: 34879269 DOI: 10.1016/j.celrep.2021.110097] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/26/2021] [Accepted: 11/14/2021] [Indexed: 01/07/2023] Open
Abstract
RNA-DNA hybrids are often associated with genome instability and also function as a cellular regulator in many biological processes. In this study, we show that accumulated RNA-DNA hybrids cause multiple defects in budding yeast meiosis, including decreased sporulation efficiency and spore viability. Further analysis shows that these RNA-DNA hybrid foci colocalize with RPA/Rad51 foci on chromosomes. The efficient formation of RNA-DNA hybrid foci depends on Rad52 and ssDNA ends of meiotic DNA double-strand breaks (DSBs), and their number is correlated with DSB frequency. Interestingly, RNA-DNA hybrid foci and recombination foci show similar dynamics. The excessive accumulation of RNA-DNA hybrids around DSBs competes with Rad51/Dmc1, impairs homolog bias, and decreases crossover and noncrossover recombination. Furthermore, precocious removal of RNA-DNA hybrids by RNase H1 overexpression also impairs meiotic recombination similarly. Taken together, our results demonstrate that RNA-DNA hybrids form at ssDNA ends of DSBs to actively regulate meiotic recombination.
Collapse
|
57
|
Lin R, Zhong X, Zhou Y, Geng H, Hu Q, Huang Z, Hu J, Fu XD, Chen L, Chen JY. R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation. Nucleic Acids Res 2021; 50:D303-D315. [PMID: 34792163 PMCID: PMC8728142 DOI: 10.1093/nar/gkab1103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/28/2021] [Accepted: 10/21/2021] [Indexed: 11/13/2022] Open
Abstract
R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.
Collapse
Affiliation(s)
- Ruoyao Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiaoming Zhong
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Yongli Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Huichao Geng
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qingxi Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zhihao Huang
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| |
Collapse
|
58
|
Kemiha S, Poli J, Lin YL, Lengronne A, Pasero P. Toxic R-loops: Cause or consequence of replication stress? DNA Repair (Amst) 2021; 107:103199. [PMID: 34399314 DOI: 10.1016/j.dnarep.2021.103199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 01/08/2023]
Abstract
Transcription-replication conflicts (TRCs) represent a potential source of endogenous replication stress (RS) and genomic instability in eukaryotic cells but the mechanisms that underlie this instability remain poorly understood. Part of the problem could come from non-B DNA structures called R-loops, which are formed of a RNA:DNA hybrid and a displaced ssDNA loop. In this review, we discuss different scenarios in which R-loops directly or indirectly interfere with DNA replication. We also present other types of TRCs that may not depend on R-loops to impede fork progression. Finally, we discuss alternative models in which toxic RNA:DNA hybrids form at stalled forks as a consequence - but not a cause - of replication stress and interfere with replication resumption.
Collapse
Affiliation(s)
- Samira Kemiha
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France.
| |
Collapse
|
59
|
Kim A, Wang GG. R-loop and its functions at the regulatory interfaces between transcription and (epi)genome. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194750. [PMID: 34461314 PMCID: PMC8627470 DOI: 10.1016/j.bbagrm.2021.194750] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 01/08/2023]
Abstract
R-loop represents a prevalent and specialized chromatin structure critically involved in a wide range of biological processes. In particular, co-transcriptional R-loops, produced often due to RNA polymerase pausing or RNA biogenesis malfunction, can initiate molecular events to context-dependently regulate local gene transcription and crosstalk with chromatin modifications. Cellular "readers" of R-loops are identified, exerting crucial impacts on R-loop homeostasis and gene regulation. Mounting evidence also supports R-loop deregulation as a frequent, sometimes initiating, event during the development of human pathologies, notably cancer and neurological disorder. The purpose of this review is to cover recent advances in understanding the fundamentals of R-loop biology, which have started to unveil complex interplays of R-loops with factors involved in various biological processes such as transcription, RNA processing and epitranscriptomic modification (such as N6-methyladenosine), DNA damage sensing and repair, and epigenetic regulation.
Collapse
Affiliation(s)
- Arum Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
| |
Collapse
|
60
|
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.
Collapse
Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK;
| |
Collapse
|
61
|
Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
Collapse
Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
| |
Collapse
|
62
|
Guha S, Bhaumik SR. Transcription-coupled DNA double-strand break repair. DNA Repair (Amst) 2021; 109:103211. [PMID: 34883263 DOI: 10.1016/j.dnarep.2021.103211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 12/20/2022]
Abstract
The genomic DNA is constantly under attack by cellular and/or environmental factors. Fortunately, the cell is armed to safeguard its genome by various mechanisms such as nucleotide excision, base excision, mismatch and DNA double-strand break repairs. While these processes maintain the integrity of the genome throughout, DNA repair occurs preferentially faster at the transcriptionally active genes. Such transcription-coupled repair phenomenon plays important roles to maintain active genome integrity, failure of which would interfere with transcription, leading to an altered gene expression (and hence cellular pathologies/diseases). Among the various DNA damages, DNA double-strand breaks are quite toxic to the cells. If DNA double-strand break occurs at the active gene, it would interfere with transcription/gene expression, thus threatening cellular viability. Such DNA double-strand breaks are found to be repaired faster at the active gene in comparison to its inactive state or the inactive gene, thus supporting the existence of a new phenomenon of transcription-coupled DNA double-strand break repair. Here, we describe the advances of this repair process.
Collapse
Affiliation(s)
- Shalini Guha
- 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.
| |
Collapse
|
63
|
Molinaro C, Martoriati A, Cailliau K. Proteins from the DNA Damage Response: Regulation, Dysfunction, and Anticancer Strategies. Cancers (Basel) 2021; 13:3819. [PMID: 34359720 PMCID: PMC8345162 DOI: 10.3390/cancers13153819] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells respond to genotoxic stress through a series of complex protein pathways called DNA damage response (DDR). These monitoring mechanisms ensure the maintenance and the transfer of a correct genome to daughter cells through a selection of DNA repair, cell cycle regulation, and programmed cell death processes. Canonical or non-canonical DDRs are highly organized and controlled to play crucial roles in genome stability and diversity. When altered or mutated, the proteins in these complex networks lead to many diseases that share common features, and to tumor formation. In recent years, technological advances have made it possible to benefit from the principles and mechanisms of DDR to target and eliminate cancer cells. These new types of treatments are adapted to the different types of tumor sensitivity and could benefit from a combination of therapies to ensure maximal efficiency.
Collapse
Affiliation(s)
| | | | - Katia Cailliau
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France; (C.M.); (A.M.)
| |
Collapse
|
64
|
Jia N, Guo C, Nakazawa Y, van den Heuvel D, Luijsterburg MS, Ogi T. Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders. DNA Repair (Amst) 2021; 106:103192. [PMID: 34358806 DOI: 10.1016/j.dnarep.2021.103192] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 12/15/2022]
Abstract
Transcription-blocking DNA lesions (TBLs) in genomic DNA are triggered by a wide variety of DNA-damaging agents. Such lesions cause stalling of elongating RNA polymerase II (RNA Pol II) enzymes and fully block transcription when unresolved. The toxic impact of DNA damage on transcription progression is commonly referred to as transcription stress. In response to RNA Pol II stalling, cells activate and employ transcription-coupled repair (TCR) machineries to repair cytotoxic TBLs and resume transcription. Increasing evidence indicates that the modification and processing of stalled RNA Pol II is an integral component of the cellular response to and the repair of TBLs. If TCR pathways fail, the prolonged stalling of RNA Pol II will impede global replication and transcription as well as block the access of other DNA repair pathways that may act upon the TBL. Consequently, such prolonged stalling will trigger profound genome instability and devastating clinical features. In this review, we will discuss the mechanisms by which various types of TBLs are repaired by distinct TCR pathways and how RNA Pol II processing is regulated during these processes. We will also discuss the clinical consequences of transcription stress and genotype-phenotype correlations of related TCR-deficiency disorders.
Collapse
Affiliation(s)
- Nan Jia
- Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
| |
Collapse
|
65
|
Visser H, Thomas AD. MicroRNAs, damage levels, and DNA damage response control. Trends Genet 2021; 37:963-965. [PMID: 34281698 DOI: 10.1016/j.tig.2021.06.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
DNA damage-inducible miRNAs are likely to be functional in the DNA damage response. This response can elicit damage resolution and cell survival or apoptosis. The current, albeit incomplete, picture suggests that miRNAs can affect cell fate via modulation of key response proteins, but the question is, who's in charge?
Collapse
Affiliation(s)
- Hartwig Visser
- Centre for Research in Bioscience, University of the West of England, Bristol, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Adam D Thomas
- Centre for Research in Bioscience, University of the West of England, Bristol, Coldharbour Lane, Bristol, BS16 1QY, UK.
| |
Collapse
|
66
|
Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet 2021; 37:973-985. [PMID: 34238592 DOI: 10.1016/j.tig.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Defective DNA replication, known as 'replication stress', is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.
Collapse
Affiliation(s)
- Charlotte Audoynaud
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
| |
Collapse
|
67
|
Wang W, Li K, Yang Z, Hou Q, Zhao WW, Sun Q. RNase H1C collaborates with ssDNA binding proteins WHY1/3 and recombinase RecA1 to fulfill the DNA damage repair in Arabidopsis chloroplasts. Nucleic Acids Res 2021; 49:6771-6787. [PMID: 34133716 PMCID: PMC8266629 DOI: 10.1093/nar/gkab479] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/25/2021] [Accepted: 05/19/2021] [Indexed: 12/28/2022] Open
Abstract
Proper repair of damaged DNA is crucial for genetic integrity and organismal survival. As semi-autonomous organelles, plastids have their own genomes whose integrity must be preserved. Several factors have been shown to participate in plastid DNA damage repair; however, the underlying mechanism remains unclear. Here, we elucidate a mechanism of homologous recombination (HR) repair in chloroplasts that involves R-loops. We find that the recombinase RecA1 forms filaments in chloroplasts during HR repair, but aggregates as puncta when RNA:DNA hybrids accumulate. ssDNA-binding proteins WHY1/3 and chloroplast RNase H1 AtRNH1C are recruited to the same genomic sites to promote HR repair. Depletion of AtRNH1C or WHY1/3 significantly suppresses the binding of RNA polymerase to the damaged DNA, thus reducing HR repair and modulating microhomology-mediated double-strand break repair. Furthermore, we show that DNA polymerase IB works with AtRNH1C genetically to complete the DNA damage repair process. This study reveals the positive role of R-loops in facilitating the activities of WHY1/3 and RecA1, which in turn secures HR repair and organellar development.
Collapse
Affiliation(s)
- Wenjie Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Zhuo Yang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Quancan Hou
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei W Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| |
Collapse
|
68
|
Ortega P, Mérida-Cerro JA, Rondón AG, Gómez-González B, Aguilera A. DNA-RNA hybrids at DSBs interfere with repair by homologous recombination. eLife 2021; 10:e69881. [PMID: 34236317 PMCID: PMC8289408 DOI: 10.7554/elife.69881] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand breaks (DSBs) are the most harmful DNA lesions and their repair is crucial for cell viability and genome integrity. The readout of DSB repair may depend on whether DSBs occur at transcribed versus non-transcribed regions. Some studies have postulated that DNA-RNA hybrids form at DSBs to promote recombinational repair, but others have challenged this notion. To directly assess whether hybrids formed at DSBs promote or interfere with the recombinational repair, we have used plasmid and chromosomal-based systems for the analysis of DSB-induced recombination in Saccharomyces cerevisiae. We show that, as expected, DNA-RNA hybrid formation is stimulated at DSBs. In addition, mutations that promote DNA-RNA hybrid accumulation, such as hpr1∆ and rnh1∆ rnh201∆, cause high levels of plasmid loss when DNA breaks are induced at sites that are transcribed. Importantly, we show that high levels or unresolved DNA-RNA hybrids at the breaks interfere with their repair by homologous recombination. This interference is observed for both plasmid and chromosomal recombination and is independent of whether the DSB is generated by endonucleolytic cleavage or by DNA replication. These data support a model in which DNA-RNA hybrids form fortuitously at DNA breaks during transcription and need to be removed to allow recombinational repair, rather than playing a positive role.
Collapse
Affiliation(s)
- Pedro Ortega
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de OlavideSevilleSpain
| | - José Antonio Mérida-Cerro
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de OlavideSevilleSpain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de OlavideSevilleSpain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de OlavideSevilleSpain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de OlavideSevilleSpain
| |
Collapse
|
69
|
Fijen C, Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021; 105:103170. [PMID: 34256335 DOI: 10.1016/j.dnarep.2021.103170] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Formation of biomolecular condensates is increasingly recognized as a mechanism employed by cells to deal with stress and to optimize enzymatic reactions. Recent studies have characterized several DNA repair foci as phase-separated condensates, behaving like liquid droplets. Concomitantly, the apparent importance of long non-coding RNAs and RNA-binding proteins for the repair of double-strand breaks has raised many questions about their exact contribution to the repair process. Here we discuss how RNA molecules can participate in condensate formation and how RNA-binding proteins can act as molecular scaffolds. We furthermore summarize our current knowledge about how properties of condensates can influence the choice of repair pathway (homologous recombination or non-homologous end joining) and identify the open questions in this field of emerging importance.
Collapse
Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| |
Collapse
|
70
|
Non-canonical function of DGCR8 in DNA double-strand break repair signaling and tumor radioresistance. Nat Commun 2021; 12:4033. [PMID: 34188037 PMCID: PMC8242032 DOI: 10.1038/s41467-021-24298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), repair proteins are recruited to the damaged sites. Ubiquitin signaling plays a critical role in coordinating protein recruitment during the DNA damage response. Here, we find that the microRNA biogenesis factor DGCR8 promotes tumor resistance to X-ray radiation independently of its Drosha-binding ability. Upon radiation, the kinase ATM and the deubiquitinase USP51 mediate the activation and stabilization of DGCR8 through phosphorylation and deubiquitination. Specifically, radiation-induced ATM-dependent phosphorylation of DGCR8 at serine 677 facilitates USP51 to bind, deubiquitinate, and stabilize DGCR8, which leads to the recruitment of DGCR8 and DGCR8’s binding partner RNF168 to MDC1 and RNF8 at DSBs. This, in turn, promotes ubiquitination of histone H2A, repair of DSBs, and radioresistance. Altogether, these findings reveal the non-canonical function of DGCR8 in DSB repair and suggest that radiation treatment may result in therapy-induced tumor radioresistance through ATM- and USP51-mediated activation and upregulation of DGCR8. The molecular mechanisms underlying cancer cell radioresistance need to be elucidated. In this study, the authors show that the microRNA biogenesis factor DGCR8 is stabilized by USP51 and ATM upon irradiation and by consequence it promotes the repair of DNA double-strand breaks and radioresistance by recruiting RNF168 to sites of damage.
Collapse
|
71
|
Ngo GHP, Grimstead JW, Baird DM. UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair. Nat Commun 2021; 12:3849. [PMID: 34158508 PMCID: PMC8219777 DOI: 10.1038/s41467-021-24201-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome. The induction of DNA-RNA hybrids strongly affects the repair of these DSBs, but the nature of these structures and how they are formed remain poorly understood. Here we provide evidence that R loops, three-stranded structures containing DNA-RNA hybrids and the displaced single-stranded DNA (ssDNA) can form at sub-telomeric DSBs. These R loops are generated independently of DNA resection but are induced alongside two-stranded DNA-RNA hybrids that form on ssDNA generated by DNA resection. We further identified UPF1, an RNA/DNA helicase, as a crucial factor that drives the formation of these R loops and DNA-RNA hybrids to stimulate DNA resection, homologous recombination, microhomology-mediated end joining and DNA damage checkpoint activation. Our data show that R loops and DNA-RNA hybrids are actively generated at DSBs to facilitate DNA repair.
Collapse
Affiliation(s)
- Greg H P Ngo
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Julia W Grimstead
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK.
| |
Collapse
|
72
|
Chang A, Liu L, Ashby JM, Wu D, Chen Y, O'Neill SS, Huang S, Wang J, Wang G, Cheng D, Tan X, Petty WJ, Pasche BC, Xiang R, Zhang W, Sun P. Recruitment of KMT2C/MLL3 to DNA Damage Sites Mediates DNA Damage Responses and Regulates PARP Inhibitor Sensitivity in Cancer. Cancer Res 2021; 81:3358-3373. [PMID: 33853832 PMCID: PMC8260460 DOI: 10.1158/0008-5472.can-21-0688] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
When recruited to promoters, histone 3 lysine 4 (H3K4) methyltransferases KMT2 (KMT2A-D) activate transcription by opening chromatin through H3K4 methylation. Here, we report that KMT2 mutations occur frequently in non-small cell lung cancer (NSCLC) and are associated with high mutation loads and poor survival. KMT2C regulated DNA damage responses (DDR) through direct recruitment to DNA damage sites by Ago2 and small noncoding DNA damage response RNA, where it mediates H3K4 methylation, chromatin relaxation, secondary recruitment of DDR factors, and amplification of DDR signals along chromatin. Furthermore, by disrupting homologous recombination (HR)-mediated DNA repair, KMT2C/D mutations sensitized NSCLC to Poly(ADP-ribose) polymerase inhibitors (PARPi), whose efficacy is unclear in NSCLC due to low BRCA1/2 mutation rates. These results demonstrate a novel, transcription-independent role of KMT2C in DDR and identify high-frequency KMT2C/D mutations as much-needed biomarkers for PARPi therapies in NSCLC and other cancers with infrequent BRCA1/2 mutations. SIGNIFICANCE: This study uncovers a critical role for KMT2C in DDR via direct recruitment to DNA damage sites, identifying high-frequency KMT2C/D mutations as biomarkers for response to PARP inhibition in cancer.
Collapse
MESH Headings
- Animals
- Apoptosis
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Cell Proliferation
- DNA Damage
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Homologous Recombination
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Nude
- Mutation
- Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
- Prognosis
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Antao Chang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
- Nankai University School of Medicine, Tianjin, China
| | - Liang Liu
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Justin M Ashby
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Dan Wu
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Yanan Chen
- Nankai University School of Medicine, Tianjin, China
| | - Stacey S O'Neill
- Department of Pathology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Shan Huang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
- Nankai University School of Medicine, Tianjin, China
| | - Juan Wang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
- Nankai University School of Medicine, Tianjin, China
| | - Guanwen Wang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
- Nankai University School of Medicine, Tianjin, China
| | - Dongmei Cheng
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Xiaoming Tan
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
- Department of Respiratory Disease, South Campus, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - W J Petty
- Department of Internal Medicine, Division of Hematology and Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Boris C Pasche
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Rong Xiang
- Nankai University School of Medicine, Tianjin, China
| | - Wei Zhang
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina
| | - Peiqing Sun
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Medical Center Blvd, Winston-Salem, North Carolina.
| |
Collapse
|
73
|
Dettori LG, Torrejon D, Chakraborty A, Dutta A, Mohamed M, Papp C, Kuznetsov VA, Sung P, Feng W, Bah A. A Tale of Loops and Tails: The Role of Intrinsically Disordered Protein Regions in R-Loop Recognition and Phase Separation. Front Mol Biosci 2021; 8:691694. [PMID: 34179096 PMCID: PMC8222781 DOI: 10.3389/fmolb.2021.691694] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
R-loops are non-canonical, three-stranded nucleic acid structures composed of a DNA:RNA hybrid, a displaced single-stranded (ss)DNA, and a trailing ssRNA overhang. R-loops perform critical biological functions under both normal and disease conditions. To elucidate their cellular functions, we need to understand the mechanisms underlying R-loop formation, recognition, signaling, and resolution. Previous high-throughput screens identified multiple proteins that bind R-loops, with many of these proteins containing folded nucleic acid processing and binding domains that prevent (e.g., topoisomerases), resolve (e.g., helicases, nucleases), or recognize (e.g., KH, RRMs) R-loops. However, a significant number of these R-loop interacting Enzyme and Reader proteins also contain long stretches of intrinsically disordered regions (IDRs). The precise molecular and structural mechanisms by which the folded domains and IDRs synergize to recognize and process R-loops or modulate R-loop-mediated signaling have not been fully explored. While studying one such modular R-loop Reader, the Fragile X Protein (FMRP), we unexpectedly discovered that the C-terminal IDR (C-IDR) of FMRP is the predominant R-loop binding site, with the three N-terminal KH domains recognizing the trailing ssRNA overhang. Interestingly, the C-IDR of FMRP has recently been shown to undergo spontaneous Liquid-Liquid Phase Separation (LLPS) assembly by itself or in complex with another non-canonical nucleic acid structure, RNA G-quadruplex. Furthermore, we have recently shown that FMRP can suppress persistent R-loops that form during transcription, a process that is also enhanced by LLPS via the assembly of membraneless transcription factories. These exciting findings prompted us to explore the role of IDRs in R-loop processing and signaling proteins through a comprehensive bioinformatics and computational biology study. Here, we evaluated IDR prevalence, sequence composition and LLPS propensity for the known R-loop interactome. We observed that, like FMRP, the majority of the R-loop interactome, especially Readers, contains long IDRs that are highly enriched in low complexity sequences with biased amino acid composition, suggesting that these IDRs could directly interact with R-loops, rather than being “mere flexible linkers” connecting the “functional folded enzyme or binding domains”. Furthermore, our analysis shows that several proteins in the R-loop interactome are either predicted to or have been experimentally demonstrated to undergo LLPS or are known to be associated with phase separated membraneless organelles. Thus, our overall results present a thought-provoking hypothesis that IDRs in the R-loop interactome can provide a functional link between R-loop recognition via direct binding and downstream signaling through the assembly of LLPS-mediated membrane-less R-loop foci. The absence or dysregulation of the function of IDR-enriched R-loop interactors can potentially lead to severe genomic defects, such as the widespread R-loop-mediated DNA double strand breaks that we recently observed in Fragile X patient-derived cells.
Collapse
Affiliation(s)
- Leonardo G Dettori
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Diego Torrejon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Mohamed Mohamed
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Csaba Papp
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States.,Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Vladimir A Kuznetsov
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States.,Bioinformatics Institute, ASTAR Biomedical Institutes, Singapore, Singapore
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| |
Collapse
|
74
|
Palancade B, Rothstein R. The Ultimate (Mis)match: When DNA Meets RNA. Cells 2021; 10:cells10061433. [PMID: 34201169 PMCID: PMC8227541 DOI: 10.3390/cells10061433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/20/2022] Open
Abstract
RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. We summarize how in vivo and in vitro experiments support the contribution of DNA polymerases and homologous recombination proteins in the formation of RNA-containing structures, and we discuss the role of DNA repair enzymes in their removal. The diversity of pathways that are thus affected by RNA insertions likely reflects the ancestral function of RNA molecules in genome maintenance and transmission.
Collapse
Affiliation(s)
- Benoit Palancade
- Institut Jacques Monod, Université de Paris, CNRS, F-75006 Paris, France
- Correspondence: (B.P.); (R.R.)
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Correspondence: (B.P.); (R.R.)
| |
Collapse
|
75
|
Perfecting DNA double-strand break repair on transcribed chromatin. Essays Biochem 2021; 64:705-719. [PMID: 32309851 DOI: 10.1042/ebc20190094] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
Timely repair of DNA double-strand break (DSB) entails coordination with the local higher order chromatin structure and its transaction activities, including transcription. Recent studies are uncovering how DSBs trigger transient suppression of nearby transcription to permit faithful DNA repair, failing of which leads to elevated chromosomal aberrations and cell hypersensitivity to DNA damage. Here, we summarize the molecular bases for transcriptional control during DSB metabolism, and discuss how the exquisite coordination between the two DNA-templated processes may underlie maintenance of genome stability and cell homeostasis.
Collapse
|
76
|
Senataxin Ortholog Sen1 Limits DNA:RNA Hybrid Accumulation at DNA Double-Strand Breaks to Control End Resection and Repair Fidelity. Cell Rep 2021; 31:107603. [PMID: 32375052 DOI: 10.1016/j.celrep.2020.107603] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/07/2020] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
An important but still enigmatic function of DNA:RNA hybrids is their role in DNA double-strand break (DSB) repair. Here, we show that Sen1, the budding yeast ortholog of the human helicase Senataxin, is recruited at an HO endonuclease-induced DSB and limits the local accumulation of DNA:RNA hybrids. In the absence of Sen1, hybrid accumulation proximal to the DSB promotes increased binding of the Ku70-80 (KU) complex at the break site, mutagenic non-homologous end joining (NHEJ), micro-homology-mediated end joining (MMEJ), and chromosome translocations. We also show that homology-directed recombination (HDR) by gene conversion is mostly proficient in sen1 mutants after single DSB. However, in the absence of Sen1, DNA:RNA hybrids, Mre11, and Dna2 initiate resection through a non-canonical mechanism. We propose that this resection mechanism through local DNA:RNA hybrids acts as a backup to prime HDR when canonical pathways are altered, but at the expense of genome integrity.
Collapse
|
77
|
Lee SR, Pollard DA, Galati DF, Kelly ML, Miller B, Mong C, Morris MN, Roberts-Nygren K, Kapler GM, Zinkgraf M, Dang HQ, Branham E, Sasser J, Tessier E, Yoshiyama C, Matsumoto M, Turman G. Disruption of a ∼23-24 nucleotide small RNA pathway elevates DNA damage responses in Tetrahymena thermophila. Mol Biol Cell 2021; 32:1335-1346. [PMID: 34010017 PMCID: PMC8694037 DOI: 10.1091/mbc.e20-10-0631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endogenous RNA interference (RNAi) pathways regulate a wide range of cellular processes in diverse eukaryotes, yet in the ciliated eukaryote, Tetrahymena thermophila, the cellular purpose of RNAi pathways that generate ∼23–24 nucleotide (nt) small (s)RNAs has remained unknown. Here, we investigated the phenotypic and gene expression impacts on vegetatively growing cells when genes involved in ∼23–24 nt sRNA biogenesis are disrupted. We observed slower proliferation and increased expression of genes involved in DNA metabolism and chromosome organization and maintenance in sRNA biogenesis mutants RSP1Δ, RDN2Δ, and RDF2Δ. In addition, RSP1Δ and RDN2Δ cells frequently exhibited enlarged chromatin extrusion bodies, which are nonnuclear, DNA-containing structures that may be akin to mammalian micronuclei. Expression of homologous recombination factor Rad51 was specifically elevated in RSP1Δ and RDN2Δ strains, with Rad51 and double-stranded DNA break marker γ-H2A.X localized to discrete macronuclear foci. In addition, an increase in Rad51 and γ-H2A.X foci was also found in knockouts of TWI8, a macronucleus-localized PIWI protein. Together, our findings suggest that an evolutionarily conserved role for RNAi pathways in maintaining genome integrity may be extended even to the early branching eukaryotic lineage that gave rise to Tetrahymena thermophila.
Collapse
Affiliation(s)
- Suzanne R Lee
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Daniel A Pollard
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Domenico F Galati
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Megan L Kelly
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Brian Miller
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Christina Mong
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Megan N Morris
- Biology Department, Western Washington University, Bellingham, WA 98225
| | | | - Geoffrey M Kapler
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Matthew Zinkgraf
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Hung Q Dang
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Erica Branham
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Jason Sasser
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Erin Tessier
- Biology Department, Western Washington University, Bellingham, WA 98225
| | | | - Maya Matsumoto
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Gaea Turman
- Biology Department, Western Washington University, Bellingham, WA 98225
| |
Collapse
|
78
|
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.
Collapse
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
| |
Collapse
|
79
|
Abbasi S, Parmar G, Kelly RD, Balasuriya N, Schild-Poulter C. The Ku complex: recent advances and emerging roles outside of non-homologous end-joining. Cell Mol Life Sci 2021; 78:4589-4613. [PMID: 33855626 PMCID: PMC11071882 DOI: 10.1007/s00018-021-03801-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022]
Abstract
Since its discovery in 1981, the Ku complex has been extensively studied under multiple cellular contexts, with most work focusing on Ku in terms of its essential role in non-homologous end-joining (NHEJ). In this process, Ku is well-known as the DNA-binding subunit for DNA-PK, which is central to the NHEJ repair process. However, in addition to the extensive study of Ku's role in DNA repair, Ku has also been implicated in various other cellular processes including transcription, the DNA damage response, DNA replication, telomere maintenance, and has since been studied in multiple contexts, growing into a multidisciplinary point of research across various fields. Some advances have been driven by clarification of Ku's structure, including the original Ku crystal structure and the more recent Ku-DNA-PKcs crystallography, cryogenic electron microscopy (cryoEM) studies, and the identification of various post-translational modifications. Here, we focus on the advances made in understanding the Ku heterodimer outside of non-homologous end-joining, and across a variety of model organisms. We explore unique structural and functional aspects, detail Ku expression, conservation, and essentiality in different species, discuss the evidence for its involvement in a diverse range of cellular functions, highlight Ku protein interactions and recent work concerning Ku-binding motifs, and finally, we summarize the clinical Ku-related research to date.
Collapse
Affiliation(s)
- Sanna Abbasi
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Gursimran Parmar
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Rachel D Kelly
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Nileeka Balasuriya
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute and Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5B7, Canada.
| |
Collapse
|
80
|
Salifou K, Burnard C, Basavarajaiah P, Grasso G, Helsmoortel M, Mac V, Depierre D, Franckhauser C, Beyne E, Contreras X, Dejardin J, Rouquier S, Cuvier O, Kiernan R. Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. SCIENCE ADVANCES 2021; 7:7/21/eabb2947. [PMID: 34020942 PMCID: PMC8139584 DOI: 10.1126/sciadv.abb2947] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/31/2021] [Indexed: 05/05/2023]
Abstract
MRN-MDC1 plays a central role in the DNA damage response (DDR) and repair. Using proteomics of isolated chromatin fragments, we identified DDR factors, such as MDC1, among those highly associating with a genomic locus upon transcriptional activation. Purification of MDC1 in the absence of exogenous DNA damage revealed interactions with factors involved in gene expression and RNA processing, in addition to DDR factors. ChIP-seq showed that MRN subunits, MRE11 and NBS1, colocalized throughout the genome, notably at TSSs and bodies of actively transcribing genes, which was dependent on the RNAPII transcriptional complex rather than transcription per se. Depletion of MRN increased RNAPII abundance at MRE11/NBS1-bound genes. Prolonged MRE11 or NBS1 depletion induced single-nucleotide polymorphisms across actively transcribing MRN target genes. These data suggest that association of MRN with the transcriptional machinery constitutively scans active genes for transcription-induced DNA damage to preserve the integrity of the coding genome.
Collapse
Affiliation(s)
- Kader Salifou
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Callum Burnard
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Poornima Basavarajaiah
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Giuseppa Grasso
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Marion Helsmoortel
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Victor Mac
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - David Depierre
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Céline Franckhauser
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Emmanuelle Beyne
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Xavier Contreras
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Jérôme Dejardin
- CNRS-UMR 9002, IGH/University of Montpellier, Biology of Repeated Sequences Lab, 34396, France
| | - Sylvie Rouquier
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France
| | - Olivier Cuvier
- Center of Integrative Biology (CBI) CNRS/Université de Toulouse (UMR 5077), 31000, France
| | - Rosemary Kiernan
- CNRS-UMR 9002, Institute of Human Genetics (IGH)/University of Montpellier, Gene Regulation Lab, 34396, France.
| |
Collapse
|
81
|
Jimeno S, Balestra FR, Huertas P. The Emerging Role of RNA Modifications in DNA Double-Strand Break Repair. Front Mol Biosci 2021; 8:664872. [PMID: 33996910 PMCID: PMC8116738 DOI: 10.3389/fmolb.2021.664872] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/08/2021] [Indexed: 11/14/2022] Open
Abstract
The correct repair of DNA double-strand breaks is essential for maintaining the stability of the genome, thus ensuring the survival and fitness of any living organism. Indeed, the repair of these lesions is a complicated affair, in which several pathways compete for the DNA ends in a complex balance. Thus, the fine-tuning of the DNA double-strand break repair pathway choice relies on the different regulatory layers that respond to environmental cues. Among those different tiers of regulation, RNA modifications have just emerged as a promising field.
Collapse
Affiliation(s)
- Sonia Jimeno
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Fernando R. Balestra
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Pablo Huertas
- Departamento de Genética, Universidad de Sevilla, Seville, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| |
Collapse
|
82
|
Ren J, Wu Y, Wang Y, Zhao Y, Li Y, Hao S, Lin L, Zhang S, Xu X, Wang H. CtIP suppresses primary microRNA maturation and promotes metastasis of colon cancer cells in a xenograft mouse model. J Biol Chem 2021; 296:100707. [PMID: 33901493 PMCID: PMC8164041 DOI: 10.1016/j.jbc.2021.100707] [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: 11/26/2020] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022] Open
Abstract
miRNAs are important regulators of eukaryotic gene expression. The post-transcriptional maturation of miRNAs is controlled by the Drosha-DiGeorge syndrome critical region gene 8 (DGCR8) microprocessor. Dysregulation of miRNA biogenesis has been implicated in the pathogenesis of human diseases, including cancers. C-terminal-binding protein-interacting protein (CtIP) is a well-known DNA repair factor that promotes the processing of DNA double-strand break (DSB) to initiate homologous recombination-mediated DSB repair. However, it was unclear whether CtIP has other unknown cellular functions. Here, we aimed to uncover the roles of CtIP in miRNA maturation and cancer cell metastasis. We found that CtIP is a potential regulatory factor that suppresses the processing of miRNA primary transcripts (pri-miRNA). CtIP directly bound to both DGCR8 and pri-miRNAs through a conserved Sae2-like domain, reduced the binding of Drosha to DGCR8 and pri-miRNA substrate, and inhibited processing activity of Drosha complex. CtIP depletion significantly increased the expression levels of a subset of mature miRNAs, including miR-302 family members that are associated with tumor progression and metastasis in several cancer types. We also found that CtIP-inhibited miRNAs, such as miR-302 family members, are not crucial for DSB repair. However, increase of miR-302b levels or loss of CtIP function severely suppressed human colon cancer cell line tumor cell metastasis in a mouse xenograft model. These studies reveal a previously unrecognized mechanism of CtIP in miRNA processing and tumor metastasis that represents a new function of CtIP in cancer.
Collapse
Affiliation(s)
- Jianping Ren
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yan Wu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Ya Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Yuqin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Youhang Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Lixiu Lin
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Shuyuan Zhang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, China Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing, China.
| |
Collapse
|
83
|
Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
Collapse
|
84
|
Long Q, Liu Z, Gullerova M. Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks. Front Mol Biosci 2021; 8:655786. [PMID: 33959637 PMCID: PMC8096065 DOI: 10.3389/fmolb.2021.655786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022] Open
Abstract
Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.
Collapse
Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
85
|
Almozyan S, Coulton J, Babaei-Jadidi R, Nateri AS. FLYWCH1, a Multi-Functional Zinc Finger Protein Contributes to the DNA Repair Pathway. Cells 2021; 10:cells10040889. [PMID: 33924684 PMCID: PMC8069811 DOI: 10.3390/cells10040889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Over recent years, several Cys2-His2 (C2H2) domain-containing proteins have emerged as critical players in repairing DNA-double strand breaks. Human FLYWCH1 is a newly characterised nuclear transcription factor with (C2H2)-type zinc-finger DNA-binding domains. Yet, our knowledge about FLYWCH1 is still in its infancy. This study explores the expression, role and regulation of FLYWCH1 in the context of DNA damage and repair. We provide evidence suggesting a potential contribution of FLYWCH1 in facilitating the recruitment of DNA-damage response proteins (DDRPs). We found that FLYWCH1 colocalises with γH2AX in normal fibroblasts and colorectal cancer (CRC) cell lines. Importantly, our results showed that enforced expression of FLYWCH1 induces the expression of γH2AX, ATM and P53 proteins. Using an ATM-knockout (ATMKO) model, we indicated that FLYWCH1 mediates the phosphorylation of H2AX (Ser139) independently to ATM expression. On the other hand, the induction of DNA damage using UV-light induces the endogenous expression of FLYWCH1. Conversely, cisplatin treatment reduces the endogenous level of FLYWCH1 in CRC cell lines. Together, our findings uncover a novel FLYWCH1/H2AX phosphorylation axis in steady-state conditions and during the induction of the DNA-damage response (DDR). Although the role of FLYWCH1 within the DDR machinery remains largely uncharacterised and poorly understood, we here report for the first-time findings that implicate FLYWCH1 as a potential participant in the DNA damage response signaling pathways.
Collapse
Affiliation(s)
- Sheema Almozyan
- Cancer Genetics & Stem Cell Group, BioDiscovery Institute, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (S.A.); (J.C.)
| | - James Coulton
- Cancer Genetics & Stem Cell Group, BioDiscovery Institute, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (S.A.); (J.C.)
| | - Roya Babaei-Jadidi
- Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK;
| | - Abdolrahman S. Nateri
- Cancer Genetics & Stem Cell Group, BioDiscovery Institute, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK; (S.A.); (J.C.)
- Correspondence:
| |
Collapse
|
86
|
R-loops as Janus-faced modulators of DNA repair. Nat Cell Biol 2021; 23:305-313. [PMID: 33837288 DOI: 10.1038/s41556-021-00663-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 02/01/2023]
Abstract
R-loops are non-B DNA structures with intriguing dual consequences for gene expression and genome stability. In addition to their recognized roles in triggering DNA double-strand breaks (DSBs), R-loops have recently been demonstrated to accumulate in cis to DSBs, especially those induced in transcriptionally active loci. In this Review, we discuss whether R-loops actively participate in DSB repair or are detrimental by-products that must be removed to avoid genome instability.
Collapse
|
87
|
Cabrini M, Roncador M, Galbiati A, Cipolla L, Maffia A, Iannelli F, Sabbioneda S, d'Adda di Fagagna F, Francia S. DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end joining. J Cell Sci 2021; 134:jcs.249706. [PMID: 33558311 PMCID: PMC8015226 DOI: 10.1242/jcs.249706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/23/2021] [Indexed: 11/20/2022] Open
Abstract
The DNA damage response (DDR) is the signaling cascade that recognizes DNA double-strand breaks (DSBs) and promotes their resolution via the DNA repair pathways of non-homologous end joining (NHEJ) or homologous recombination (HR). We and others have shown that DDR activation requires DROSHA; however, whether DROSHA exerts its functions by associating with damage sites, what controls its recruitment, and how DROSHA influences DNA repair remains poorly understood. Here, we show that DROSHA associates with DSBs independently of transcription. Neither H2AX, nor ATM or DNA-PK kinase activities are required for recruitment of DROSHA to break sites. Rather, DROSHA interacts with RAD50, and inhibition of the MRN complex by mirin treatment abolishes this interaction. MRN complex inactivation by RAD50 knockdown or mirin treatment prevents DROSHA recruitment to DSBs and, as a consequence, also prevents 53BP1 (also known as TP53BP1) recruitment. During DNA repair, DROSHA inactivation reduces NHEJ and boosts HR frequency. Indeed, DROSHA knockdown also increases the association of downstream HR factors such as RAD51 to DNA ends. Overall, our results demonstrate that DROSHA is recruited at DSBs by the MRN complex and directs DNA repair towards NHEJ.
Collapse
Affiliation(s)
- Matteo Cabrini
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy.,IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Marco Roncador
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Alessandro Galbiati
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Lina Cipolla
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Antonio Maffia
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Fabio Iannelli
- IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Fabrizio d'Adda di Fagagna
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy .,IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| | - Sofia Francia
- Istituto di Genetica Molecolare, CNR - Consiglio Nazionale delle Ricerche, Pavia 27100, Italy .,IFOM Foundation - The FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
| |
Collapse
|
88
|
Sessa G, Gómez-González B, Silva S, Pérez-Calero C, Beaurepere R, Barroso S, Martineau S, Martin C, Ehlén Å, Martínez JS, Lombard B, Loew D, Vagner S, Aguilera A, Carreira A. BRCA2 promotes DNA-RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repair‡. EMBO J 2021; 40:e106018. [PMID: 33634895 DOI: 10.15252/embj.2020106018] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
The BRCA2 tumor suppressor is a DNA double-strand break (DSB) repair factor essential for maintaining genome integrity. BRCA2-deficient cells spontaneously accumulate DNA-RNA hybrids, a known source of genome instability. However, the specific role of BRCA2 on these structures remains poorly understood. Here we identified the DEAD-box RNA helicase DDX5 as a BRCA2-interacting protein. DDX5 associates with DNA-RNA hybrids that form in the vicinity of DSBs, and this association is enhanced by BRCA2. Notably, BRCA2 stimulates the DNA-RNA hybrid-unwinding activity of DDX5 helicase. An impaired BRCA2-DDX5 interaction, as observed in cells expressing the breast cancer variant BRCA2-T207A, reduces the association of DDX5 with DNA-RNA hybrids, decreases the number of RPA foci, and alters the kinetics of appearance of RAD51 foci upon irradiation. Our findings are consistent with DNA-RNA hybrids constituting an impediment for the repair of DSBs by homologous recombination and reveal BRCA2 and DDX5 as active players in their removal.
Collapse
Affiliation(s)
- Gaetana Sessa
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Belén Gómez-González
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, University of Seville, Seville, Spain
| | - Sonia Silva
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, University of Seville, Seville, Spain
| | - Carmen Pérez-Calero
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, University of Seville, Seville, Spain
| | - Romane Beaurepere
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Sonia Barroso
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, University of Seville, Seville, Spain
| | - Sylvain Martineau
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Charlotte Martin
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Åsa Ehlén
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Juan S Martínez
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Bérangère Lombard
- Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Stephan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| | - Andrés Aguilera
- Andalusian Molecular Biology and Regenerative Medicine Centre-CABIMER, University of Seville-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, University of Seville, Seville, Spain
| | - Aura Carreira
- Institut Curie, Université PSL, CNRS UMR3348, Orsay, France.,Université Paris-Saclay, CNRS UMR3348, Orsay, France
| |
Collapse
|
89
|
Jiang X, Prabhakar A, Van der Voorn SM, Ghatpande P, Celona B, Venkataramanan S, Calviello L, Lin C, Wang W, Black BL, Floor SN, Lagna G, Hata A. Control of ribosomal protein synthesis by the Microprocessor complex. Sci Signal 2021; 14:14/671/eabd2639. [PMID: 33622983 DOI: 10.1126/scisignal.abd2639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribosome biogenesis in eukaryotes requires the coordinated production and assembly of 80 ribosomal proteins and four ribosomal RNAs (rRNAs), and its rate must be synchronized with cellular growth. Here, we showed that the Microprocessor complex, which mediates the first step of microRNA processing, potentiated the transcription of ribosomal protein genes by eliminating DNA/RNA hybrids known as R-loops. Nutrient deprivation triggered the nuclear export of Drosha, a key component of the Microprocessor complex, and its subsequent degradation by the E3 ubiquitin ligase Nedd4, thereby reducing ribosomal protein production and protein synthesis. In mouse erythroid progenitors, conditional deletion of Drosha led to the reduced production of ribosomal proteins, translational inhibition of the mRNA encoding the erythroid transcription factor Gata1, and impaired erythropoiesis. This phenotype mirrored the clinical presentation of human "ribosomopathies." Thus, the Microprocessor complex plays a pivotal role in synchronizing protein synthesis capacity with cellular growth rate and is a potential drug target for anemias caused by ribosomal insufficiency.
Collapse
Affiliation(s)
- Xuan Jiang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amit Prabhakar
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie M Van der Voorn
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medical Physiology, University Medical Center Utrecht, Utrecht, 3584 CM, Netherlands
| | - Prajakta Ghatpande
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Barbara Celona
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chuwen Lin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Wanpeng Wang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Giorgio Lagna
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Akiko Hata
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| |
Collapse
|
90
|
Emerging roles of centromeric RNAs in centromere formation and function. Genes Genomics 2021; 43:217-226. [PMID: 33523401 DOI: 10.1007/s13258-021-01041-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Centromeres are specialized chromosomal domains involved in kinetochore formation and faithful chromosome segregation. Despite a high level of functional conservation, centromeres are not identified by DNA sequences, but by epigenetic means. Universally, centromeres are typically formed on highly repetitive DNA, which were previously considered to be silent. However, recent studies have shown that transcription occurs in this region, known as centromeric-derived RNAs (cenRNAs). CenRNAs that contribute to fundamental aspects of centromere function have been recently investigated in detail. However, the distribution, behavior and contributions of centromeric transcripts are still poorly understood. OBJECTIVE The aim of this article is to provide an overview of the roles of cenRNAs in centromere formation and function. METHODS We describe the structure and DNA sequence of centromere from yeast to human. In addition, we briefly introduce the roles of cenRNAs in centromere formation and function, kinetochore structure, accurate chromosome segregation, and pericentromeric heterochromatin assembly. Centromeric circular RNAs (circRNAs) and R-loops are rising stars in centromere function. CircRNAs have been successfully identified in various species with the assistance of high-throughput sequencing and novel computational approaches for non-polyadenylated RNA transcripts. Centromeric R-loops can be identified by the single-strand DNA ligation-based library preparation technique. But the molecular features and function of these centromeric R-loops and circRNAs are still being investigated. CONCLUSION In this review, we summarize recent findings on the epigenetic regulation of cenRNAs across species, which would provide useful information about cenRNAs and interesting hints for further studies.
Collapse
|
91
|
de Polo A, Labbé DP. Diet-Dependent Metabolic Regulation of DNA Double-Strand Break Repair in Cancer: More Choices on the Menu. Cancer Prev Res (Phila) 2021; 14:403-414. [PMID: 33509805 DOI: 10.1158/1940-6207.capr-20-0470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/27/2020] [Accepted: 01/21/2021] [Indexed: 11/16/2022]
Abstract
Despite several epidemiologic and preclinical studies supporting the role of diet in cancer progression, the complexity of the diet-cancer link makes it challenging to deconvolute the underlying mechanisms, which remain scantly elucidated. This review focuses on genomic instability as one of the cancer hallmarks affected by diet-dependent metabolic alterations. We discuss how altered dietary intake of metabolites of the one-carbon metabolism, including methionine, folate, and vitamins B and C, can impact the methylation processes and thereby tumorigenesis. We present the concept that the protumorigenic effect of certain diets, such as the Western diet, is in part due to a diet-induced erosion of the DNA repair capacity caused by altered epigenetic and epitranscriptomic landscapes, while the protective effect of other dietary patterns, such as the Mediterranean diet, can be partly explained by their ability to sustain a proficient DNA repair. In particular, considering that diet-dependent alterations of the one-carbon metabolism can impact the rate of methylation processes, changes in dietary patterns can affect the activity of writers and erasers of histone and RNA methyl marks and consequently impair their role in ensuring a proficient DNA damage repair.
Collapse
Affiliation(s)
- Anna de Polo
- Division of Urology, Department of Surgery, McGill University and Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - David P Labbé
- Division of Urology, Department of Surgery, McGill University and Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada.
| |
Collapse
|
92
|
Rinaldi C, Pizzul P, Longhese MP, Bonetti D. Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability. Front Cell Dev Biol 2021; 8:618157. [PMID: 33505970 PMCID: PMC7829580 DOI: 10.3389/fcell.2020.618157] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/02/2020] [Indexed: 12/14/2022] Open
Abstract
DNA transcription and replication are two essential physiological processes that can turn into a threat for genome integrity when they compete for the same DNA substrate. During transcription, the nascent RNA strongly binds the template DNA strand, leading to the formation of a peculiar RNA-DNA hybrid structure that displaces the non-template single-stranded DNA. This three-stranded nucleic acid transition is called R-loop. Although a programed formation of R-loops plays important physiological functions, these structures can turn into sources of DNA damage and genome instability when their homeostasis is altered. Indeed, both R-loop level and distribution in the genome are tightly controlled, and the list of factors involved in these regulatory mechanisms is continuously growing. Over the last years, our knowledge of R-loop homeostasis regulation (formation, stabilization, and resolution) has definitely increased. However, how R-loops affect genome stability and how the cellular response to their unscheduled formation is orchestrated are still not fully understood. In this review, we will report and discuss recent findings about these questions and we will focus on the role of ATM- and Rad3-related (ATR) and Ataxia-telangiectasia-mutated (ATM) kinases in the activation of an R-loop-dependent DNA damage response.
Collapse
Affiliation(s)
- Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| |
Collapse
|
93
|
Sharma S, Anand R, Zhang X, Francia S, Michelini F, Galbiati A, Williams H, Ronato DA, Masson JY, Rothenberg E, Cejka P, d'Adda di Fagagna F. MRE11-RAD50-NBS1 Complex Is Sufficient to Promote Transcription by RNA Polymerase II at Double-Strand Breaks by Melting DNA Ends. Cell Rep 2021; 34:108565. [PMID: 33406426 PMCID: PMC7788559 DOI: 10.1016/j.celrep.2020.108565] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex supports the synthesis of damage-induced long non-coding RNA (dilncRNA) by RNA polymerase II (RNAPII) from DNA double-strand breaks (DSBs) by an unknown mechanism. Here, we show that recombinant human MRN and native RNAPII are sufficient to reconstitute a minimal functional transcriptional apparatus at DSBs. MRN recruits and stabilizes RNAPII at DSBs. Unexpectedly, transcription is promoted independently from MRN nuclease activities. Rather, transcription depends on the ability of MRN to melt DNA ends, as shown by the use of MRN mutants and specific allosteric inhibitors. Single-molecule FRET assays with wild-type and mutant MRN show a tight correlation between the ability to melt DNA ends and to promote transcription. The addition of RPA enhances MRN-mediated transcription, and unpaired DNA ends allow MRN-independent transcription by RNAPII. These results support a model in which MRN generates single-strand DNA ends that favor the initiation of transcription by RNAPII.
Collapse
Affiliation(s)
- Sheetal Sharma
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland
| | - Xuzhu Zhang
- NYU Langone Medical Center, 450 East 29th Street, New York, NY, USA
| | - Sofia Francia
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy; Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia 2700, Italy
| | - Flavia Michelini
- IFOM-The FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | | | | | - Daryl A Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 2J6, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 2J6, Canada
| | - Eli Rothenberg
- NYU Langone Medical Center, 450 East 29th Street, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera Italiana (USI), Faculty of Biomedical Sciences, Bellinzona 6500, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich 8093, Switzerland.
| | - 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 2700, Italy.
| |
Collapse
|
94
|
Regulation of DNA break repair by RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:23-33. [PMID: 33385412 DOI: 10.1016/j.pbiomolbio.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Genomic stability is critical for cell survival and its effective repair when damaged is a vital process for preserving genetic information. Failure to correctly repair the genome can lead to the accumulation of mutations that ultimately drives carcinogenesis. Life has evolved sophisticated surveillance, repair pathways, and mechanisms to recognize and mend genomic lesions to preserve its integrity. Many of these pathways involve a cascade of protein effectors that act to identify the type of damage, such as double-strand (ds) DNA breaks, propagate the damage signal, and recruit an array of other protein factors to resolve the damage without loss of genetic information. It is now becoming increasingly clear that there are a number of RNA processing factors, such as the transcriptional machinery, and microRNA biogenesis components, as well as RNA itself, that facilitate the repair of DNA damage. Here, some of the recent work unravelling the role of RNA in the DNA Damage Response (DDR), in particular the dsDNA break repair pathway, will be reviewed.
Collapse
|
95
|
Lee SY, Kim JJ, Miller KM. Emerging roles of RNA modifications in genome integrity. Brief Funct Genomics 2020; 20:106-112. [PMID: 33279952 DOI: 10.1093/bfgp/elaa022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Post-translational modifications of proteins are well-established participants in DNA damage response (DDR) pathways, which function in the maintenance of genome integrity. Emerging evidence is starting to reveal the involvement of modifications on RNA in the DDR. RNA modifications are known regulators of gene expression but how and if they participate in DNA repair and genome maintenance has been poorly understood. Here, we review several studies that have now established RNA modifications as key components of DNA damage responses. RNA modifying enzymes and the binding proteins that recognize these modifications localize to and participate in the repair of UV-induced and DNA double-strand break lesions. RNA modifications have a profound effect on DNA-RNA hybrids (R-loops) at DNA damage sites, a structure known to be involved in DNA repair and genome stability. Given the importance of the DDR in suppressing mutations and human diseases such as neurodegeneration, immunodeficiencies, cancer and aging, RNA modification pathways may be involved in human diseases not solely through their roles in gene expression but also by their ability to impact DNA repair and genome stability.
Collapse
Affiliation(s)
- Seo Yun Lee
- Miller laboratory at the University of Texas at Austin
| | - Jae Jin Kim
- Miller laboratory at the University of Texas at Austin
| | | |
Collapse
|
96
|
Vågbø CB, Slupphaug G. RNA in DNA repair. DNA Repair (Amst) 2020; 95:102927. [DOI: 10.1016/j.dnarep.2020.102927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022]
|
97
|
Rzeszutek I, Betlej G. The Role of Small Noncoding RNA in DNA Double-Strand Break Repair. Int J Mol Sci 2020; 21:ijms21218039. [PMID: 33126669 PMCID: PMC7663326 DOI: 10.3390/ijms21218039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 02/01/2023] Open
Abstract
DNA damage is a common phenomenon promoted through a variety of exogenous and endogenous factors. The DNA damage response (DDR) pathway involves a wide range of proteins, and as was indicated, small noncoding RNAs (sncRNAs). These are double-strand break-induced RNAs (diRNAs) and DNA damage response small RNA (DDRNA). Moreover, RNA binding proteins (RBPs) and RNA modifications have also been identified to modulate diRNA and DDRNA function in the DDR process. Several theories have been formulated regarding the synthesis and function of these sncRNAs during DNA repair; nevertheless, these pathways’ molecular details remain unclear. Here, we review the current knowledge regarding the mechanisms of diRNA and DDRNA biosynthesis and discuss the role of sncRNAs in maintaining genome stability.
Collapse
Affiliation(s)
- Iwona Rzeszutek
- Institute of Biology and Biotechnology, Department of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
- Correspondence: ; Tel.: +48-17-851-86-20; Fax: +48-17-851-87-64
| | - Gabriela Betlej
- Institute of Physical Culture Studies, College of Medical Sciences, University of Rzeszow, 35-310 Rzeszow, Poland;
| |
Collapse
|
98
|
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.
Collapse
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
| |
Collapse
|
99
|
Gómez-González B, Aguilera A. Origin matters: spontaneous DNA-RNA hybrids do not form in trans as a source of genome instability. Curr Genet 2020; 67:93-97. [PMID: 33095299 DOI: 10.1007/s00294-020-01117-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 12/30/2022]
Abstract
Multiple exogenous and endogenous genotoxic agents threaten the integrity of the genome, but one major source of spontaneous DNA damage is the formation of unscheduled DNA-RNA hybrids. These can be genetically detected by their ability to induce recombination. The origin of spontaneous hybrids has been mainly attributed to the nascent RNA formed co-transcriptionally in cis invading its own DNA template. However, it was unclear whether hybrids could also be spontaneously generated by RNA produced in a different locus (in trans). Using new genetic systems in the yeast Saccharomyces cerevisiae, we recently tested whether hybrids could be formed in trans and compromise genome integrity. Whereas we detected recombinogenic DNA-RNA hybrids in cis and in a Rad51-independent manner, we found no evidence for recombinogenic DNA-RNA hybrids to be formed with RNAs produced in trans. Here, we further discuss the implications in the field for the origin of genetic instability and the threats coming from RNAs.
Collapse
Affiliation(s)
- Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC, Seville, Spain. .,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
| |
Collapse
|
100
|
Fóthi Á, Biró O, Erdei Z, Apáti Á, Orbán TI. Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster. RNA Biol 2020; 18:1170-1180. [PMID: 33052778 DOI: 10.1080/15476286.2020.1836457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3' end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional 'fine-tuning' can differentiate among miRNAs that are expressed simultaneously from a common precursor.
Collapse
Affiliation(s)
- Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Biró
- Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Erdei
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| |
Collapse
|