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Iwamoto N, Liu Y, Frank-Kamenetsky M, Maguire A, Tseng WC, Taborn K, Kothari N, Akhtar A, Bowman K, Shelke JD, Lamattina A, Hu XS, Jang HG, Kandasamy P, Liu F, Longo K, Looby R, Meena, Metterville J, Pan Q, Purcell-Estabrook E, Shimizu M, Prakasha PS, Standley S, Upadhyay H, Yang H, Yin Y, Zhao A, Francis C, Byrne M, Dale E, Verdine GL, Vargeese C. Preclinical evaluation of stereopure antisense oligonucleotides for allele-selective lowering of mutant HTT. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102246. [PMID: 39027419 PMCID: PMC11255113 DOI: 10.1016/j.omtn.2024.102246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Huntington's disease (HD) is an autosomal dominant disease caused by the expansion of cytosine-adenine-guanine (CAG) repeats in one copy of the HTT gene (mutant HTT, mHTT). The unaffected HTT gene encodes wild-type HTT (wtHTT) protein, which supports processes important for the health and function of the central nervous system. Selective lowering of mHTT for the treatment of HD may provide a benefit over nonselective HTT-lowering approaches, as it aims to preserve the beneficial activities of wtHTT. Targeting a heterozygous single-nucleotide polymorphism (SNP) where the targeted variant is on the mHTT gene is one strategy for achieving allele-selective activity. Herein, we investigated whether stereopure phosphorothioate (PS)- and phosphoryl guanidine (PN)-containing oligonucleotides can direct allele-selective mHTT lowering by targeting rs362273 (SNP3). We demonstrate that our SNP3-targeting molecules are potent, durable, and selective for mHTT in vitro and in vivo in mouse models. Through comparisons with a surrogate for the nonselective investigational compound tominersen, we also demonstrate that allele-selective molecules display equivalent potency toward mHTT with improved durability while sparing wtHTT. Our preclinical findings support the advancement of WVE-003, an investigational allele-selective compound currently in clinical testing (NCT05032196) for the treatment of patients with HD.
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Affiliation(s)
| | | | | | | | | | | | | | - Ali Akhtar
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | | | - Fangjun Liu
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Ken Longo
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Meena
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | - Qianli Pan
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | | | | | | | - Hailin Yang
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Yuan Yin
- Wave Life Sciences, Cambridge, MA 02138, USA
| | | | | | - Mike Byrne
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Elena Dale
- Wave Life Sciences, Cambridge, MA 02138, USA
| | - Gregory L. Verdine
- Department of Stem Cell and Regenerative Biology, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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2
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Kaur R, Frederickson A, Wetmore SD. Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- PpoI. Phys Chem Chem Phys 2024; 26:8919-8931. [PMID: 38426850 DOI: 10.1039/d3cp06201e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Homing endonucleases (HEs) are highly specific DNA cleaving enzymes, with I-PpoI having been suggested to use a single metal to accelerate phosphodiester bond cleavage. Although an I-PpoI mechanism has been proposed based on experimental structural data, no consensus has been reached regarding the roles of the metal or key active site amino acids. This study uses QM cluster and QM/MM calculations to provide atomic-level details of the I-PpoI catalytic mechanism. Minimal QM cluster and large-scale QM/MM models demonstrate that the experimentally-proposed pathway involving direct Mg2+ coordination to the substrate coupled with leaving group protonation through a metal-activated water is not feasible due to an inconducive I-PpoI active site alignment. Despite QM cluster models of varying size uncovering a pathway involving leaving group protonation by a metal-activated water, indirect (water-mediated) metal coordination to the substrate is required to afford this pathway, which renders this mechanism energetically infeasible. Instead, QM cluster models reveal that the preferred pathway involves direct Mg2+-O3' coordination to stabilize the charged substrate and assist leaving group departure, while H98 activates the water nucleophile. These calculations also underscore that both catalytic residues that directly interact with the substrate and secondary amino acids that position or stabilize these residues are required for efficient catalysis. QM/MM calculations on the solvated enzyme-DNA complex verify the preferred mechanism, which is fully consistent with experimental kinetic, structural, and mutational data. The fundamental understanding of the I-PpoI mechanism of action, gained from the present work can be used to further explore potential uses of this enzyme in biotechnology and medicine, and direct future computational investigations of other members of the understudied HE family.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.
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3
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Jaiswal AS, Dutta A, Srinivasan G, Yuan Y, Zhou D, Shaheen M, Sadideen D, Kirby A, Williamson E, Gupta Y, Olsen SK, Xu M, Loranc E, Mukhopadhyay P, Pertsemlidis A, Bishop AR, Sung P, Nickoloff J, Hromas R. TATDN2 resolution of R-loops is required for survival of BRCA1-mutant cancer cells. Nucleic Acids Res 2023; 51:12224-12241. [PMID: 37953292 PMCID: PMC10711561 DOI: 10.1093/nar/gkad952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638-5p, resulted in synthetic lethality in BRCA1-deficient cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3' exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.
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Affiliation(s)
- Aruna S Jaiswal
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Gayathri Srinivasan
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Montaser Shaheen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Doraid T Sadideen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Austin Kirby
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Elizabeth A Williamson
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yogesh K Gupta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Shaun K Olsen
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Mingjiang Xu
- Department of Molecular Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Eva Loranc
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Pramiti Mukhopadhyay
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander Pertsemlidis
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
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4
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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5
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Li J, Zhao J, Gan X, Wang Y, Jiang D, Chen L, Wang F, Xu J, Pei H, Huang J, Chen X. The RPA-RNF20-SNF2H cascade promotes proper chromosome segregation and homologous recombination repair. Proc Natl Acad Sci U S A 2023; 120:e2303479120. [PMID: 37155876 PMCID: PMC10193940 DOI: 10.1073/pnas.2303479120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/27/2023] [Indexed: 05/10/2023] Open
Abstract
The human tumor suppressor Ring finger protein 20 (RNF20)-mediated histone H2B monoubiquitination (H2Bub) is essential for proper chromosome segregation and DNA repair. However, what is the precise function and mechanism of RNF20-H2Bub in chromosome segregation and how this pathway is activated to preserve genome stability remain unknown. Here, we show that the single-strand DNA-binding factor Replication protein A (RPA) interacts with RNF20 mainly in the S and G2/M phases and recruits RNF20 to mitotic centromeres in a centromeric R-loop-dependent manner. In parallel, RPA recruits RNF20 to chromosomal breaks upon DNA damage. Disruption of the RPA-RNF20 interaction or depletion of RNF20 increases mitotic lagging chromosomes and chromosome bridges and impairs BRCA1 and RAD51 loading and homologous recombination repair, leading to elevated chromosome breaks, genome instability, and sensitivities to DNA-damaging agents. Mechanistically, the RPA-RNF20 pathway promotes local H2Bub, H3K4 dimethylation, and subsequent SNF2H recruitment, ensuring proper Aurora B kinase activation at centromeres and efficient loading of repair proteins at DNA breaks. Thus, the RPA-RNF20-SNF2H cascade plays a broad role in preserving genome stability by coupling H2Bub to chromosome segregation and DNA repair.
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Affiliation(s)
- Jimin Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Jingyu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
| | - Fangwei Wang
- The Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210009, China
| | - Huadong Pei
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057
| | - Jun Huang
- The Ministry of Education Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan 430072, China
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6
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Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z. Syntheses of Pyrimidine-Modified Seleno-DNAs as Stable Antisense Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539140. [PMID: 37205589 PMCID: PMC10187239 DOI: 10.1101/2023.05.02.539140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Chemically modified antisense oligonucleotides (ASO) currently in pre-clinical and clinical experiments mainly focus on the 2'-position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2'-modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO's binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno-modification at 5-position of thymidine, as well as its Se-oligonucleotides. Via X-ray crystal structural study, we found that the Se-modification was located in the major groove of nucleic acid duplex and didn't cause the thermal and structural perturbations. Surprisingly, our nucleobase-modified Se-DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. This affords a novel avenue for potential antisense modification in the form of Se-antisense oligonucleotides (Se-ASO).
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Affiliation(s)
- Ziyuan Fang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Cen Chen
- Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
- SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, 618000, P. R. China
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7
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Stoy H, Zwicky K, Kuster D, Lang KS, Krietsch J, Crossley MP, Schmid JA, Cimprich KA, Merrikh H, Lopes M. Direct visualization of transcription-replication conflicts reveals post-replicative DNA:RNA hybrids. Nat Struct Mol Biol 2023; 30:348-359. [PMID: 36864174 PMCID: PMC10023573 DOI: 10.1038/s41594-023-00928-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/23/2023] [Indexed: 03/04/2023]
Abstract
Transcription-replication collisions (TRCs) are crucial determinants of genome instability. R-loops were linked to head-on TRCs and proposed to obstruct replication fork progression. The underlying mechanisms, however, remained elusive due to the lack of direct visualization and of non-ambiguous research tools. Here, we ascertained the stability of estrogen-induced R-loops on the human genome, visualized them directly by electron microscopy (EM), and measured R-loop frequency and size at the single-molecule level. Combining EM and immuno-labeling on locus-specific head-on TRCs in bacteria, we observed the frequent accumulation of DNA:RNA hybrids behind replication forks. These post-replicative structures are linked to fork slowing and reversal across conflict regions and are distinct from physiological DNA:RNA hybrids at Okazaki fragments. Comet assays on nascent DNA revealed a marked delay in nascent DNA maturation in multiple conditions previously linked to R-loop accumulation. Altogether, our findings suggest that TRC-associated replication interference entails transactions that follow initial R-loop bypass by the replication fork.
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Affiliation(s)
- Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Katharina Zwicky
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Danina Kuster
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Kevin S Lang
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonas A Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Houra Merrikh
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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8
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Shi X, Teng H, Sun Z. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops. Brief Bioinform 2022; 23:6751149. [PMID: 36208174 PMCID: PMC9677470 DOI: 10.1093/bib/bbac441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple types of non-canonical nucleic acid structures play essential roles in DNA recombination and replication, transcription, and genomic instability and have been associated with several human diseases. Thus, an increasing number of experimental and bioinformatics methods have been developed to identify these structures. To date, most reviews have focused on the features of non-canonical DNA/RNA structure formation, experimental approaches to mapping these structures, and the association of these structures with diseases. In addition, two reviews of computational algorithms for the prediction of non-canonical nucleic acid structures have been published. One of these reviews focused only on computational approaches for G4 detection until 2020. The other mainly summarized the computational tools for predicting cruciform, H-DNA and Z-DNA, in which the algorithms discussed were published before 2012. Since then, several experimental and computational methods have been developed. However, a systematic review including the conformation, sequencing mapping methods and computational prediction strategies for these structures has not yet been published. The purpose of this review is to provide an updated overview of conformation, current sequencing technologies and computational identification methods for non-canonical nucleic acid structures, as well as their strengths and weaknesses. We expect that this review will aid in understanding how these structures are characterised and how they contribute to related biological processes and diseases.
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Affiliation(s)
- Xiaohui Shi
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Ouhai District, Wenzhou 325000, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Ouhai District, Wenzhou 325000, China
| | - Zhongsheng Sun
- Corresponding author: Zhongsheng Sun, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The 1st Affiliated Hospital of WMU, Nanbaixiang Wenyi Yiyuan Xinyuan District, Ouhai District, Wenzhou 325000, China. E-mail:
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9
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Misic J, Milenkovic D, Al-Behadili A, Xie X, Jiang M, Jiang S, Filograna R, Koolmeister C, Siira S, Jenninger L, Filipovska A, Clausen A, Caporali L, Valentino M, La Morgia C, Carelli V, Nicholls T, Wredenberg A, Falkenberg M, Larsson NG. Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion. Nucleic Acids Res 2022; 50:8749-8766. [PMID: 35947649 PMCID: PMC9410905 DOI: 10.1093/nar/gkac661] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/08/2022] [Accepted: 08/04/2022] [Indexed: 12/24/2022] Open
Abstract
The in vivo role for RNase H1 in mammalian mitochondria has been much debated. Loss of RNase H1 is embryonic lethal and to further study its role in mtDNA expression we characterized a conditional knockout of Rnaseh1 in mouse heart. We report that RNase H1 is essential for processing of RNA primers to allow site-specific initiation of mtDNA replication. Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is initiated at non-canonical sites and becomes impaired. Importantly, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed accompanied by mtDNA depletion. The steady-state levels of mitochondrial transcripts follow the levels of mtDNA, and RNA processing is not altered in the absence of RNase H1. Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain of RNase H1 causing impaired mtDNA replication. In contrast to catalytically inactive variants of RNase H1, this mutant version has enhanced enzyme activity but shows impaired primer formation. This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.
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Affiliation(s)
- Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | | | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Min Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia
| | - Louise Jenninger
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Maria Lucia Valentino
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
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10
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Karlowicz A, Dubiel AB, Czerwinska J, Bledea A, Purzycki P, Grzelewska M, McAuley RJ, Szczesny RJ, Brzuska G, Krol E, Szczesny B, Szymanski MR. In vitro reconstitution reveals a key role of human mitochondrial EXOG in RNA primer processing. Nucleic Acids Res 2022; 50:7991-8007. [PMID: 35819194 PMCID: PMC9371904 DOI: 10.1093/nar/gkac581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/01/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022] Open
Abstract
The removal of RNA primers is essential for mitochondrial DNA (mtDNA) replication. Several nucleases have been implicated in RNA primer removal in human mitochondria, however, no conclusive mechanism has been elucidated. Here, we reconstituted minimal in vitro system capable of processing RNA primers into ligatable DNA ends. We show that human 5'-3' exonuclease, EXOG, plays a fundamental role in removal of the RNA primer. EXOG cleaves short and long RNA-containing flaps but also in cooperation with RNase H1, processes non-flap RNA-containing intermediates. Our data indicate that the enzymatic activity of both enzymes is necessary to process non-flap RNA-containing intermediates and that regardless of the pathway, EXOG-mediated RNA cleavage is necessary prior to ligation by DNA Ligase III. We also show that upregulation of EXOG levels in mitochondria increases ligation efficiency of RNA-containing substrates and discover physical interactions, both in vitro and in cellulo, between RNase H1 and EXOG, Pol γA, Pol γB and Lig III but not FEN1, which we demonstrate to be absent from mitochondria of human lung epithelial cells. Together, using human mtDNA replication enzymes, we reconstitute for the first time RNA primer removal reaction and propose a novel model for RNA primer processing in human mitochondria.
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Affiliation(s)
- Anna Karlowicz
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Andrzej B Dubiel
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Jolanta Czerwinska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106 Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw 02-106, Poland
| | - Adela Bledea
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Piotr Purzycki
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Marta Grzelewska
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Ryan J McAuley
- Department of Ophthalmology and Visual Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Roman J Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, ul. Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Gabriela Brzuska
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Ewelina Krol
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
| | - Bartosz Szczesny
- Department of Ophthalmology and Visual Sciences, The University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Michal R Szymanski
- Structural Biology Laboratory, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, ul. Abrahama 58, 80-307 Gdansk, Poland
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11
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RNA modifications can affect RNase H1-mediated PS-ASO activity. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:814-828. [PMID: 35664704 PMCID: PMC9136273 DOI: 10.1016/j.omtn.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/07/2022] [Indexed: 11/21/2022]
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12
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Abstract
RNase H1 has become an essential tool to uncover the physiological and pathological roles of R-loops, three-stranded structures consisting of and RNA-DNA hybrid opposite to a single DNA strand (ssDNA). RNase H1 degrades the RNA portion of the R-loops returning the two DNA strands to double-stranded form (dsDNA). Overexpression of RNase H1 in different systems has helped to address the questions of where R-loops are located, their abundance, and mechanisms of formation, stability, and degradation. In this chapter we review multiple studies that used RNase H1 as an instrument to investigate R-loops multiple functions and their relevance in health and diseases.
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Affiliation(s)
- Susana M Cerritelli
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kiran Sakhuja
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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13
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Masaki Y, Tabira A, Hattori S, Wakatsuki S, Seio K. Insertion of a methylene group into the backbone of an antisense oligonucleotide reveals the importance of deoxyribose recognition by RNase H. Org Biomol Chem 2022; 20:8917-8924. [DOI: 10.1039/d2ob01667b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Methylene-inserted oligonucleotides showed an inserted-position-dependent inhibitory effect on cleavage reaction which suggested the importance of deoxyribose recognition.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
- PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Ayano Tabira
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Shihori Hattori
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Shunsuke Wakatsuki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259-J2-16 Nagatsuta, Midori, Yokohama, Kanagawa, 226-8501, Japan
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14
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Silva S, Guillén-Mendoza C, Aguilera A. RNase H1 Hybrid-Binding Domain-Based Tools for Cellular Biology Studies of DNA-RNA Hybrids in Mammalian Cells. Methods Mol Biol 2022; 2528:115-125. [PMID: 35704188 DOI: 10.1007/978-1-0716-2477-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
R loops are abundant noncanonical DNA-RNA hybrid structures that can occur during DNA-based processes, such as transcription, replication and DNA damage, and can lead both to physiologically favorable and pathological outcomes. With an increasing body of work feeding the field of R loop biology, our understanding of the processes in which R loops intervene and the consequences of meddling with R loop formation and dissolution has greatly increased but it has also led to new questions and sometimes opposing possibilities. Proper detection of these structures is a crucial factor to advance our knowledge about R loops and factors associated with their formation and removal. Here, we describe the use of fluorescently tagged HBD, the hybrid-binding domain of RNase H1, as a tool for analyzing DNA-RNA hybrids in different contexts using live-cell microscopy and immunofluorescence experiments.
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Affiliation(s)
- Sónia Silva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Cristina Guillén-Mendoza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 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-Universidad Pablo de Olavide, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
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15
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Endogenous reverse transcriptase and RNase H-mediated antiviral mechanism in embryonic stem cells. Cell Res 2021; 31:998-1010. [PMID: 34158624 PMCID: PMC8217788 DOI: 10.1038/s41422-021-00524-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleic acid-based systems play important roles in antiviral defense, including CRISPR/Cas that adopts RNA-guided DNA cleavage to prevent DNA phage infection and RNA interference (RNAi) that employs RNA-guided RNA cleavage to defend against RNA virus infection. Here, we report a novel type of nucleic acid-based antiviral system that exists in mouse embryonic stem cells (mESCs), which suppresses RNA virus infection by DNA-mediated RNA cleavage. We found that the viral RNA of encephalomyocarditis virus can be reverse transcribed into complementary DNA (vcDNA) by the reverse transcriptase (RTase) encoded by endogenous retrovirus-like elements in mESCs. The vcDNA is negative-sense single-stranded and forms DNA/RNA hybrid with viral RNA. The viral RNA in the heteroduplex is subsequently destroyed by cellular RNase H1, leading to robust suppression of viral growth. Furthermore, either inhibition of the RTase activity or depletion of endogenous RNase H1 results in the promotion of virus proliferation. Altogether, our results provide intriguing insights into the antiviral mechanism of mESCs and the antiviral function of endogenized retroviruses and cellular RNase H. Such a natural nucleic acid-based antiviral mechanism in mESCs is referred to as ERASE (endogenous RTase/RNase H-mediated antiviral system), which is an addition to the previously known nucleic acid-based antiviral mechanisms including CRISPR/Cas in bacteria and RNAi in plants and invertebrates.
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16
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Crossley MP, Brickner JR, Song C, Zar SMT, Maw SS, Chédin F, Tsai MS, Cimprich KA. Catalytically inactive, purified RNase H1: A specific and sensitive probe for RNA-DNA hybrid imaging. J Cell Biol 2021; 220:212458. [PMID: 34232287 PMCID: PMC8266564 DOI: 10.1083/jcb.202101092] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures with both physiological and pathological roles in cells. R-loop imaging generally relies on detection of the RNA-DNA hybrid component of these structures using the S9.6 antibody. We show that the use of this antibody for imaging can be problematic because it readily binds to double-stranded RNA (dsRNA) in vitro and in vivo, giving rise to nonspecific signal. In contrast, purified, catalytically inactive human RNase H1 tagged with GFP (GFP-dRNH1) is a more specific reagent for imaging RNA-DNA hybrids. GFP-dRNH1 binds strongly to RNA-DNA hybrids but not to dsRNA oligonucleotides in fixed human cells and is not susceptible to binding endogenous RNA. Furthermore, we demonstrate that purified GFP-dRNH1 can be applied to fixed cells to detect hybrids after their induction, thereby bypassing the need for cell line engineering. GFP-dRNH1 therefore promises to be a versatile tool for imaging and quantifying RNA-DNA hybrids under a wide range of conditions.
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Affiliation(s)
- Magdalena P Crossley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Chenlin Song
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Su Mon Thin Zar
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Su S Maw
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, Davis, CA
| | - Miaw-Sheue Tsai
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
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17
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RAD51 Inhibition Induces R-Loop Formation in Early G1 Phase of the Cell Cycle. Int J Mol Sci 2021; 22:ijms22073740. [PMID: 33916766 PMCID: PMC8038378 DOI: 10.3390/ijms22073740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/30/2022] Open
Abstract
R-loops are three-stranded structures generated by annealing of nascent transcripts to the template DNA strand, leaving the non-template DNA strand exposed as a single-stranded loop. Although R-loops play important roles in physiological processes such as regulation of gene expression, mitochondrial DNA replication, or immunoglobulin class switch recombination, dysregulation of the R-loop metabolism poses a threat to the stability of the genome. A previous study in yeast has shown that the homologous recombination machinery contributes to the formation of R-loops and associated chromosome instability. On the contrary, here, we demonstrate that depletion of the key homologous recombination factor, RAD51, as well as RAD51 inhibition by the B02 inhibitor did not prevent R-loop formation induced by the inhibition of spliceosome assembly in human cells. However, we noticed that treatment of cells with B02 resulted in RAD51-dependent accumulation of R-loops in an early G1 phase of the cell cycle accompanied by a decrease in the levels of chromatin-bound ORC2 protein, a component of the pre-replication complex, and an increase in DNA synthesis. Our results suggest that B02-induced R-loops might cause a premature origin firing.
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18
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Zhang L, Vickers TA, Sun H, Liang XH, Crooke ST. Binding of phosphorothioate oligonucleotides with RNase H1 can cause conformational changes in the protein and alter the interactions of RNase H1 with other proteins. Nucleic Acids Res 2021; 49:2721-2739. [PMID: 33577678 PMCID: PMC7969025 DOI: 10.1093/nar/gkab078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 02/06/2023] Open
Abstract
We recently found that toxic PS-ASOs can cause P54nrb and PSF nucleolar mislocalization in an RNase H1-dependent manner. To better understand the underlying mechanisms of these observations, here we utilize different biochemical approaches to demonstrate that PS-ASO binding can alter the conformations of the bound proteins, as illustrated using recombinant RNase H1, P54nrb, PSF proteins and various isolated domains. While, in general, binding of PS-ASOs or ASO/RNA duplexes stabilizes the conformations of these proteins, PS-ASO binding may also cause the unfolding of RNase H1, including both the hybrid binding domain and the catalytic domain. The extent of conformational change correlates with the binding affinity of PS-ASOs to the proteins. Consequently, PS-ASO binding to RNase H1 induces the interaction of RNase H1 with P54nrb or PSF in a 2′-modification and sequence dependent manner, and toxic PS-ASOs tend to induce more interactions than non-toxic PS-ASOs. PS-ASO binding also enhances the interaction between P54nrb and PSF. However, the interaction between RNase H1 and P32 protein can be disrupted upon binding of PS-ASOs. Together, these results suggest that stronger binding of PS-ASOs can cause greater conformational changes of the bound proteins, subsequently affecting protein–protein interactions. These observations thus provide deeper understanding of the molecular basis of PS-ASO-induced protein mislocalization or degradation observed in cells and advance our understanding of why some PS-ASOs are cytotoxic.
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Affiliation(s)
- Lingdi Zhang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Timothy A Vickers
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Antisense Drug discovery, Ionis Pharmaceuticals, Inc. Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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19
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Chédin F, Hartono SR, Sanz LA, Vanoosthuyse V. Best practices for the visualization, mapping, and manipulation of R-loops. EMBO J 2021; 40:e106394. [PMID: 33411340 PMCID: PMC7883053 DOI: 10.15252/embj.2020106394] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/25/2020] [Accepted: 11/10/2020] [Indexed: 01/12/2023] Open
Abstract
R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution has significant impacts on genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here, we review the main existing methodologies for R-loop mapping and assess their limitations as well as the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we propose a possible resolution for the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.
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Affiliation(s)
- Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Stella R Hartono
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome CenterUniversity of California, DavisDavisCAUSA
| | - Vincent Vanoosthuyse
- Laboratoire de Biologie et Modélisation de la CelluleCNRSUMR 5239Univ LyonÉcole Normale Supérieure de LyonLyonFrance
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20
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Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
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Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
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21
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González de Cózar JM, Carretero-Junquera M, Ciesielski GL, Miettinen SM, Varjosalo M, Kaguni LS, Dufour E, Jacobs HT. A second hybrid-binding domain modulates the activity of Drosophila ribonuclease H1. J Biochem 2020; 168:515-533. [PMID: 32589740 PMCID: PMC7657459 DOI: 10.1093/jb/mvaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 11/14/2022] Open
Abstract
In eukaryotes, ribonuclease H1 (RNase H1) is involved in the processing and removal of RNA/DNA hybrids in both nuclear and mitochondrial DNA. The enzyme comprises a C-terminal catalytic domain and an N-terminal hybrid-binding domain (HBD), separated by a linker of variable length, 115 amino acids in Drosophila melanogaster (Dm). Molecular modelling predicted this extended linker to fold into a structure similar to the conserved HBD. Based on a deletion series, both the catalytic domain and the conserved HBD were required for high-affinity binding to heteroduplex substrates, while loss of the novel HBD led to an ∼90% drop in Kcat with a decreased KM, and a large increase in the stability of the RNA/DNA hybrid-enzyme complex, supporting a bipartite-binding model in which the second HBD facilitates processivity. Shotgun proteomics following in vivo cross-linking identified single-stranded DNA-binding proteins from both nuclear and mitochondrial compartments, respectively RpA-70 and mtSSB, as prominent interaction partners of Dm RNase H1. However, we were not able to document direct and stable interactions with mtSSB when the proteins were co-overexpressed in S2 cells, and functional interactions between them in vitro were minor.
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Affiliation(s)
| | | | - Grzegorz L Ciesielski
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, USA
| | - Sini M Miettinen
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Laurie S Kaguni
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Eric Dufour
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
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22
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Wood M, Quinet A, Lin YL, Davis AA, Pasero P, Ayala YM, Vindigni A. TDP-43 dysfunction results in R-loop accumulation and DNA replication defects. J Cell Sci 2020; 133:jcs244129. [PMID: 32989039 PMCID: PMC7648616 DOI: 10.1242/jcs.244129] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
TAR DNA-binding protein 43 (TDP-43; also known as TARDBP) is an RNA-binding protein whose aggregation is a hallmark of the neurodegenerative disorders amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43 loss increases DNA damage and compromises cell viability, but the actual function of TDP-43 in preventing genome instability remains unclear. Here, we show that loss of TDP-43 increases R-loop formation in a transcription-dependent manner and results in DNA replication stress. TDP-43 nucleic-acid-binding and self-assembly activities are important in inhibiting R-loop accumulation and preserving normal DNA replication. We also found that TDP-43 cytoplasmic aggregation impairs TDP-43 function in R-loop regulation. Furthermore, increased R-loop accumulation and DNA damage is observed in neurons upon loss of TDP-43. Together, our findings indicate that TDP-43 function and normal protein homeostasis are crucial in maintaining genomic stability through a co-transcriptional process that prevents aberrant R-loop accumulation. We propose that the increased R-loop formation and genomic instability associated with TDP-43 loss are linked to the pathogenesis of TDP-43 proteinopathies.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yea-Lih Lin
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier 34396, France
| | - Albert A Davis
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS et Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier 34396, France
| | - Yuna M Ayala
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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23
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Langner HK, Jastrzebska K, Caruthers MH. Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras. J Am Chem Soc 2020; 142:16240-16253. [PMID: 32866014 DOI: 10.1021/jacs.0c04335] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This Article outlines the optimized chemical synthesis and preliminary biochemical characterization of a new oligonucleotide analogue called thiophosphoramidate morpholinos (TMOs). Their rational design hinges upon integrating two well-studied pharmacophores, namely, phosphorothioates (pS) and morpholinos, to create morpholino-pS hybrid oligonucleotides. Our simple synthesis strategy enables the easy incorporation of morpholino-pS moieties and therapeutically relevant sugar modifications in tandem to create novel oligonucleotide (ON) analogues that are hitherto unexplored in the oligotherapeutics arena. Exclusively TMO-modified ONs demonstrate high stability toward 3'-exonuclease. Hybridization studies show that TMO chimeras consisting of alternating TMO and DNA-pS subunits exhibit higher binding affinity toward complementary RNA relative to the canonical DNA/RNA duplex (∼10 °C). Oligonucleotides that consist entirely of TMO linkages also show higher RNA binding affinity but do not recruit ribonuclease H1 (RNase H1). Chimeric TMO analogues demonstrate high gene silencing efficacy, comparable to that of a chimeric 2'-OMe-pS/pO control, during in vitro bioassay screens designed to evaluate their potential as microRNA inhibitors of hsa-miR-15b-5p in HeLa cells.
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Affiliation(s)
- Heera K Langner
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Katarzyna Jastrzebska
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
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24
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Crooke ST, Seth PP, Vickers TA, Liang XH. The Interaction of Phosphorothioate-Containing RNA Targeted Drugs with Proteins Is a Critical Determinant of the Therapeutic Effects of These Agents. J Am Chem Soc 2020; 142:14754-14771. [PMID: 32786803 DOI: 10.1021/jacs.0c04928] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent progress in understanding phosphorothioate antisense oligonucleotide (PS-ASO) interactions with proteins has revealed that proteins play deterministic roles in the absorption, distribution, cellular uptake, subcellular distribution, molecular mechanisms of action, and toxicity of PS-ASOs. Similarly, such interactions can alter the fates of many intracellular proteins. These and other advances have opened new avenues for the medicinal chemistry of PS-ASOs and research on all elements of the molecular pharmacology of these molecules. These advances have recently been reviewed. In this Perspective article, we summarize some of those learnings, the general principles that have emerged, and a few of the exciting new questions that can now be addressed.
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Affiliation(s)
- Stanley T Crooke
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Punit P Seth
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Timothy A Vickers
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
| | - Xue-Hai Liang
- Ionis Pharmaceuticals, Inc., Carlsbad, California 92010-6670, United States
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25
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Crooke ST, Vickers TA, Liang XH. Phosphorothioate modified oligonucleotide-protein interactions. Nucleic Acids Res 2020; 48:5235-5253. [PMID: 32356888 PMCID: PMC7261153 DOI: 10.1093/nar/gkaa299] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antisense oligonucleotides (ASOs) interact with target RNAs via hybridization to modulate gene expression through different mechanisms. ASO therapeutics are chemically modified and include phosphorothioate (PS) backbone modifications and different ribose and base modifications to improve pharmacological properties. Modified PS ASOs display better binding affinity to the target RNAs and increased binding to proteins. Moreover, PS ASO protein interactions can affect many aspects of their performance, including distribution and tissue delivery, cellular uptake, intracellular trafficking, potency and toxicity. In this review, we summarize recent progress in understanding PS ASO protein interactions, highlighting the proteins with which PS ASOs interact, the influence of PS ASO protein interactions on ASO performance, and the structure activity relationships of PS ASO modification and protein interactions. A detailed understanding of these interactions can aid in the design of safer and more potent ASO drugs, as illustrated by recent findings that altering ASO chemical modifications dramatically improves therapeutic index.
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26
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Li Y, Song Y, Xu W, Li Q, Wang X, Li K, Wang J, Liu Z, Velychko S, Ye R, Xia Q, Wang L, Guo R, Dong X, Zheng Z, Dai Y, Li H, Yao M, Xue Y, Schöler HR, Sun Q, Yao H. R-loops coordinate with SOX2 in regulating reprogramming to pluripotency. SCIENCE ADVANCES 2020; 6:eaba0777. [PMID: 32704541 PMCID: PMC7360481 DOI: 10.1126/sciadv.aba0777] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/09/2020] [Indexed: 05/06/2023]
Abstract
R-loops modulate genome stability and regulate gene expression, but the functions and the regulatory mechanisms of R-loops in stem cell biology are still unclear. Here, we profiled R-loops during somatic cell reprogramming and found that dynamic changes in R-loops are essential for reprogramming and occurred before changes in gene expression. Disrupting the homeostasis of R-loops by depleting RNaseH1 or catalytic inactivation of RNaseH1 at D209 (RNaseH1D209N) blocks reprogramming. Sox2, but not any other factor in the Yamanaka cocktail, overcomes the inhibitory effects of RNaseH1 activity loss on reprogramming. Sox2 interacts with the reprogramming barrier factor Ddx5 and inhibits the resolvase activity of Ddx5 on R-loops and thus facilitates reprogramming. Furthermore, reprogramming efficiency can be modulated by dCas9-mediated RNaseH1/RNaseH1D209N targeting the specific R-loop regions. Together, these results show that R-loops play important roles in reprogramming and shed light on the regulatory module of Sox2/Ddx5 on R-loops during reprogramming.
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Affiliation(s)
- Yaoyi Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Xu
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qin Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinxiu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Kuan Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Juehan Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zicong Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Medical Faculty, University of Muenster, Münster 48149, Germany
| | - Rong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Xia
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhikai Zheng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yushuang Dai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Haojie Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hans R. Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Medical Faculty, University of Muenster, Münster 48149, Germany
- Medical Faculty, University of Muenster, Domagkstrasse 3, 48149 Muenster, Germany
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Corresponding author. (Q.S.); (H.Y.)
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding author. (Q.S.); (H.Y.)
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27
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Vickers TA, Rahdar M, Prakash TP, Crooke ST. Kinetic and subcellular analysis of PS-ASO/protein interactions with P54nrb and RNase H1. Nucleic Acids Res 2020; 47:10865-10880. [PMID: 31495875 PMCID: PMC6846478 DOI: 10.1093/nar/gkz771] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
The rapid RNase H1-dependent mislocalization of heterodimer proteins P54nrb and PSF to nucleoli is an early event in the pathway that explains the effects of most toxic phosphorothioate ASOs (PS-ASOs). Using a recently developed NanoLuciferace (NLuc)-based structural complementation reporter system which allows us to observe ASO/protein interactions in real time in live cells, we have determined that safe and toxic PS-ASOs associate with these proteins with kinetics and impact on subcellular localization that differ. Toxic PS-ASOs interact in a complex that includes RNase H1, P54nrb and PSF; but RNase H1/P54nrb complexes were observed in only the cells treated with toxic, but not safe PS-ASOs. In addition, experiments performed in vitro suggest that RNA is also a required component of the complex. The protein–protein interaction between P54nrb and RNase H1 requires the spacer region of RNAse H1, while the P54nrb core domains are required for association with RNase H1. In addition, we have determined that PS-ASOs bind P54nrb via RRM1 and RRM2, while they bind RNase H1 primarily via the hybrid binding domain, however catalytic domain interactions also contribute to overall affinity. These ASO–protein interactions are highly influenced by the chemistry of the PS-ASO binding environment, however little correlation between affinity for specific proteins and PS-ASO toxicity was observed.
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Affiliation(s)
- Timothy A Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Meghdad Rahdar
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Thazha P Prakash
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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28
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Reyes A, Rusecka J, Tońska K, Zeviani M. RNase H1 Regulates Mitochondrial Transcription and Translation via the Degradation of 7S RNA. Front Genet 2020; 10:1393. [PMID: 32082360 PMCID: PMC7006045 DOI: 10.3389/fgene.2019.01393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/19/2019] [Indexed: 02/02/2023] Open
Abstract
RNase H1 is able to recognize DNA/RNA heteroduplexes and to degrade their RNA component. As a consequence, it has been implicated in different aspects of mtDNA replication such as primer formation, primer removal, and replication termination, and significant differences have been reported between control and mutant RNASEH1 skin fibroblasts from patients. However, neither mtDNA depletion nor the presence of deletions have been described in skin fibroblasts while still presenting signs of mitochondrial dysfunction (lower mitochondrial membrane potential, reduced oxygen consumption, slow growth in galactose). Here, we show that RNase H1 has an effect on mtDNA transcripts, most likely through the regulation of 7S RNA and other R-loops. The observed effect on both mitochondrial mRNAs and 16S rRNA results in decreased mitochondrial translation and subsequently mitochondrial dysfunction in cells carrying mutations in RNASEH1.
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Affiliation(s)
- Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Aurelio Reyes, ; Massimo Zeviani,
| | - Joanna Rusecka
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Katarzyna Tońska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Aurelio Reyes, ; Massimo Zeviani,
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29
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Hyjek M, Figiel M, Nowotny M. RNases H: Structure and mechanism. DNA Repair (Amst) 2019; 84:102672. [PMID: 31371183 DOI: 10.1016/j.dnarep.2019.102672] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/05/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022]
Abstract
RNases H are a family of endonucleases that hydrolyze RNA residues in various nucleic acids. These enzymes are present in all branches of life, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements. RNases H are divided into two main classes (RNases H1 and H2 or type 1 and type 2 enzymes) with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. Additionally, a third class is found in some Archaea and bacteria. Besides distinct cellular functions specific for each type of RNases H, this family of proteins is generally involved in the maintenance of genome stability with overlapping and cooperative role in removal of R-loops thus preventing their accumulation. Extensive biochemical and structural studies of RNases H provided not only a comprehensive and complete picture of their mechanism but also revealed key basic principles of nucleic acid recognition and processing. RNase H1 is present in prokaryotes and eukaryotes and cleaves RNA in RNA/DNA hybrids. Its main function is hybrid removal, notably in the context of R-loops. RNase H2, which is also present in all branches of life, can play a similar role but it also has a specialized function in the cleavage of single ribonucleotides embedded in the DNA. RNase H3 is present in Archaea and bacteria and is closely related to RNase H2 in sequence and structure but has RNase H1-like biochemical properties. This review summarizes the mechanisms of substrate recognition and enzymatic cleavage by different classes of RNases H with particular insights into structural features of nucleic acid binding, specificity towards RNA and/or DNA strands and catalysis.
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Affiliation(s)
- Malwina Hyjek
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Marcin Nowotny
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
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30
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Carreño-Gago L, Blázquez-Bermejo C, Díaz-Manera J, Cámara Y, Gallardo E, Martí R, Torres-Torronteras J, García-Arumí E. Identification and Characterization of New RNASEH1 Mutations Associated With PEO Syndrome and Multiple Mitochondrial DNA Deletions. Front Genet 2019; 10:576. [PMID: 31258551 PMCID: PMC6588129 DOI: 10.3389/fgene.2019.00576] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/31/2019] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA (mtDNA) depletion and deletion syndrome encompasses a group of disorders caused by mutations in genes involved in mtDNA replication and maintenance. The clinical phenotype ranges from fatal infantile hepatocerebral forms to mild adult onset progressive external ophthalmoplegia (PEO). We report the case of a patient with PEO and multiple mtDNA deletions, with two new homozygous mutations in RNASEH1. The first mutation (c.487T>C) is located in the same catalytic domain as the four previously reported mutations, and the second (c.258_260del) is located in the connection domain, where no mutations have been reported. In silico study of the mutations predicted only the first mutation as pathogenic, but functional studies showed that both mutations cause loss of ribonuclease H1 activity. mtDNA replication dysfunction was demonstrated in patient fibroblasts, which were unable to recover normal mtDNA copy number after ethidium bromide-induced mtDNA depletion. Our results demonstrate the pathogenicity of two new RNASEH1 variants found in a patient with PEO syndrome, multiple deletions, and mild mitochondrial myopathy.
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Affiliation(s)
- Lidia Carreño-Gago
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Cora Blázquez-Bermejo
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Jordi Díaz-Manera
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Servei de Neurologia, Malalties Neuromusculars, Hospital de la Santa Creu i Sant Pau i Institut de Recerca de HSCSP, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yolanda Cámara
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Eduard Gallardo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Servei de Neurologia, Malalties Neuromusculars, Hospital de la Santa Creu i Sant Pau i Institut de Recerca de HSCSP, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ramon Martí
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Javier Torres-Torronteras
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Elena García-Arumí
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain.,Àrea de Genètica Clínica i Molecular, Hospital Universitari Vall d'Hebron, Barcelona, Spain
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31
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Chromatin modifiers Mdm2 and RNF2 prevent RNA:DNA hybrids that impair DNA replication. Proc Natl Acad Sci U S A 2018; 115:E11311-E11320. [PMID: 30413623 DOI: 10.1073/pnas.1809592115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The p53-Mdm2 system is key to tumor suppression. We have recently reported that p53 as well as Mdm2 are capable of supporting DNA replication fork progression. On the other hand, we found that Mdm2 is a modifier of chromatin, modulating polycomb repressor complex (PRC)-driven histone modifications. Here we show that, similar to Mdm2 knockdown, the depletion of PRC members impairs DNA synthesis, as determined in fiber assays. In particular, the ubiquitin ligase and PRC1 component RNF2/Ring1B is required to support DNA replication, similar to Mdm2. Moreover, the Ring finger domain of Mdm2 is not only essential for its ubiquitin ligase activity, but also for proper DNA replication. Strikingly, Mdm2 overexpression can rescue RNF2 depletion with regard to DNA replication fork progression, and vice versa, strongly suggesting that the two ubiquitin ligases perform overlapping functions in this context. H2A overexpression also rescues fork progression upon depletion of Mdm2 or RNF2, but only when the ubiquitination sites K118/K119 are present. Depleting the H2A deubiquitinating enzyme BAP1 reduces the fork rate, suggesting that both ubiquitination and deubiquitination of H2A are required to support fork progression. The depletion of Mdm2 elicits the accumulation of RNA/DNA hybrids, suggesting R-loop formation as a mechanism of impaired DNA replication. Accordingly, RNase H overexpression or the inhibition of the transcription elongation kinase CDK9 each rescues DNA replication upon depletion of Mdm2 or RNF2. Taken together, our results suggest that chromatin modification by Mdm2 and PRC1 ensures smooth DNA replication through the avoidance of R-loop formation.
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32
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TRF1 participates in chromosome end protection by averting TRF2-dependent telomeric R loops. Nat Struct Mol Biol 2018; 25:147-153. [PMID: 29358759 PMCID: PMC5808845 DOI: 10.1038/s41594-017-0021-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/26/2017] [Indexed: 12/12/2022]
Abstract
The shelterin protein TRF2 assembles protective T loops at chromosome ends by stimulating intramolecular invasion of the telomeric G-rich single-stranded DNA (ssDNA) overhang into the duplex telomeric array. The other shelterin factor, TRF1, is thought to mainly facilitate telomeric dsDNA replication without directly participating in end protection. Here we show that in vitro human TRF2 stimulates invasion of G-rich TERRA-like RNA into telomeric dsDNA, leading to formation of telomeric RNA-DNA hybrids (telR loops). The N-terminal basic domain of TRF2 binds to TERRA-like RNA and enables TRF2 to promote efficient RNA invasion. TRF1, through its N-terminal acidic domain, counteracts TRF2-mediated RNA invasion but not ssDNA invasion. In vivo, when TRF1 is depleted or replaced with a variant lacking the acidic domain, TRF2 induces formation of telR loops, which in turn cause telomere loss. Hence, uncontrolled TRF2 threatens telomere integrity, and TRF1 directly supports end protection by suppressing harmful telR loops.
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33
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Kabeche L, Nguyen HD, Buisson R, Zou L. A mitosis-specific and R loop-driven ATR pathway promotes faithful chromosome segregation. Science 2017; 359:108-114. [PMID: 29170278 DOI: 10.1126/science.aan6490] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/22/2017] [Accepted: 11/09/2017] [Indexed: 01/04/2023]
Abstract
The ataxia telangiectasia mutated and Rad3-related (ATR) kinase is crucial for DNA damage and replication stress responses. Here, we describe an unexpected role of ATR in mitosis. Acute inhibition or degradation of ATR in mitosis induces whole-chromosome missegregation. The effect of ATR ablation is not due to altered cyclin-dependent kinase 1 (CDK1) activity, DNA damage responses, or unscheduled DNA synthesis but to loss of an ATR function at centromeres. In mitosis, ATR localizes to centromeres through Aurora A-regulated association with centromere protein F (CENP-F), allowing ATR to engage replication protein A (RPA)-coated centromeric R loops. As ATR is activated at centromeres, it stimulates Aurora B through Chk1, preventing formation of lagging chromosomes. Thus, a mitosis-specific and R loop-driven ATR pathway acts at centromeres to promote faithful chromosome segregation, revealing functions of R loops and ATR in suppressing chromosome instability.
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Affiliation(s)
- Lilian Kabeche
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Rémi Buisson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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34
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Shen W, Sun H, De Hoyos CL, Bailey JK, Liang XH, Crooke ST. Dynamic nucleoplasmic and nucleolar localization of mammalian RNase H1 in response to RNAP I transcriptional R-loops. Nucleic Acids Res 2017; 45:10672-10692. [PMID: 28977560 PMCID: PMC5737507 DOI: 10.1093/nar/gkx710] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022] Open
Abstract
An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migration of RNase H1 and R-loops from nucleoli to perinucleolar ring structures was observed upon inhibition of RNAP I transcription. Treatment with camptothecin which transiently stabilized nucleolar R-loops recruited RNase H1 to the nucleoli. It has been reported that the absence of Topoisomerase and RNase H activity in Escherichia coli or Saccharomyces cerevisiae caused R-loop accumulation along rDNA. We found that the distribution of RNase H1 and Top1 along rDNA coincided at sites where R-loops accumulated in mammalian cells. Loss of either RNase H1 or Top1 caused R-loop accumulation, and the accumulation of R-loops was exacerbated when both proteins were depleted. Importantly, we observed that protein levels of Top1 were negatively correlated with the abundance of RNase H1. We conclude that Top1 and RNase H1 are partially functionally redundant in mammalian cells to suppress RNAP I transcription-associate R-loops.
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Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jeffrey K Bailey
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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35
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Influence of mismatched and bulged nucleotides on SNP-preferential RNase H cleavage of RNA-antisense gapmer heteroduplexes. Sci Rep 2017; 7:12532. [PMID: 28970564 PMCID: PMC5624880 DOI: 10.1038/s41598-017-12844-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
This study focused on determining design rules for gapmer-type antisense oligonucleotides (ASOs), that can differentiate cleavability of two SNP variants of RNA in the presence of ribonuclease H based on the mismatch type and position in the heteroduplex. We describe the influence of structural motifs formed by several arrangements of multiple mismatches (various types of mismatches and their position within the ASO/target RNA duplex) on RNase H cleavage selectivity of five different SNP types. The targets were mRNA fragments of APP, SCA3, SNCA and SOD1 genes, carrying C-to-G, G-to-C, G-to-A, A-to-G and C-to-U substitutions. The results show that certain arrangements of mismatches enhance discrimination between wild type and mutant SNP alleles of RNA in vitro as well as in HeLa cells. Among the over 120 gapmers tested, we found two gapmers that caused preferential degradation of the mutant allele APP 692 G and one that led to preferential cleavage of the mutant SNCA 53 A allele, both in vitro and in cells. However, several gapmers promoted selective cleavage of mRNA mutant alleles in in vitro experiments only.
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36
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Nguyen HD, Yadav T, Giri S, Saez B, Graubert TA, Zou L. Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1. Mol Cell 2017; 65:832-847.e4. [PMID: 28257700 DOI: 10.1016/j.molcel.2017.01.029] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability.
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Affiliation(s)
- Hai Dang Nguyen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Tribhuwan Yadav
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sumanprava Giri
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Borja Saez
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Timothy A Graubert
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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37
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Parajuli S, Teasley DC, Murali B, Jackson J, Vindigni A, Stewart SA. Human ribonuclease H1 resolves R-loops and thereby enables progression of the DNA replication fork. J Biol Chem 2017; 292:15216-15224. [PMID: 28717002 DOI: 10.1074/jbc.m117.787473] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/21/2017] [Indexed: 11/06/2022] Open
Abstract
Faithful DNA replication is essential for genome stability. To ensure accurate replication, numerous complex and redundant replication and repair mechanisms function in tandem with the core replication proteins to ensure DNA replication continues even when replication challenges are present that could impede progression of the replication fork. A unique topological challenge to the replication machinery is posed by RNA-DNA hybrids, commonly referred to as R-loops. Although R-loops play important roles in gene expression and recombination at immunoglobulin sites, their persistence is thought to interfere with DNA replication by slowing or impeding replication fork progression. Therefore, it is of interest to identify DNA-associated enzymes that help resolve replication-impeding R-loops. Here, using DNA fiber analysis, we demonstrate that human ribonuclease H1 (RNH1) plays an important role in replication fork movement in the mammalian nucleus by resolving R-loops. We found that RNH1 depletion results in accumulation of RNA-DNA hybrids, slowing of replication forks, and increased DNA damage. Our data uncovered a role for RNH1 in global DNA replication in the mammalian nucleus. Because accumulation of RNA-DNA hybrids is linked to various human cancers and neurodegenerative disorders, our study raises the possibility that replication fork progression might be impeded, adding to increased genomic instability and contributing to disease.
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Affiliation(s)
| | | | - Bhavna Murali
- From the Departments of Cell Biology and Physiology and
| | - Jessica Jackson
- the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Alessandro Vindigni
- the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 .,Siteman Cancer Center, and
| | - Sheila A Stewart
- From the Departments of Cell Biology and Physiology and .,Siteman Cancer Center, and.,Medicine.,Integrating Communications within the Cancer Environment (ICCE) Institute, Washington University School of Medicine, St. Louis, Missouri 63110 and
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38
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Vickers TA, Crooke ST. Development of a Quantitative BRET Affinity Assay for Nucleic Acid-Protein Interactions. PLoS One 2016; 11:e0161930. [PMID: 27571227 PMCID: PMC5003356 DOI: 10.1371/journal.pone.0161930] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
Protein-nucleic acid interactions play a crucial role in the regulation of diverse biological processes. Elucidating the roles that protein-nucleic acid complexes play in the regulation of transcription, translation, DNA replication, repair and recombination, and RNA processing continues to be a crucial aspect of understanding of cell biology and the mechanisms of disease. In addition, proteins have been demonstrated to interact with antisense oligonucleotide therapeutics in a sequence and chemistry dependent manner, influencing ASO potency and distribution in cells and in vivo. While many assays have been developed to measure protein-nucleic acid interactions, many suffer from lack of throughput and sensitivity, or challenges with protein purification and scalability. In this report we present a new BRET assay for the analysis of DNA-protein interactions which makes use of an extremely bright luciferase as a tag for the binding protein, along with a long-wavelength fluorophore conjugated to the nucleic acid. The resulting assay is high throughput, sensitive, does not require protein purification, and even allows for quantitative characterization of these interactions within the biologically relevant context of whole cells.
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Affiliation(s)
- Timothy A. Vickers
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, United States of America
- * E-mail:
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, United States of America
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39
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Lima WF, Murray HM, Damle SS, Hart CE, Hung G, De Hoyos CL, Liang XH, Crooke ST. Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function. Nucleic Acids Res 2016; 44:5299-312. [PMID: 27131367 PMCID: PMC4914116 DOI: 10.1093/nar/gkw350] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/19/2016] [Indexed: 11/12/2022] Open
Abstract
Viable constitutive and tamoxifen inducible liver-specific RNase H1 knockout mice that expressed no RNase H1 activity in hepatocytes showed increased R-loop levels and reduced mitochondrial encoded DNA and mRNA levels, suggesting impaired mitochondrial R-loop processing, transcription and mitochondrial DNA replication. These changes resulted in mitochondrial dysfunction with marked changes in mitochondrial fusion, fission, morphology and transcriptional changes reflective of mitochondrial damage and stress. Liver degeneration ensued, as indicated by apoptosis, fibrosis and increased transaminase levels. Antisense oligonucleotides (ASOs) designed to serve as substrates for RNase H1 were inactive in the hepatocytes from the RNase H1 knockout mice and in vivo, demonstrating that RNase H1 is necessary for the activity of DNA-like ASOs. During liver regeneration, a clone of hepatocytes that expressed RNase H1 developed and partially restored mitochondrial and liver function.
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Affiliation(s)
- Walt F Lima
- Department of Core Antisense Research, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Heather M Murray
- Department of Core Antisense Research, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Sagar S Damle
- Department of Functional Genomics, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Christopher E Hart
- Department of Functional Genomics, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Gene Hung
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl Li De Hoyos
- Department of Core Antisense Research, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
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40
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Tresini M, Warmerdam DO, Kolovos P, Snijder L, Vrouwe MG, Demmers JA, van IJcken WF, Grosveld FG, Medema RH, Hoeijmakers JH, Mullenders LH, Vermeulen W, Marteijn JA. The core spliceosome as target and effector of non-canonical ATM signalling. Nature 2015; 523:53-8. [PMID: 26106861 PMCID: PMC4501432 DOI: 10.1038/nature14512] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/11/2015] [Indexed: 01/19/2023]
Abstract
In response to DNA damage, tissue homoeostasis is ensured by protein networks promoting DNA repair, cell cycle arrest or apoptosis. DNA damage response signalling pathways coordinate these processes, partly by propagating gene-expression-modulating signals. DNA damage influences not only the abundance of messenger RNAs, but also their coding information through alternative splicing. Here we show that transcription-blocking DNA lesions promote chromatin displacement of late-stage spliceosomes and initiate a positive feedback loop centred on the signalling kinase ATM. We propose that initial spliceosome displacement and subsequent R-loop formation is triggered by pausing of RNA polymerase at DNA lesions. In turn, R-loops activate ATM, which signals to impede spliceosome organization further and augment ultraviolet-irradiation-triggered alternative splicing at the genome-wide level. Our findings define R-loop-dependent ATM activation by transcription-blocking lesions as an important event in the DNA damage response of non-replicating cells, and highlight a key role for spliceosome displacement in this process.
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Affiliation(s)
- Maria Tresini
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Daniël O. Warmerdam
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Petros Kolovos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Loes Snijder
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mischa G. Vrouwe
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen A.A. Demmers
- Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Frank G. Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René H. Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jan H.J. Hoeijmakers
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Leon H.F. Mullenders
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurgen A. Marteijn
- Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
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41
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Reyes A, Melchionda L, Nasca A, Carrara F, Lamantea E, Zanolini A, Lamperti C, Fang M, Zhang J, Ronchi D, Bonato S, Fagiolari G, Moggio M, Ghezzi D, Zeviani M. RNASEH1 Mutations Impair mtDNA Replication and Cause Adult-Onset Mitochondrial Encephalomyopathy. Am J Hum Genet 2015; 97:186-93. [PMID: 26094573 DOI: 10.1016/j.ajhg.2015.05.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/21/2015] [Indexed: 11/27/2022] Open
Abstract
Chronic progressive external ophthalmoplegia (CPEO) is common in mitochondrial disorders and is frequently associated with multiple mtDNA deletions. The onset is typically in adulthood, and affected subjects can also present with general muscle weakness. The underlying genetic defects comprise autosomal-dominant or recessive mutations in several nuclear genes, most of which play a role in mtDNA replication. Next-generation sequencing led to the identification of compound-heterozygous RNASEH1 mutations in two singleton subjects and a homozygous mutation in four siblings. RNASEH1, encoding ribonuclease H1 (RNase H1), is an endonuclease that is present in both the nucleus and mitochondria and digests the RNA component of RNA-DNA hybrids. Unlike mitochondria, the nucleus harbors a second ribonuclease (RNase H2). All affected individuals first presented with CPEO and exercise intolerance in their twenties, and these were followed by muscle weakness, dysphagia, and spino-cerebellar signs with impaired gait coordination, dysmetria, and dysarthria. Ragged-red and cytochrome c oxidase (COX)-negative fibers, together with impaired activity of various mitochondrial respiratory chain complexes, were observed in muscle biopsies of affected subjects. Western blot analysis showed the virtual absence of RNase H1 in total lysate from mutant fibroblasts. By an in vitro assay, we demonstrated that altered RNase H1 has a reduced capability to remove the RNA from RNA-DNA hybrids, confirming their pathogenic role. Given that an increasing amount of evidence indicates the presence of RNA primers during mtDNA replication, this result might also explain the accumulation of mtDNA deletions and underscores the importance of RNase H1 for mtDNA maintenance.
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Affiliation(s)
- Aurelio Reyes
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK
| | - Laura Melchionda
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Alessia Nasca
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Franco Carrara
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Eleonora Lamantea
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Alice Zanolini
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Costanza Lamperti
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Mingyan Fang
- Beijing Genomic Institute, Shenzhen 518083, China
| | | | - Dario Ronchi
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan 20122, Italy
| | - Sara Bonato
- Neurology Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan 20122, Italy
| | - Gigliola Fagiolari
- Neuromuscular Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan 20122, Italy
| | - Maurizio Moggio
- Neuromuscular Unit, Neuroscience Section, Department of Pathophysiology and Transplantation, Dino Ferrari Center, IRCCS Fondazione Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan 20122, Italy
| | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy.
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK.
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Legros P, Malapert A, Niinuma S, Bernard P, Vanoosthuyse V. RNA processing factors Swd2.2 and Sen1 antagonize RNA Pol III-dependent transcription and the localization of condensin at Pol III genes. PLoS Genet 2014; 10:e1004794. [PMID: 25392932 PMCID: PMC4230746 DOI: 10.1371/journal.pgen.1004794] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/02/2014] [Indexed: 11/19/2022] Open
Abstract
Condensin-mediated chromosome condensation is essential for genome stability upon cell division. Genetic studies have indicated that the association of condensin with chromatin is intimately linked to gene transcription, but what transcription-associated feature(s) direct(s) the accumulation of condensin remains unclear. Here we show in fission yeast that condensin becomes strikingly enriched at RNA Pol III-transcribed genes when Swd2.2 and Sen1, two factors involved in the transcription process, are simultaneously deleted. Sen1 is an ATP-dependent helicase whose orthologue in Saccharomyces cerevisiae contributes both to terminate transcription of some RNA Pol II transcripts and to antagonize the formation of DNA:RNA hybrids in the genome. Using two independent mapping techniques, we show that DNA:RNA hybrids form in abundance at Pol III-transcribed genes in fission yeast but we demonstrate that they are unlikely to faciliate the recruitment of condensin. Instead, we show that Sen1 forms a stable and abundant complex with RNA Pol III and that Swd2.2 and Sen1 antagonize both the interaction of RNA Pol III with chromatin and RNA Pol III-dependent transcription. When Swd2.2 and Sen1 are lacking, the increased concentration of RNA Pol III and condensin at Pol III-transcribed genes is accompanied by the accumulation of topoisomerase I and II and by local nucleosome depletion, suggesting that Pol III-transcribed genes suffer topological stress. We provide evidence that this topological stress contributes to recruit and/or stabilize condensin at Pol III-transcribed genes in the absence of Swd2.2 and Sen1. Our data challenge the idea that a processive RNA polymerase hinders the binding of condensin and suggest that transcription-associated topological stress could in some circumstances facilitate the association of condensin. Failure to condense chromosomes prior to anaphase onset can lead to genome instability. The evolutionary-conserved condensin complex drives chromosome condensation, probably by changing the topology of chromatin around its binding sites. Condensin localizes to regions of high transcription, suggesting that some transcription-associated feature(s) direct its association with chromatin. Here we considered that transcription-dependent DNA:RNA hybrids or topological stress could be involved in recruiting condensin. Our data show that condensin is indeed enriched at regions accumulating DNA:RNA hybrids but that they are not involved in its recruitment. Rather, we identify a mutant combination where increased transcription by RNA Pol III is associated locally with stronger topological stress. Strikingly the localization of condensin is dramatically enhanced at the same loci and we show that topological stress contributes to this enhanced association. Our data strengthen the idea that transcription creates the environment necessary to recruit condensin in mitosis.
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Affiliation(s)
- Pénélope Legros
- CNRS, Université Lyon 01, UMR5239, LBMC; Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Amélie Malapert
- CNRS, Université Lyon 01, UMR5239, LBMC; Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Sho Niinuma
- CNRS, Université Lyon 01, UMR5239, LBMC; Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Pascal Bernard
- CNRS, Université Lyon 01, UMR5239, LBMC; Ecole Normale Supérieure de Lyon, Lyon, France.
| | - Vincent Vanoosthuyse
- CNRS, Université Lyon 01, UMR5239, LBMC; Ecole Normale Supérieure de Lyon, Lyon, France.
- * E-mail:
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Arora R, Lee Y, Wischnewski H, Brun CM, Schwarz T, Azzalin CM. RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat Commun 2014; 5:5220. [PMID: 25330849 PMCID: PMC4218956 DOI: 10.1038/ncomms6220] [Citation(s) in RCA: 316] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/10/2014] [Indexed: 12/21/2022] Open
Abstract
A fraction of cancer cells maintain telomeres through the telomerase-independent, ‘Alternative Lengthening of Telomeres’ (ALT) pathway. ALT relies on homologous recombination (HR) between telomeric sequences; yet, what makes ALT telomeres recombinogenic remains unclear. Here we show that the RNA endonuclease RNaseH1 regulates the levels of RNA–DNA hybrids between telomeric DNA and the long noncoding RNA TERRA, and is a key mediator of telomere maintenance in ALT cells. RNaseH1 associated to telomeres specifically in ALT cells and its depletion led to telomeric hybrid accumulation, exposure of single-stranded telomeric DNA, activation of replication protein A at telomeres and abrupt telomere excision. Conversely, overexpression of RNaseH1 weakened the recombinogenic nature of ALT telomeres and led to telomere shortening. Altering cellular RNaseH1 levels did not perturb telomere homoeostasis in telomerase-positive cells. RNaseH1 maintains regulated levels of telomeric RNA–DNA hybrids at ALT telomeres to trigger HR without compromising telomere integrity too severely. A subset of cancers maintains telomere length independently of telomerase by activating alternative lengthening of telomeres (ALT) pathways. Here the authors show that RNaseH1 modulates telomeric homologous recombination frequencies in ALT cells by regulating the levels of RNA–DNA hybrids between TERRA and telomeric DNA.
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Affiliation(s)
- Rajika Arora
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Yongwoo Lee
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Harry Wischnewski
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Catherine M Brun
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Tobias Schwarz
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
| | - Claus M Azzalin
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich (ETHZ), Zürich CH-8093, Switzerland
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Wu H, Sun H, Liang X, Lima WF, Crooke ST. Human RNase H1 is associated with protein P32 and is involved in mitochondrial pre-rRNA processing. PLoS One 2013; 8:e71006. [PMID: 23990920 PMCID: PMC3750045 DOI: 10.1371/journal.pone.0071006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/28/2013] [Indexed: 11/19/2022] Open
Abstract
Mammalian RNase H1 has been implicated in mitochondrial DNA replication and RNA processing and is required for embryonic development. We identified the mitochondrial protein P32 that binds specifically to human RNase H1, but not human RNase H2. P32 binds human RNase H1 via the hybrid-binding domain of the enzyme at an approximately 1∶1 ratio. P32 enhanced the cleavage activity of RNase H1 by reducing the affinity of the enzyme for the heteroduplex substrate and enhancing turnover, but had no effect on the cleavage pattern. RNase H1 and P32 were partially co-localized in mitochondria and reduction of P32 or RNase H1 levels resulted in accumulation of mitochondrial pre ribosomal RNA [12S/16S] in HeLa cells. P32 also co-immunoprecipitated with MRPP1, a mitochondrial RNase P protein required for mitochondrial pre-rRNA processing. The P32-RNase H1 complex was shown to physically interact with mitochondrial DNA and pre-rRNA. These results expand the potential roles for RNase H1 to include assuring proper transcription and processing of guanosine-cytosine rich pre-ribosomal RNA in mitochondria. Further, the results identify P32 as a member of the ‘RNase H1 degradosome’ and the key P32 enhances the enzymatic efficiency of human RNase H1.
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Affiliation(s)
- Hongjiang Wu
- Department of Core Antisense Research, Isis Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Hong Sun
- Department of Core Antisense Research, Isis Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Xuehai Liang
- Department of Core Antisense Research, Isis Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Walt F. Lima
- Department of Core Antisense Research, Isis Pharmaceuticals, Inc., Carlsbad, California, United States of America
| | - Stanley T. Crooke
- Department of Core Antisense Research, Isis Pharmaceuticals, Inc., Carlsbad, California, United States of America
- * E-mail:
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Maláč K, Barvík I. Complex between Human RNase HI and the phosphonate-DNA/RNA duplex: Molecular dynamics study. J Mol Graph Model 2013; 44:81-90. [DOI: 10.1016/j.jmgm.2013.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 04/30/2013] [Accepted: 05/05/2013] [Indexed: 10/26/2022]
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R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 2012; 45:814-25. [PMID: 22387027 DOI: 10.1016/j.molcel.2012.01.017] [Citation(s) in RCA: 588] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/08/2011] [Accepted: 01/10/2012] [Indexed: 12/31/2022]
Abstract
CpG islands (CGIs) function as promoters for approximately 60% of human genes. Most of these elements remain protected from CpG methylation, a prevalent epigenetic modification associated with transcriptional silencing. Here, we report that methylation-resistant CGI promoters are characterized by significant strand asymmetry in the distribution of guanines and cytosines (GC skew) immediately downstream from their transcription start sites. Using innovative genomics methodologies, we show that transcription through regions of GC skew leads to the formation of long R loop structures. Furthermore, we show that GC skew and R loop formation potential is correlated with and predictive of the unmethylated state of CGIs. Finally, we provide evidence that R loop formation protects from DNMT3B1, the primary de novo DNA methyltransferase in early development. Altogether, these results suggest that protection from DNA methylation is a built-in characteristic of the DNA sequence of CGI promoters that is revealed by the cotranscriptional formation of R loop structures.
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Nguyen TA, Tak YS, Lee CH, Kang YH, Cho IT, Seo YS. Analysis of subunit assembly and function of the Saccharomyces cerevisiae RNase H2 complex. FEBS J 2011; 278:4927-42. [PMID: 22004424 DOI: 10.1111/j.1742-4658.2011.08394.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
RNase H2 of Saccharomyces cerevisiae consists of three essential subunits (Rnh201, Rnh202 and Rnh203) and plays a critical role in the removal of RNA incorporated in duplex DNA. In the present study, we purified individual subunits and heterodimeric subcomplexes to examine the assembly and biochemical function of subunits of RNase H2 in vitro. Reconstitution experiments revealed that Rnh202 and Rnh203 first form a subcomplex, followed by the recruitment of Rnh201 to complete complex formation. Rnh201 alone or in combination with Rnh203 showed neither substrate-binding, nor catalytic activity, indicating that both activities of Rnh201 are latent until it becomes an integral part of the complex. However, Rnh202 by itself showed substrate-binding activity. RNase H2 containing mutant Rnh202 defective in substrate binding had decreased substrate-binding activity, indicating that Rnh202 contributes directly to substrate binding. Reconstitution of RNase H2 complexes with various mutant subunits allowed us to assess the influence of conserved amino acid residues in either Rnh201 or Rnh202 on substrate-binding and catalytic activities. We found that the substrate-binding activities of both Rnh201 and Rnh202 were critical for cleavage of the phosphodiester bond present between DNA and RNA in RNase H2 substrates.
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Affiliation(s)
- Tuan Anh Nguyen
- Center for DNA Replication and Genome Instability, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Rosta E, Nowotny M, Yang W, Hummer G. Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc 2011; 133:8934-41. [PMID: 21539371 PMCID: PMC3110985 DOI: 10.1021/ja200173a] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use quantum mechanics/molecular mechanics simulations to study the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal catalysis to process nucleic acids. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA-cleavage reaction and characterize its mechanism. We find that the reaction proceeds in two steps. In a first step, catalyzed primarily by magnesium ion A and its ligands, a water molecule attacks the scissile phosphate. Consistent with thiol-substitution experiments, a water proton is transferred to the downstream phosphate group. The transient phosphorane formed as a result of this nucleophilic attack decays by breaking the bond between the phosphate and the ribose oxygen. In the resulting intermediate, the dissociated but unprotonated leaving group forms an alkoxide coordinated to magnesium ion B. In a second step, the reaction is completed by protonation of the leaving group, with a neutral Asp132 as a likely proton donor. The overall reaction barrier of ∼15 kcal mol(-1), encountered in the first step, together with the cost of protonating Asp132, is consistent with the slow measured rate of ∼1-100/min. The two-step mechanism is also consistent with the bell-shaped pH dependence of the reaction rate. The nonmonotonic relative motion of the magnesium ions along the reaction pathway agrees with X-ray crystal structures. Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction.
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Affiliation(s)
- Edina Rosta
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, U.S.A
| | - Gerhard Hummer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
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Elsässer B, Fels G. Nucleotide docking: prediction of reactant state complexes for ribonuclease enzymes. J Mol Model 2010; 17:1953-62. [PMID: 21120556 DOI: 10.1007/s00894-010-0900-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/10/2010] [Indexed: 12/29/2022]
Abstract
Ribonuclease enzymes (RNases) play key roles in the maturation and metabolism of all RNA molecules. Computational simulations of the processes involved can help to elucidate the underlying enzymatic mechanism and is often employed in a synergistic approach together with biochemical experiments. Theoretical calculations require atomistic details regarding the starting geometries of the molecules involved, which, in the absence of crystallographic data, can only be achieved from computational docking studies. Fortunately, docking algorithms have improved tremendously in recent years, so that reliable structures of enzyme-ligand complexes can now be successfully obtained from computation. However, most docking programs are not particularly optimized for nucleotide docking. In order to assist our studies on the cleavage of RNA by the two most important ribonuclease enzymes, RNase A and RNase H, we evaluated four docking tools-MOE2009, Glide 5.5, QXP-Flo+0802, and Autodock 4.0-for their ability to simulate complexes between these enzymes and RNA oligomers. To validate our results, we analyzed the docking results with respect to the known key interactions between the protein and the nucleotide. In addition, we compared the predicted complexes with X-ray structures of the mutated enzyme as well as with structures obtained from previous calculations. In this manner, we were able to prepare the desired reaction state complex so that it could be used as the starting structure for further DFT/B3LYP QM/MM reaction mechanism studies.
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Affiliation(s)
- Brigitta Elsässer
- Department of Chemistry, University of Paderborn, Warburgerstr. 100, 33098 Paderborn, Germany.
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50
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Jongruja N, You DJ, Kanaya E, Koga Y, Takano K, Kanaya S. The N-terminal hybrid binding domain of RNase HI from Thermotoga maritima is important for substrate binding and Mg2+-dependent activity. FEBS J 2010; 277:4474-89. [DOI: 10.1111/j.1742-4658.2010.07834.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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