1
|
Brachova P, Alvarez NS, Hong X, Gunewardena S, Vincent KA, Latham KE, Christenson LK. Inosine RNA modifications are enriched at the codon wobble position in mouse oocytes and eggs†. Biol Reprod 2020; 101:938-949. [PMID: 31346607 DOI: 10.1093/biolre/ioz130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/07/2019] [Accepted: 07/12/2019] [Indexed: 12/30/2022] Open
Abstract
Mammalian oocytes and eggs are transcriptionally quiescent and depend on post-transcriptional mechanisms for proper maturation. Post-transcriptional mRNA modifications comprise an important regulatory mechanism that can alter protein and miRNA recognition sites, splicing, stability, secondary structure, and protein coding. We discovered that fully grown mouse germinal vesicle oocytes and metaphase II eggs display abundant inosine mRNA modifications compared to growing oocytes from postnatal day 12 oocytes. These inosines were enriched in mRNA protein coding regions (CDS) and specifically located at the third codon base, or wobble position. Inosines, observed at lower frequencies in CDS of somatic tissues, were similarly enriched at the codon wobble position. In oocytes and eggs, inosine modifications lead primarily to synonymous changes in mRNA transcripts. Inosines may ultimately affect maternal mRNA stability by changing codon usage, thereby altering translational efficiency and translationally coupled mRNA degradation. These important observations advance our understanding of post-transcriptional mechanisms contributing to mammalian oocyte maturation.
Collapse
Affiliation(s)
- Pavla Brachova
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Nehemiah S Alvarez
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.,De Novo Genomics, Kansas City, KS, USA
| | - Xiaoman Hong
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Sumedha Gunewardena
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kailey A Vincent
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| |
Collapse
|
2
|
Insights into the role of endonuclease V in RNA metabolism in Trypanosoma brucei. Sci Rep 2017; 7:8505. [PMID: 28819113 PMCID: PMC5561087 DOI: 10.1038/s41598-017-08910-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/14/2017] [Indexed: 01/05/2023] Open
Abstract
Inosine may arise in DNA as a result of oxidative deamination of adenine or misincorporation of deoxyinosine triphosphate during replication. On the other hand, the occurrence of inosine in RNA is considered a normal and essential modification induced by specific adenosine deaminases acting on mRNA and tRNA. In prokaryotes, endonuclease V (EndoV) can recognize and cleave inosine-containing DNA. In contrast, mammalian EndoVs preferentially cleave inosine-containing RNA, suggesting a role in RNA metabolism for the eukaryotic members of this protein family. We have performed a biochemical characterization of EndoV from the protozoan parasite Trypanosoma brucei. In vitro, TbEndoV efficiently processes single-stranded RNA oligonucleotides with inosine, including A to I-edited tRNA-like substrates but exhibits weak activity over DNA, except when a ribonucleotide is placed 3' to the inosine. Immunolocalization studies performed in procyclic forms indicate that TbEndoV is mainly cytosolic yet upon nutritional stress it redistributes and accumulates in stress granules colocalizing with the DEAD-box helicase TbDhh1. RNAi-mediated depletion of TbEndoV results in moderate growth defects in procyclic cells while the two EndoV alleles could be readily knocked out in bloodstream forms. Taken together, these observations suggest an important role of TbEndoV in RNA metabolism in procyclic forms of the parasite.
Collapse
|
3
|
Mannion NM, Greenwood SM, Young R, Cox S, Brindle J, Read D, Nellåker C, Vesely C, Ponting CP, McLaughlin PJ, Jantsch MF, Dorin J, Adams IR, Scadden ADJ, Ohman M, Keegan LP, O'Connell MA. The RNA-editing enzyme ADAR1 controls innate immune responses to RNA. Cell Rep 2014; 9:1482-94. [PMID: 25456137 PMCID: PMC4542304 DOI: 10.1016/j.celrep.2014.10.041] [Citation(s) in RCA: 497] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 09/01/2014] [Accepted: 10/14/2014] [Indexed: 12/12/2022] Open
Abstract
The ADAR RNA-editing enzymes deaminate adenosine bases to inosines in cellular RNAs. Aberrant interferon expression occurs in patients in whom ADAR1 mutations cause Aicardi-Goutières syndrome (AGS) or dystonia arising from striatal neurodegeneration. Adar1 mutant mouse embryos show aberrant interferon induction and die by embryonic day E12.5. We demonstrate that Adar1 embryonic lethality is rescued to live birth in Adar1; Mavs double mutants in which the antiviral interferon induction response to cytoplasmic double-stranded RNA (dsRNA) is prevented. Aberrant immune responses in Adar1 mutant mouse embryo fibroblasts are dramatically reduced by restoring the expression of editing-active cytoplasmic ADARs. We propose that inosine in cellular RNA inhibits antiviral inflammatory and interferon responses by altering RLR interactions. Transfecting dsRNA oligonucleotides containing inosine-uracil base pairs into Adar1 mutant mouse embryo fibroblasts reduces the aberrant innate immune response. ADAR1 mutations causing AGS affect the activity of the interferon-inducible cytoplasmic isoform more severely than the nuclear isoform. Adar1 mutant mouse embryonic lethality is rescued in Adar1; Mavs double mutants Aberrant antiviral responses in the Adar1 mutant are due to loss of RNA editing Human ADAR1 mutations causing AGS affect primarily the interferon-inducible isoform We propose that inosine helps innate immunity to distinguish cellular from viral RNA
Collapse
Affiliation(s)
- Niamh M Mannion
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Sam M Greenwood
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Robert Young
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Sarah Cox
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - James Brindle
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - David Read
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Christoffer Nellåker
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Cornelia Vesely
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Paul J McLaughlin
- Institute of Structural and Molecular Biology, Michael Swann Building, School of Biological Sciences, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, UK
| | - Michael F Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9/5, 1030 Vienna, Austria
| | - Julia Dorin
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ian R Adams
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - A D J Scadden
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Marie Ohman
- Department of Molecular Biosciences, Wenner Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Liam P Keegan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Mary A O'Connell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK; Department of Molecular Biosciences, Wenner Gren Institute, Stockholm University, 106 91 Stockholm, Sweden.
| |
Collapse
|