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Nejad C, Pillman KA, Siddle KJ, Pépin G, Änkö ML, McCoy CE, Beilharz TH, Quintana-Murci L, Goodall GJ, Bracken CP, Gantier MP. miR-222 isoforms are differentially regulated by type-I interferon. RNA 2018; 24:332-341. [PMID: 29263133 PMCID: PMC5824353 DOI: 10.1261/rna.064550.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
Endogenous microRNAs (miRNAs) often exist as multiple isoforms (known as "isomiRs") with predominant variation around their 3'-end. Increasing evidence suggests that different isomiRs of the same family can have diverse functional roles, as recently demonstrated with the example of miR-222-3p 3'-end variants. While isomiR levels from a same miRNA family can vary between tissues and cell types, change of templated isomiR stoichiometry to stimulation has not been reported to date. Relying on small RNA-sequencing analyses, we demonstrate here that miR-222-3p 3'-end variants >23 nt are specifically decreased upon interferon (IFN) β stimulation of human fibroblasts, while shorter isoforms are spared. This length-dependent dynamic regulation of long miR-222-3p 3'-isoforms and >40 other miRNA families was confirmed in human monocyte-derived dendritic cells following infection with Salmonella Typhimurium, underlining the breadth of 3'-length regulation by infection, beyond the example of miR-222-3p. We further show that stem-loop miRNA Taqman RT-qPCR exhibits selectivity between 3'-isoforms, according to their length, and that this can lead to misinterpretation of results when these isoforms are differentially regulated. Collectively, and to our knowledge, this work constitutes the first demonstration that the stoichiometry of highly abundant templated 3'-isoforms of a same miRNA family can be dynamically regulated by a stimulus. Given that such 3'-isomiRs can have different functions, our study underlines the need to consider isomiRs when investigating miRNA-based regulation.
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Affiliation(s)
- Charlotte Nejad
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, South Australia 5000, Australia
| | - Katherine J Siddle
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Geneviève Pépin
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
| | - Minna-Liisa Änkö
- Department of Anatomy and Developmental Biology, Monash University, Victoria 3800, Australia
- Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Claire E McCoy
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Traude H Beilharz
- Development and Stem Cells Program, Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Lluís Quintana-Murci
- Institut Pasteur, Unit of Human Evolutionary Genetics, CNRS URA3012, Paris 75015, France
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, South Australia 5000, Australia
- Department of Medicine, University of Adelaide, Adelaide, South Australia 5005, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria 3168, Australia
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