Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes
Background. RNA editing is a post-transcriptional regulatory mechanism that can alter the coding sequences of certain genes in response to physiological demands. We previously identified C-to-U RNA editing (C136U, R46X) which inactivates a small fraction of succinate dehydrogenase (SDH; mitochondria...
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PeerJ Inc.
2013-09-01
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| Online Access: | https://peerj.com/articles/152.pdf |
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| author | Bora E. Baysal Kitty De Jong Biao Liu Jianmin Wang Santosh K. Patnaik Paul K. Wallace Robert T. Taggart |
| author_facet | Bora E. Baysal Kitty De Jong Biao Liu Jianmin Wang Santosh K. Patnaik Paul K. Wallace Robert T. Taggart |
| author_sort | Bora E. Baysal |
| collection | DOAJ |
| description | Background. RNA editing is a post-transcriptional regulatory mechanism that can alter the coding sequences of certain genes in response to physiological demands. We previously identified C-to-U RNA editing (C136U, R46X) which inactivates a small fraction of succinate dehydrogenase (SDH; mitochondrial complex II) subunit B gene (SDHB) mRNAs in normal steady-state peripheral blood mononuclear cells (PBMCs). SDH is a heterotetrameric tumor suppressor complex which when mutated causes paraganglioma tumors that are characterized by constitutive activation of hypoxia inducible pathways. Here, we studied regulation, extent and cell type origin of SDHB RNA editing.Methods. We used short-term cultured PBMCs obtained from random healthy platelet donors, performed monocyte enrichment by cold aggregation, employed a novel allele-specific quantitative PCR method, flow cytometry, immunologic cell separation, gene expression microarray, database analysis and high-throughput RNA sequencing.Results. While the editing rate is low in uncultured monocyte-enriched PBMCs (average rate 2.0%, range 0.4%–6.3%, n = 42), it is markedly upregulated upon exposure to 1% oxygen tension (average rate 18.2%, range 2.8%–49.4%, n = 14) and during normoxic macrophage differentiation in the presence of serum (average rate 10.1%, range 2.7%–18.8%, n = 17). The normoxic induction of SDHB RNA editing was associated with the development of dense adherent aggregates of monocytes in culture. CD14-positive monocyte isolation increased the percentages of C136U transcripts by 1.25-fold in normoxic cultures (n = 5) and 1.68-fold in hypoxic cultures (n = 4). CD14-negative lymphocytes showed no evidence of SDHB editing. The SDHB genomic DNA remained wild-type during increased RNA editing. Microarray analysis showed expression changes in wound healing and immune response pathway genes as the editing rate increased in normoxic cultures. High-throughput sequencing of SDHB and SDHD transcripts confirmed the induction of C136U RNA editing in normoxic cultures but showed no additional verifiable coding edits. Analysis of SDHB RNA sequence data from 16 normal human tissues from the Illumina Body Map and from 45 samples representing 23 different cell types from the ENCODE projects confirmed the occurrence of site-specific C136U editing in whole blood (1.7%) and two primary CD14+ monocyte samples (1.9% and 2.6%). In contrast, the other cell types showed an average of 0.2% and 0.1% C136U editing rates in the two databases, respectively.Conclusions. These findings demonstrate that C-to-U coding RNA editing of certain genes is dynamically induced by physiologically relevant environmental factors and suggest that epigenetic downregulation of SDHB by site-specific RNA editing plays a role in hypoxia adaptation in monocytes. |
| first_indexed | 2024-03-09T06:40:10Z |
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| language | English |
| last_indexed | 2024-03-09T06:40:10Z |
| publishDate | 2013-09-01 |
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| spelling | doaj.art-591b3fe9e9284be7a799fef3c9137b522023-12-03T10:51:36ZengPeerJ Inc.PeerJ2167-83592013-09-011e15210.7717/peerj.152152Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytesBora E. Baysal0Kitty De Jong1Biao Liu2Jianmin Wang3Santosh K. Patnaik4Paul K. Wallace5Robert T. Taggart6Departments of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY, USADepartments of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY, USABiostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USABiostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USAThoracic Surgery, Roswell Park Cancer Institute, Buffalo, NY, USADepartments of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY, USADepartments of Pathology and Laboratory Medicine, Roswell Park Cancer Institute, Buffalo, NY, USABackground. RNA editing is a post-transcriptional regulatory mechanism that can alter the coding sequences of certain genes in response to physiological demands. We previously identified C-to-U RNA editing (C136U, R46X) which inactivates a small fraction of succinate dehydrogenase (SDH; mitochondrial complex II) subunit B gene (SDHB) mRNAs in normal steady-state peripheral blood mononuclear cells (PBMCs). SDH is a heterotetrameric tumor suppressor complex which when mutated causes paraganglioma tumors that are characterized by constitutive activation of hypoxia inducible pathways. Here, we studied regulation, extent and cell type origin of SDHB RNA editing.Methods. We used short-term cultured PBMCs obtained from random healthy platelet donors, performed monocyte enrichment by cold aggregation, employed a novel allele-specific quantitative PCR method, flow cytometry, immunologic cell separation, gene expression microarray, database analysis and high-throughput RNA sequencing.Results. While the editing rate is low in uncultured monocyte-enriched PBMCs (average rate 2.0%, range 0.4%–6.3%, n = 42), it is markedly upregulated upon exposure to 1% oxygen tension (average rate 18.2%, range 2.8%–49.4%, n = 14) and during normoxic macrophage differentiation in the presence of serum (average rate 10.1%, range 2.7%–18.8%, n = 17). The normoxic induction of SDHB RNA editing was associated with the development of dense adherent aggregates of monocytes in culture. CD14-positive monocyte isolation increased the percentages of C136U transcripts by 1.25-fold in normoxic cultures (n = 5) and 1.68-fold in hypoxic cultures (n = 4). CD14-negative lymphocytes showed no evidence of SDHB editing. The SDHB genomic DNA remained wild-type during increased RNA editing. Microarray analysis showed expression changes in wound healing and immune response pathway genes as the editing rate increased in normoxic cultures. High-throughput sequencing of SDHB and SDHD transcripts confirmed the induction of C136U RNA editing in normoxic cultures but showed no additional verifiable coding edits. Analysis of SDHB RNA sequence data from 16 normal human tissues from the Illumina Body Map and from 45 samples representing 23 different cell types from the ENCODE projects confirmed the occurrence of site-specific C136U editing in whole blood (1.7%) and two primary CD14+ monocyte samples (1.9% and 2.6%). In contrast, the other cell types showed an average of 0.2% and 0.1% C136U editing rates in the two databases, respectively.Conclusions. These findings demonstrate that C-to-U coding RNA editing of certain genes is dynamically induced by physiologically relevant environmental factors and suggest that epigenetic downregulation of SDHB by site-specific RNA editing plays a role in hypoxia adaptation in monocytes.https://peerj.com/articles/152.pdfEpigeneticEnvironmentRNA editingCytidine deaminaseMonocyteMacrophage |
| spellingShingle | Bora E. Baysal Kitty De Jong Biao Liu Jianmin Wang Santosh K. Patnaik Paul K. Wallace Robert T. Taggart Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes PeerJ Epigenetic Environment RNA editing Cytidine deaminase Monocyte Macrophage |
| title | Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes |
| title_full | Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes |
| title_fullStr | Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes |
| title_full_unstemmed | Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes |
| title_short | Hypoxia-inducible C-to-U coding RNA editing downregulates SDHB in monocytes |
| title_sort | hypoxia inducible c to u coding rna editing downregulates sdhb in monocytes |
| topic | Epigenetic Environment RNA editing Cytidine deaminase Monocyte Macrophage |
| url | https://peerj.com/articles/152.pdf |
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