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• 1. [Article] Mitochondria-derived Small Non-coding RNAs in Extreme Anoxia Tolerance

  Mitochondria are critical sensors of oxygen and play a major role in the regulation of the cellular response to oxygen deprivation. Understanding mitochondrial function during transitions into and out ...

  Citation × Citation Citation Abstract Copy Title: Mitochondria-derived Small Non-coding RNAs in Extreme Anoxia Tolerance Author: Riggs, Claire L., Podrabsky, Jason E. Year: 2017 Mitochondria are critical sensors of oxygen and play a major role in the regulation of the cellular response to oxygen deprivation. Understanding mitochondrial function during transitions into and out of anoxia in species that can tolerate anoxia may lend new insights into the role that mitochondria play in cellular homeostasis in response to fluctuating levels of oxygen. The objective of this study was to examine the potential role of small RNAs in long-term vertebrate anoxia tolerance. Expression patterns of small RNAs were determined using RNAseq in the most anoxia tolerant vertebrate, embryos of the annual killifishAustrofundulus limnaeus. Anoxia tolerance varies during development in this species in a way that allows for the comparison of developmental stages with extreme anoxia tolerance to stages with a more typical vertebrate anoxia tolerance. Embryos of 4 different developmental stages were exposed to anoxia, followed by aerobic recovery, and small RNA expression was determined with Illumina RNAseq under aerobic conditions, anoxia, and during aerobic recovery. A large proportion of the differentially expressed small RNAs were found to be encoded in the mitochondrial genome. About 12% of the unique small RNAs identified were encoded within the mitochondrial genome, and around 20% of the highly differentially expressed RNAs in response to anoxia were mitochondrial in origin. Of the differentially expressed sequences mapping to the mitochondrial genome, small RNAs derived from mitochondrial tRNAs were particularly enriched, with sequences up-regulated during anoxia and aerobic recovery from anoxia. These small RNAs of interest localize to anoxia sensitive tissues, such as the brain and heart, providing further evidence for a potential role in supporting anoxia tolerance. These same small RNAs have been detected in cell cultures derived from A. limnaeus embryos, by RNAseq and in situ hybridization. Cell culture expression patterns corroborated whole-embryo sequence expression patterns. This work highlights a potential new class of small RNAs derived from the mitochondrial genome that may act to mediate and coordinate the physiological response to anoxia in this species. Further understanding the biology of these mitochondrially-derived small RNAs and their role in anoxia tolerance may provide novel insight into combating cellular damage induced by heart attack and stroke, two lethal consequences of heart disease in humans. Title: Mitochondria-derived Small Non-coding RNAs in Extreme Anoxia Tolerance Author: Riggs, Claire L., Podrabsky, Jason E. Year: 2017 Mitochondria are critical sensors of oxygen and play a major role in the regulation of the cellular response to oxygen deprivation. Understanding mitochondrial function during transitions into and out of anoxia in species that can tolerate anoxia may lend new insights into the role that mitochondria play in cellular homeostasis in response to fluctuating levels of oxygen. The objective of this study was to examine the potential role of small RNAs in long-term vertebrate anoxia tolerance. Expression patterns of small RNAs were determined using RNAseq in the most anoxia tolerant vertebrate, embryos of the annual killifishAustrofundulus limnaeus. Anoxia tolerance varies during development in this species in a way that allows for the comparison of developmental stages with extreme anoxia tolerance to stages with a more typical vertebrate anoxia tolerance. Embryos of 4 different developmental stages were exposed to anoxia, followed by aerobic recovery, and small RNA expression was determined with Illumina RNAseq under aerobic conditions, anoxia, and during aerobic recovery. A large proportion of the differentially expressed small RNAs were found to be encoded in the mitochondrial genome. About 12% of the unique small RNAs identified were encoded within the mitochondrial genome, and around 20% of the highly differentially expressed RNAs in response to anoxia were mitochondrial in origin. Of the differentially expressed sequences mapping to the mitochondrial genome, small RNAs derived from mitochondrial tRNAs were particularly enriched, with sequences up-regulated during anoxia and aerobic recovery from anoxia. These small RNAs of interest localize to anoxia sensitive tissues, such as the brain and heart, providing further evidence for a potential role in supporting anoxia tolerance. These same small RNAs have been detected in cell cultures derived from A. limnaeus embryos, by RNAseq and in situ hybridization. Cell culture expression patterns corroborated whole-embryo sequence expression patterns. This work highlights a potential new class of small RNAs derived from the mitochondrial genome that may act to mediate and coordinate the physiological response to anoxia in this species. Further understanding the biology of these mitochondrially-derived small RNAs and their role in anoxia tolerance may provide novel insight into combating cellular damage induced by heart attack and stroke, two lethal consequences of heart disease in humans. Close

• 2. [Article] Small Noncoding RNA Expression During Extreme Anoxia Tolerance of Annual Killifish (Austrofundulus limnaeus) Embryos

  Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially ...

  Citation × Citation Citation Abstract Copy Title: Small Noncoding RNA Expression During Extreme Anoxia Tolerance of Annual Killifish (Austrofundulus limnaeus) Embryos Author: Riggs, Claire L., Podrabsky, Jason E. Year: 2017 Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days at their peak tolerance at 25°C. Their anoxia tolerance and physiology vary over development, such that both anoxia-tolerant and anoxia-sensitive phenotypes comprise the species. This allows for a robust comparison to identify sncRNAs essential to anoxia-tolerance. For this study, RNA sequencing was used to identify and quantify expression of sncRNAs in four embryonic stages of A. limnaeus in response to an exposure to anoxia and subsequent aerobic recovery. Unique stage-specific patterns of expression were identified that correlate with anoxia tolerance. In addition, embryos of A. limnaeus appear to constitutively express stress-responsive miRNAs. Most differentially expressed sncRNAs were expressed at higher levels during recovery. Many novel groups of sncRNAs with expression profiles suggesting a key role in anoxia tolerance were identified, including sncRNAs derived from mitochondrial tRNAs. This global analysis has revealed groups of candidate sncRNAs that we hypothesize support anoxia tolerance. Title: Small Noncoding RNA Expression During Extreme Anoxia Tolerance of Annual Killifish (Austrofundulus limnaeus) Embryos Author: Riggs, Claire L., Podrabsky, Jason E. Year: 2017 Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days at their peak tolerance at 25°C. Their anoxia tolerance and physiology vary over development, such that both anoxia-tolerant and anoxia-sensitive phenotypes comprise the species. This allows for a robust comparison to identify sncRNAs essential to anoxia-tolerance. For this study, RNA sequencing was used to identify and quantify expression of sncRNAs in four embryonic stages of A. limnaeus in response to an exposure to anoxia and subsequent aerobic recovery. Unique stage-specific patterns of expression were identified that correlate with anoxia tolerance. In addition, embryos of A. limnaeus appear to constitutively express stress-responsive miRNAs. Most differentially expressed sncRNAs were expressed at higher levels during recovery. Many novel groups of sncRNAs with expression profiles suggesting a key role in anoxia tolerance were identified, including sncRNAs derived from mitochondrial tRNAs. This global analysis has revealed groups of candidate sncRNAs that we hypothesize support anoxia tolerance. Close