A single mammalian transcript normally encodes one protein, but the transcript of GNAS （G-protein u-subunit） contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other conf...A single mammalian transcript normally encodes one protein, but the transcript of GNAS （G-protein u-subunit） contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other confirmed GNAS-Iike dual-coding transcripts have been reported to date, even though many such candidate genes have been predicted by bioinformatics analysis. In this study, we constructed a series of vectors to test how two protein products were translated from a single transcript in vitro. The length of the ORF （open reading frame）, position of the first AUG and the Kozak motif were found to be important factors. These factors, as well as 55-bp NMD （nonsense-mediated mRNA decay） rule, were used in a bioinformatics search for candidate dual-coding transcripts. A total of 1307, 750 and 474 two-ORF-containing transcripts were found in human, mouse and rat, respectively, of which 170, 89 and 70, respectively, were found to be potential dual-coding transcripts. Most transcripts showed low conservation among species. Interestingly, dual-coding transcripts were significantly enriched for transcripts from the zinc-finger protein family, which are usually DNA-binding proteins involved in regulation of the transcription process.展开更多
Eukaryotes have evolved a variety of mRNA surveillance mechanisms to detect and degrade aberrant mRNAs with potential deleterious outcomes.Among them,nonsense-mediated mRNA decay(NMD)functions not only as a quality co...Eukaryotes have evolved a variety of mRNA surveillance mechanisms to detect and degrade aberrant mRNAs with potential deleterious outcomes.Among them,nonsense-mediated mRNA decay(NMD)functions not only as a quality control mechanism targeting aberrant mRNAs containing a premature termination codon but also as a posttranscriptional gene regulation mechanism tar-geting numerous physiological mRNAs.Despite its well-characterized molecular basis,the regulatory scope and biological functions of NMD at an organismal level are incompletely understood.In humans,mutations in genes encoding core NMD factors cause specific developmental and neurological syndromes,suggesting a critical role of NMD in the central nervous system.Here,we review the accumulating biochemical and genetic evidence on the developmental regulation and physiological functions of NMD as well as an emerging role of NMD dysregulation in neurodegenerative diseases.展开更多
Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining （IR） transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating...Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining （IR） transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 14Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this sp!icing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay （NMD）-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.展开更多
Nonsense-mediated mRNA decay （NMD） is an important mRNA quality surveillance pathway in all eukaryotes that eliminates aberrant mRNAs derived from various sources. Three NMD factor proteins, UPF1, UPF2, and UPF3 are...Nonsense-mediated mRNA decay （NMD） is an important mRNA quality surveillance pathway in all eukaryotes that eliminates aberrant mRNAs derived from various sources. Three NMD factor proteins, UPF1, UPF2, and UPF3 are required for the NMD process and were found to be also involved in certain stress responses in mammalian and yeast cells. Using Arabidopsis thaliana mutants of UPF1 and UPF3 and UPF2-silenced lines （irUPF2）, we examined the involvement of UPF1, UPF2, and UPF3 in development and in response to stresses, wounding and infection by Pseudomonas syringae pv. tomato strain DC3000. Under the long （16 h） photoperiod condition, Arabidopsis having a defect in NMD factors exhibited altered morphologies of various organs, disturbed homeostasis of wounding-induced jasmonic acid and pathogen-elicited salicylic acid, and abnormal wounding- and methyl jasmonate-induced changes in the transcript levels of two defense-related genes, LOX2 and VSP2. Importantly, when plants were cultivated under the short （10 h） photoperiod condition, mutants of UPF1 and UPF3 and irUPF2 showed smaller differences from the wild-type plants in growth and stress-induced responses. These data suggest a complex regulatory network, likely composed of light signaling and NMD factor-mediated pathways, in influencing plant development and adaption to environmental stresses.展开更多
文摘A single mammalian transcript normally encodes one protein, but the transcript of GNAS （G-protein u-subunit） contains two reading frames and produces two structurally unrelated proteins, XLas and ALEX. No other confirmed GNAS-Iike dual-coding transcripts have been reported to date, even though many such candidate genes have been predicted by bioinformatics analysis. In this study, we constructed a series of vectors to test how two protein products were translated from a single transcript in vitro. The length of the ORF （open reading frame）, position of the first AUG and the Kozak motif were found to be important factors. These factors, as well as 55-bp NMD （nonsense-mediated mRNA decay） rule, were used in a bioinformatics search for candidate dual-coding transcripts. A total of 1307, 750 and 474 two-ORF-containing transcripts were found in human, mouse and rat, respectively, of which 170, 89 and 70, respectively, were found to be potential dual-coding transcripts. Most transcripts showed low conservation among species. Interestingly, dual-coding transcripts were significantly enriched for transcripts from the zinc-finger protein family, which are usually DNA-binding proteins involved in regulation of the transcription process.
基金Our work is supported by an NIH New Innovator Award(DP2 GM132930)the Muscular Dystrophy Association(MDA602934).J.U.G.is an NARSAD Young Investigator and a Klingenstein-Simons Fellow in NeuroscienceWe thank members of the Guo Lab for discussions。
文摘Eukaryotes have evolved a variety of mRNA surveillance mechanisms to detect and degrade aberrant mRNAs with potential deleterious outcomes.Among them,nonsense-mediated mRNA decay(NMD)functions not only as a quality control mechanism targeting aberrant mRNAs containing a premature termination codon but also as a posttranscriptional gene regulation mechanism tar-geting numerous physiological mRNAs.Despite its well-characterized molecular basis,the regulatory scope and biological functions of NMD at an organismal level are incompletely understood.In humans,mutations in genes encoding core NMD factors cause specific developmental and neurological syndromes,suggesting a critical role of NMD in the central nervous system.Here,we review the accumulating biochemical and genetic evidence on the developmental regulation and physiological functions of NMD as well as an emerging role of NMD dysregulation in neurodegenerative diseases.
文摘Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining （IR） transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 14Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this sp!icing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay （NMD）-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.
文摘Nonsense-mediated mRNA decay （NMD） is an important mRNA quality surveillance pathway in all eukaryotes that eliminates aberrant mRNAs derived from various sources. Three NMD factor proteins, UPF1, UPF2, and UPF3 are required for the NMD process and were found to be also involved in certain stress responses in mammalian and yeast cells. Using Arabidopsis thaliana mutants of UPF1 and UPF3 and UPF2-silenced lines （irUPF2）, we examined the involvement of UPF1, UPF2, and UPF3 in development and in response to stresses, wounding and infection by Pseudomonas syringae pv. tomato strain DC3000. Under the long （16 h） photoperiod condition, Arabidopsis having a defect in NMD factors exhibited altered morphologies of various organs, disturbed homeostasis of wounding-induced jasmonic acid and pathogen-elicited salicylic acid, and abnormal wounding- and methyl jasmonate-induced changes in the transcript levels of two defense-related genes, LOX2 and VSP2. Importantly, when plants were cultivated under the short （10 h） photoperiod condition, mutants of UPF1 and UPF3 and irUPF2 showed smaller differences from the wild-type plants in growth and stress-induced responses. These data suggest a complex regulatory network, likely composed of light signaling and NMD factor-mediated pathways, in influencing plant development and adaption to environmental stresses.
