Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis View Full Text


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Article Info

DATE

2022-04-19

AUTHORS

Ángel Ferrero-Serrano, Megan M. Sylvia, Peter C. Forstmeier, Andrew J. Olson, Doreen Ware, Philip C. Bevilacqua, Sarah M. Assmann

ABSTRACT

BackgroundGenome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.”ResultsWe experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation.ConclusionWe functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation. More... »

PAGES

101

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    32 schema:description BackgroundGenome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.”ResultsWe experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation.ConclusionWe functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation.
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    40 Arabidopsis accessions
    41 Arabidopsis genes
    42 Arabidopsis genome
    43 BackgroundGenome-wide association studies
    44 ConclusionWe
    45 ResultsWe
    46 abundance
    47 abundance variations
    48 accessions
    49 adaptation
    50 association
    51 association studies
    52 changes
    53 climate conditions
    54 climate descriptors
    55 conditionality
    56 conditions
    57 consequences
    58 continentality
    59 correlation
    60 demonstration
    61 descriptors
    62 differences
    63 environment
    64 environmental variation
    65 experimental demonstration
    66 expression
    67 first pan
    68 first time
    69 gene expression
    70 genes
    71 genetic variation
    72 genome
    73 genotypic variation
    74 impact
    75 information
    76 interaction
    77 local adaptation
    78 local climate conditions
    79 local environment
    80 local environmental variation
    81 mRNA
    82 mRNA structure
    83 macromolecular interactions
    84 natural environment
    85 natural genetic variation
    86 new web resource
    87 nucleotide variants
    88 pan
    89 phenotypic changes
    90 phenotypic consequences
    91 plant genomes
    92 plants
    93 polymorphism
    94 potential impact
    95 prediction
    96 presence
    97 resources
    98 respective transcripts
    99 riboSNitches
    100 role
    101 silico studies
    102 single nucleotide variants
    103 stability
    104 structure
    105 study
    106 temperature
    107 temperature variation
    108 terms
    109 time
    110 transcript abundance variation
    111 transcript stability
    112 transcription
    113 transcriptome
    114 transcripts
    115 translation
    116 v2.0
    117 variants
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    119 web resources
    120 wide prediction
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