Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both
Abstract
:1. Introduction
2. Results
2.1. Classification of the Mimulus Leaf sRNAome
2.2. Wound Responsive sRNAs
2.2.1. Micro RNA (miRNA) Loci
2.2.2. Dicer-Derived sRNA (siRNA) Loci
2.2.3. Non-Dicer Derived sRNA (nd-sRNA) Loci
2.2.4. Response Correlations at nd-sRNA Loci
2.3. Relationship between sRNA Loci and Transgenerationally Plastic DNA Methylation and Gene Expression
2.3.1. sRNA Loci and Differential Methylation
2.3.2. sRNA Loci and Differential Gene Expression
3. Discussion
3.1. sRNA Responses at the Site of Leaf Wounding
3.2. sRNA Loci Are Proximal to Differentially Methylated and Expressed Genomic Regions
3.3. sRNA Responses Do Not Predict Transgenerational Plasticity
4. Materials and Methods
4.1. RNA Extraction, Library Preparation and Read Mapping
4.2. Differential Expression Calling
4.3. Downstream Statistical Analyses
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
sRNA | small RNA |
siRNA | small interfering RNA |
miRNA | micro RNA |
tRF | tRNA derived fragment |
nd-sRNA | non-dicer derived sRNA |
LFC | log fold change |
DMR | differentially expressed region |
RdDM | RNA dependent DNA methylation |
RNAi | RNA interference |
DE | differentially expressed |
ANOVA | Analysis of Variance |
log10(rpm) | log base 10 of the read pairs mapping |
df | degrees of freedom |
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sRNA Class | Number of Identified Loci | Log(rpm) | Mean Locus Length | % Overlap with CDS 4 | % Overlap with TEs 5 |
---|---|---|---|---|---|
miRNA 1 | 44 | 1.4 | 227 | 9.3% | 29.6% |
siRNA 2 | 26,052 | 0.37 | 409 | 9.7% | 89.9% |
20 nt | 10 | 0.46 | 200 | 0 | 66.7% |
21 nt | 226 | 0.78 | 601 | 45.3% | 51.6% |
22 nt | 411 | 0.76 | 501 | 12.6% | 78.7% |
23 nt | 50 | 0.39 | 254 | 12.5% | 87.5% |
24 nt | 25,412 | 0.36 | 406 | 9.4% | 90.4% |
nd-sRNA 3 | 3775 | 0.66 | 774 | 62.7% | 30.8% |
1 h 2nd Leaf LFC | 72 h 2nd Leaf LFC | 72 h 3rd Leaf LFC | |||||||
---|---|---|---|---|---|---|---|---|---|
Term | SS | F | p | SS | F | p | SS | F | p |
mRNA Tgen Change 1 (2) | 1.01 | 0.09 | 0.08 | 12.04 | 14.10 | <0.0001 | 1.11 | 4.19 | 0.01 |
sRNA loci type 2 (1) | 0.83 | 4.18 | 0.04 | 1.71 | 4.02 | 0.04 | 0.24 | 1.86 | 0.17 |
sRNA 2 x Tgen 1 (2) | 1.20 | 3.01 | 0.05 | 10.43 | 12.21 | <0.0001 | 0.76 | 2.87 | 0.06 |
Full Model: n = 7473 | F = 4.4, p = 0.0005 | F = 37.9, p < 0.00001 | F = 1.9, p = 0.08 |
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Colicchio, J.; Kelly, J.; Hileman, L. Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both. Int. J. Mol. Sci. 2020, 21, 7552. https://doi.org/10.3390/ijms21207552
Colicchio J, Kelly J, Hileman L. Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both. International Journal of Molecular Sciences. 2020; 21(20):7552. https://doi.org/10.3390/ijms21207552
Chicago/Turabian StyleColicchio, Jack, John Kelly, and Lena Hileman. 2020. "Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both" International Journal of Molecular Sciences 21, no. 20: 7552. https://doi.org/10.3390/ijms21207552