Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both.

Jack Colicchio,John Kelly,Lena Hileman

doi:10.3390/ijms21207552

Abstract

Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated.

Highlights

The capacity of cells carrying identical DNA sequences to function in remarkably divergent ways is vital for the evolution of complex life
We determined (1) whether small-interfering RNAs (siRNA) populations differ between leaf-wounded and control plants; (2) whether proximity of small RNAs (sRNA) loci increases the probability that protein coding regions will be differentially methylated or differentially expressed in progeny of leaf wounded plants; and (3) whether sRNA abundance, gene expression or DNA methylation differences in offspring of wounded compared to control plants correlate with sRNA profiles in the parent generation after leaf wounding
At the second leaf pair of leaf wounded offspring compared to offspring of control plants, we identified 2 micro RNA (miRNA), 1 siRNA and 1 Non-dicer derived sRNA (nd-sRNA) locus with significantly different sRNA abundances (FDR < 0.05)

Summary

Introduction

The capacity of cells carrying identical DNA sequences to function in remarkably divergent ways is vital for the evolution of complex life. These programs can leave a lasting epigenetic mark on the genome in cells that have received developmental or environmental signals These lasting epigenetic modifications include DNA methylation, histone methylation and histone acetylation and can alter the RNA expression, chromatin accessibility and splicing that occurs proximal to these markings [1,2,3]. These markings can be transmitted between mitotic and sometimes meiotic cell divisions [4,5] allowing developmental and environmental cues to leave a lasting impact on a cell lineage, altering the development of cells in later life history stages or even in the generation. Autocorrelation between offspring and parent environment can favor mechanisms that establish such patterns of transgenerational plasticity [17,18], perhaps leading to natural selection that either favors or disfavors this transmission depending on local environmental patterns [11]

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Results

Conclusion