RNA Biology of Plant Embryos (Nodine Group)

MicroRNAs (miRNAs) are short non-coding RNAs that mediate target transcript repression in plants and animals. Although miRNAs are required throughout development, relatively little is known regarding their embryonic functions.

To systematically characterize embryonic miRNAs in plants, we recently developed high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout Arabidopsis thaliana (Arabidopsis) embryogenesis (Schon et al., 2018, Genome Research; Plotnikova et al., 2019, Plant Cell). We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors.

These miRNA:target interactions have a profound impact on embryonic gene expression programs, and we demonstrated that the miRNA-mediated repression of several transcription factors were individually required for proper division patterns of various embryonic cell lineages (Fig. 1). These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the Arabidopsis body plan.

Figure 1 | miRNA-Mediated Repression of Transcription Factors is Required for Morphogenesis Example of how a miRNA localized to outer cells (left) restricts its target transcript factor to inner cell types (center) to enable proper embryo morphogenesis and developmental timing (right). (For more details, see Plotnikova et al. 2019, Plant Cell)
Figure 1 | miRNA-Mediated Repression of Transcription Factors is Required for Morphogenesis Example of how a miRNA localized to outer cells (left) restricts its target transcript factor to inner cell types (center) to enable proper embryo morphogenesis and developmental timing (right). (For more details, see Plotnikova et al. 2019, Plant Cell)

Excitingly, we have also discovered a dozen miRNA:target interactions that are highly enriched in embryos and appear to be involved in various processes including hormone signaling, organelle biology, pathogen defense and DNA methylation. For example, we have found that one miRNA dynamically cleaves and represses a transcript encoding a DNA methyltransferase during embryogenesis, and this is required to prevent the ectopic methylation of thousands of genes.

By studying the dynamic activities of this single miRNA during embryogenesis, we have uncovered how it helps balance the high methyltransferase activity during early embryogenesis that is required to silence mutagenic transposable elements while preventing off-targeting (i.e. epigenetic collateral damage) of protein-coding genes.

Figure 2 | Small RNA-Mediated Establishment of Nascent Epigenome Diagram illustrating how small RNAs dynamically help establish genome-wide DNA methylation patterns during embryogenesis. CHROMOMETHYLASE 3 (CMT3) levels are high during early embryogenesis and establish DNA methylation on transposons. During mid-embryogenesis, miR823 mediates the repression of CMT3 to prevent it from ectopically methylating protein-coding genes (Papareddy et al. 2021, bioRxiv). As CMT3 levels decrease, 24 nt small interfering RNAs (siRNAs) increase and guide de novo methyltransferases (e.g. DRM2) to transposons and establish methylation and subsequent silencing (based on Papareddy et al. 2020, Genome Biology). mCHH, CHH methylation (H ≠ G) guided by siRNAs/DRM2 and CMT2; mCHG, CHG methylation activities of CMT3.
Figure 2 | Small RNA-Mediated Establishment of Nascent Epigenome Diagram illustrating how small RNAs dynamically help establish genome-wide DNA methylation patterns during embryogenesis. CHROMOMETHYLASE 3 (CMT3) levels are high during early embryogenesis and establish DNA methylation on transposons. During mid-embryogenesis, miR823 mediates the repression of CMT3 to prevent it from ectopically methylating protein-coding genes (Papareddy et al. 2021, bioRxiv). As CMT3 levels decrease, 24 nt small interfering RNAs (siRNAs) increase and guide de novo methyltransferases (e.g. DRM2) to transposons and establish methylation and subsequent silencing (based on Papareddy et al. 2020, Genome Biology). mCHH, CHH methylation (H ≠ G) guided by siRNAs/DRM2 and CMT2; mCHG, CHG methylation activities of CMT3.

We have internship and thesis projects aimed at characterizing the functions of these embryo-enriched miRNA:target interactions further. We will use a combination of microscopy, genetics, genomics and additional methods to study embryo-enriched miRNA:target interactions further.