MicroRNA Dynamics and Functions DuringArabidopsisEmbryogenesis

Abstract

MicroRNAs (miRNAs) are short non-coding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs in Arabidopsis thaliana , we developed or applied high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have a profound impact on embryonic gene expression programs, and we further demonstrated that the miRNA-mediated repression of six transcription factors were individually required for embryo morphogenesis. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.

Chromatin Regulates Bipartite-Classified Small RNA Expression to Maintain Epigenome Homeostasis in Arabidopsis

“…We recently developed a low-input small RNA sequencing (sRNA-seq) method to profile small RNA dynamics during eight stages of Arabidopsis embryogenesis, as well as floral buds and leaves [39] (Fig. 1a and Additional file 1).…”

“…1a and Additional file 1). We previously focused on the~21-nt microRNA class of small RNAs involved in post-transcriptional regulation [39] , but noticed that the vast majority of TE-derived small RNAs were 24-nt long and highly enriched in embryos compared to floral bud or leaf tissues ( Fig. 1b and Fig.…”

“…with nuclease-free water, and stored at -80°C. RNA was isolated as previously described [39,98] and genomic DNA was isolated as follows. Genomic DNA was extracted from ≥ 50 embryos per stage, floral buds and leaves using Quick-DNA TM Micro prep Kit (Zymo D3020) according to manufacturer recommendations.…”

“…sRNA-seq libraries were generated as previously described [39] , and together with publicly available datasets were analyzed in the same manner. For the model-based clustering of transposon-derived siRNAs, 24-nt siRNAs mapping to TEs annotated in the The Arabidopsis Information Resource 10 (TAIR10) genome [99] were partitioned into clusters using Mclust [42] .…”

“…The software code used for the sRNA, methylome and transcriptome analysis are available at github.com/Papareddy . [29,39,[91][92][93][94] . b Relative enrichments of 24-nt siRNAs derived from heterochromatic relative to euchromatic TEs in RdDM and related mutants.…”