MicroRNA Dynamics and Functions During Arabidopsis Embryogenesis

Abstract

MicroRNAs (miRNAs) are short noncoding 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 (Arabidopsis thaliana), we developed or applied highthroughput 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 profound effects on embryonic gene expression programs. Moreover, we demonstrated that the miRNA-mediated repression of six transcription factors are individually required for proper division patterns of various embryonic cell lineages. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and they provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.

Unravelling the developmental and functional significance of an ancient Argonaute duplication

“…For each developmental stage, we immunoprecipitated each NveAGO in two biological replicates, and included two replicates of rabbit IgG IP as negative controls. Next, we generated sRNA libraries from IP-extracted, size-selected RNA (see methods) using a modified protocol suitable for lower sRNA quantities 23 . mirDeep2 24 was used for de-novo identification and quantification of novel and known Nematostella miRNAs.…”

“…Library preparation for RNA extracted from NveAGO1 and NveAGO2 IP was size selected for 18-30 nucleotides on 15% denaturing urea polyacrylamide gel (Bio-Rad) followed by overnight RNA elution in 0.3M NaCl. Next, library preparation was carried out using NEBNext Multiplex Small RNA Library Prep Set for Illumina kit (New England Biolabs) with modified protocol 23 for improving low-input samples and sequenced with NextSeq500 (Illumina) as described above. This procedure was carried out on two distinct biological replicates for each AGO in each of the developmental stages.…”

Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress

“…For the analysis of stress response, the time series sequencing method has been used in many works to study changes at the transcriptional level [24,25,44,45]. Most of these studies compared processed samples with a control sample to obtain the differentially expressed genes.…”

“…Unlike animals, plants cannot move when the living environment changes. Some common changes in animals and plants include transcriptional regulation of transcription factors [10], alternative splicing [47], and miRNA regulation [25,44], while some studies have focused on important developmental pathways. Mitogen-activated protein kinase kinase kinase (MAPKKK) family members were found to be related to drought tolerance in maize through RNA-seq analysis [48].…”

“…The candidate genes for Fusarium wilt and sterility mosaic disease in pigeonpea have been identified by next-generation sequencing [23]. There are many similar works of time series sequencing for development and stress analysis in Arabidopsis [24,25]. Therefore, the transcriptome sequencing of time series is a good method to study the important pathways and functional changes under stress responses.In the current study, we analyzed the whole transcriptome changes under aluminum response by time series RNA sequencing (RNA-seq) in pigeonpea.…”