Architecture and Dynamics of the Jasmonic Acid Gene Regulatory Network

Abstract

Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. To advance our understanding of the architecture and dynamic regulation of the JA gene regulatory network, we performed a high-resolution RNA-seq time series of methyl JA-treated Arabidopsis thaliana at 15 time points over a 16-h period. Computational analysis showed that methyl JA (MeJA) induces a burst of transcriptional activity, generating diverse expression patterns over time that partition into distinct sectors of the JA response targeting specific biological processes. The presence of transcription factor (TF) DNA binding motifs correlated with specific TF activity during temporal MeJA-induced transcriptional reprogramming. Insight into the underlying dynamic transcriptional regulation mechanisms was captured in a chronological model of the JA gene regulatory network. Several TFs, including MYB59 and bHLH27, were uncovered as early network components with a role in pathogen and insect resistance. Analysis of subnetworks surrounding the TFs ORA47, RAP2.6L, MYB59, and ANAC055, using transcriptome profiling of overexpressors and mutants, provided insights into their regulatory role in defined modules of the JA network. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints and validates previously unknown regulators, and provides a valuable resource for functional studies on JA signaling components in plant defense and development.

Root transcriptional dynamics induced by beneficial rhizobacteria and microbial immune elicitors reveal signatures of adaptation to mutualists

“…Each biological replicate consisted of eight roots that were pooled to form one sample. RNA‐Illumina sequencing yielded on average 30 million reads per sample, of which > 90% aligned to the Arabidopsis genome after quality filtering (Van Verk et al ., ; Hickman et al ., ). The expression profiles of MYB51 and CYP71A12 quantified by RNA‐Seq were highly similar to those quantified by quantitative reverse transcriptase‐polymerase chain reaction (qRT‐PCR; Figure a), confirming that the RNA‐Seq analysis was performed correctly.…”

Foliar herbivory by caterpillars and aphids differentially affects phytohormonal signalling in roots and plant defence to a root herbivore

“…Moreover, from studies on leaf defence signalling, we know that ABA and ET are important in fine‐tuning JA responses (Pieterse et al, ). In above‐ground tissues, MeJA induction regulates over 3,500 transcripts in Arabidopsis thaliana (Hickman et al, ), and onion thrips ( Thrips tabaci ) feeding influences the transcription of about 10% of all B. oleracea genes (Sarde et al, in prep). Not all of these are involved in defence, as JA regulates many other processes, such as the regulation of root growth, formation of root hairs, lateral roots, and adventitious roots (Wasternack & Feussner, ).…”

Molecular dialogue between arbuscular mycorrhizal fungi and the nonhost plant Arabidopsis thaliana switches from initial detection to antagonism

“…For read alignment, summarization and normalization, we followed the RNA‐seq data analysis pipeline as previously described (Van Verk et al ., ; Coolen et al ., ; Hickman et al ., ). Reads were aligned to the Arabidopsis genome (TAIR version 10) and the Medicago genome (EnsemblGenomes) using TopHat v.2.0.452 (Center for Computational Biology, Baltimore, MD, USA) with the following parameter settings: ‘transcriptome‐mismatches 3’, ‘N 3’, ‘bowtie1’, ‘no‐novel‐juncs’, ‘genome‐read‐mismatches 3’, ‘p 6’, ‘read‐mismatches 3’, ‘G’, ‘min‐intron‐length 40’ and ‘max‐intron‐length 2000’.…”