Translatomics for plant stress and development
Recent Publications Harnessing the Power of Translatomics
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers,
- Carey-Fung et al. uncover a conserved upstream open reading frame in IDEF2 that represses translation and fine-tunes iron deficiency responses.
- Zhang et al. (2024) apply paired transcriptome and translatome profiling in wild-type (Col-0) and the double mutant GRP7/GRP8 under abscisic acid (ABA) treatment in Arabidopsis, exposing how RNA-binding proteins shape translation downstream of hormonal stress signals.
- Zhang et al. (2025) show that m6A methylation of CmEIN2’s 5ʹUTR dampens its translation, delaying chrysanthemum leaf senescence.
Together, these studies emphasize the central role of translational control in nutrient regulation, stress, and aging.
Discovery of a conserved translationally repressive upstream open reading frame within the iron-deficiency response regulator IDEF2
BMC Plant Biology, 2024.
Oscar Carey-Fung, Jesse T. Beasley, Ronan C. Broad, Roger P. Hellens, Alexander A. T. Johnson
While IDEF1 and IDEF2 are central to the plant response to iron deficiency, their regulation beyond transcription is poorly understood. The authors first identified putative cis-regulatory uORFs in iron-related genes using public rice ribosome profiling datasets. They then identified candidate uORFs in several Fe homeostasis genes, particularly focusing on IDEF1 and IDEF2. Using dual-luciferase reporter assays in plant leaf assays, they mutated putative start codons in the 5′ leader sequences and quantified effects on downstream main ORF, translation.
For IDEF2, mutation of conserved uORF start sites led to roughly 2- to 4-fold derepression of mORF translation, especially in wheat orthologs. The IDEF2 uORF and flanking region are highly conserved across monocots, and its regulatory effect responds to external iron levels.
These results reveal a translationally repressive uORF built into IDEF2’s 5′ leader that modulates its expression post-transcriptionally. This mechanism allows plants to fine-tune IDEF2 activity in response to iron availability without altering mRNA levels. From a practical standpoint, the work highlights uORFs as precision editing targets: by modulating or mutating these regulatory elements, one could fine-tune expression of iron-deficiency regulators like IDEF2 to improve crop nutrition and stress tolerance.
Learn more about EIRNABio’s ribosome profiling services here.
Transcriptome and translatome profiling of Col-0 and grp7grp8 under ABA treatment in Arabidopsis
Scientific Data, 2024
Jing Zhang, Yongxin Xu, Jun Xiao
This paper investigates how the phytohormone abscisic acid (ABA) regulates not only gene transcription but also mRNA translation in Arabidopsis thaliana. Although ABA-mediated transcriptional responses are well studied, the downstream translational dynamics remain poorly characterized.
Zhang, Xu and Xiao treated 3-day-old seedlings of the wild-type Col-0 and the double mutant grp7grp8—lacking the glycine-rich RNA-binding proteins GRP7 and GRP8—with either 5 µM ABA or mock solution. They then performed high-throughput RNA-seq and ribosome profiling. Additionally, they used CLIP-seq on a pGRP7::GRP7-GFP line to identify direct RNA targets of GRP7 under ABA or control treatments.
This revealed a large set of genes whose translation efficiency changes under ABA independently of transcript levels, revealing a layer of translational regulation. Moreover, the grp7grp8 mutant displayed distinct translation profiles compared to Col-0, and GRP7 was shown to bind numerous transcripts related to translational control and ABA signaling. Collectively, the dataset offers insight into how GRP7/GRP8 modulate translation downstream of ABA.
Their work underscores the importance of pairing transcriptomic and translational datasets to uncover regulation that mRNA levels alone miss. It also provides a resource for investigating ABA-mediated translation and RBP (RNA-binding protein) function in early seedling responses, opening paths to crop stress-resilience strategies.
Learn more about EIRNABio’s ribosome profiling services here.
m⁶A-mediated translational regulation of the CmEIN2 gene controls leaf senescence
Postharvest Biology & Technology, 2025.
Hua Zhang, Shiyu Sun, Yuqing Huang, Yuna Yang, Jiafu Jiang, Sumei Chen, Fadi Chen, Likai Wang
This study examines how m6A RNA methylation regulates leaf senescence in chrysanthemum by modulating translation of a key ethylene signalling gene. While m6A modifications are known to influence mRNA stability or splicing, their role in translational control in plants is less understood.
The authors found that CmEIN2, a central regulator of ethylene signaling and senescence, is subject to m6A‐mediated translational suppression. They mapped m6A sites in the 5ʹ UTR of CmEIN2 and showed that methylation reduces ribosome occupancy without significantly altering mRNA levels, indicating a post‐transcriptional regulatory effect. Using mutagenesis of m6A consensus motifs and reporter constructs, they demonstrated that loss of methylation sites led to increased translation of CmEIN2 and accelerated leaf aging phenotypes. Conversely, overexpressing methyltransferase components enhanced m6A levels and delayed senescence. They also correlated m6A levels on CmEIN2 transcripts with senescence stages, showing dynamic regulation in leaves aging.
These findings highlight a translational control layer whereby m6A installs a “brake” on CmEIN2 protein synthesis, fine‐tuning the onset of leaf senescence under developmental cues. For researchers using ribosome profiling and translational assays, this work underscores the need to integrate m6A mapping with Ribo-seq to detect methylation‐dependent regulation. In crop biology, targeting m6A machinery or editing methylation sites in senescence regulators like EIN2 may provide new strategies to delay aging, improve yield stability, or extend leaf functional lifespan under stress.
Learn more about EIRNABio’s ribosome profiling services here.
