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Astrocytes and microglia undergo dynamic and complex morphological and functional changes following ischemic stroke, which are instrumental in both inflammatory responses and neural repair. While gene expression alterations poststroke have been extensively studied, investigations into posttranscriptional regulatory mechanisms, specifically alternative splicing (AS), remain limited. Utilizing previously reported Ribo‐Tag‐seq data, this study analyzed AS alterations in poststroke astrocytes and microglia from young adult male and female mice. Our findings reveal that in astrocytes, compared to the sham group, 109 differential alternative splicing (DAS) events were observed at 4 h poststroke, which increased to 320 at day 3. In microglia, these numbers were 316 and 266, respectively. Interestingly, the disparity between DAS genes and differentially expressed genes is substantial, with fewer than 10 genes shared at both poststroke time points in astrocytes and microglia. Gene ontology enrichment analysis revealed the involvement of these DAS genes in diverse functions, encompassing immune response (Adam8, Ccr1), metabolism (Acsl6, Pcyt2, Myo5a), and developmental cell growth (App), among others. Selective DAS events were further validated by semiquantitative RT‐PCR. Overall, this study comprehensively describes the AS alterations in astrocytes and microglia during the hyperacute and acute phases of ischemic stroke and underscores the significance of certain hub DAS events in neuroinflammatory processes. [ABSTRACT FROM AUTHOR]

Summary: The phellem is a specialized boundary tissue providing the first line of defense against abiotic and biotic stresses in organs undergoing secondary growth. Phellem cells undergo several differentiation steps, which include cell wall suberization, cell expansion, and programmed cell death. Yet, the molecular players acting particularly in phellem cell differentiation remain poorly described, particularly in the widely used model plant Arabidopsis thaliana. Using specific marker lines we followed the onset and progression of phellem differentiation in A. thaliana roots and further targeted the translatome of newly developed phellem cells using translating ribosome affinity purification followed by mRNA sequencing (TRAP‐SEQ). We showed that phellem suberization is initiated early after phellogen (cork cambium) division. The specific translational landscape was organized in three main domains related to energy production, synthesis and transport of cell wall components, and response to stimulus. Novel players in phellem differentiation related to suberin monomer transport and assembly as well as novel transcription regulators were identified. This strategy provided an unprecedented resolution of the translatome of developing phellem cells, giving a detailed and specific view on the molecular mechanisms acting on cell differentiation in periderm tissues of the model plant Arabidopsis. Significance Statement: To improve our understanding of phellem differentiation into a suberized protective layer, we followed the establishment of periderm in Arabidopsis roots and sequenced the phellem‐associated translatome. We found that phellem suberization occurs shortly after pericycle cell divisions with the induction of pivotal suberin biosynthesis genes. In parallel, we detected the activation of three central genetic modules acting throughout phellem differentiation. This study provides a unique and targeted genetic resource for further functional studies of phellem tissues. [ABSTRACT FROM AUTHOR]

Summary: Understanding the impact of elevated CO2 (eCO2) in global agriculture is important given climate change projections. Breeding climate‐resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2, from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2. Significance Statement: In a domesticated and a wild Solanum species, translational and transcriptional regulation feedback onto each other and show interspecific differences in response to elevated CO2. [ABSTRACT FROM AUTHOR]

Although glutathione is well known for its reactive oxygen species ( ROS) scavenging function and plays a protective role in biotic stress, its regulatory function in abiotic stress still remains to be elucidated. Our previous study showed that exogenously applied reduced glutathione ( GSH) could improve abiotic stress tolerance in Arabidopsis. Here, we report that endogenously increased GSH also conferred tolerance to drought and salt stress in Arabidopsis. Moreover, both exogenous and endogenous GSH delayed senescence and flowering time. Polysomal profiling results showed that global translation was enhanced after GSH treatment and by the induced increase of GSH level by salt stress. By performing transcriptomic analyses of steady-state and polysome-bound mRNAs in GSH-treated plants, we reveal that GSH has a substantial impact on translation. Translational changes induced by GSH treatment target numerous hormones and stress signaling molecules, which might contribute to the enhanced stress tolerance in GSH-treated plants. Our translatome analysis also revealed that abscisic acid ( ABA), auxin and jasmonic acid ( JA) biosynthesis, as well as signaling genes, were activated during GSH treatment, which has not been reported in previously published transcriptomic data. Together, our data suggest that the increased glutathione level results in stress tolerance and global translational changes. [ABSTRACT FROM AUTHOR]

Seed dormancy, which blocks germination in apparently favourable conditions, is a key regulatory control point of plant population establishment. As germination requires de novo translation, its regulation by dormancy is likely to be related to the association of individual transcripts to polysomes., Here, the polysome-associated mRNAs, that is, the translatome, were fractionated and characterized with microarrays in dormant and nondormant sunflower ( Helianthus annuus) embryos during their imbibition at 10°C, a temperature preventing germination of dormant embryos., Profiling of mRNAs in polysomal complexes revealed that the translatome differs between germinating and nongerminating embryos. Association of transcripts with polysomes reached a maximum after 15 h of imbibition; at this time-point 194 polysome-associated transcripts were specifically found in nondormant embryos and 47 in dormant embryos only. The proteins corresponding to the polysomal mRNAs in nondormant embryos appeared to be very pertinent for germination and were involved mainly in transport, regulation of transcription or cell wall modifications., This work demonstrates that seed germination results from a timely regulated and selective recruitment of mRNAs to polysomes, thus opening novel fields of investigation for the understanding of this developmental process. [ABSTRACT FROM AUTHOR]

Oxygen deficiency, caused by flooding of all or a portion of a plant, leads to significant gene regulatory and metabolic responses associated with survival. When oxygen-deprived in light, aerial organs and root systems respond in distinct manners because of their respective autotrophy and heterotrophy, as well as intrinsic differences in cell biology and organ function. To better understand organ-specific responses to oxygen deficiency, we monitored changes in the metabolome of roots and shoots of A rabidopsis thaliana seedlings using gas chromatography-mass spectrometry and 1 H-nuclear magnetic resonance spectroscopy. Only roots accumulated high amounts of γ-aminobutyrate ( GABA) and lactate, whereas both organs accumulated alanine ( Ala) upon hypoxia. Meta-analysis of gene regulation data revealed higher induction of m RNAs coding for fermentative enzymes in roots as compared with shoots. However, the elevation in GABA level was not correlated with changes in transcript abundance, supporting the proposal that post-translational mechanisms are important in metabolic acclimation to hypoxia. The biosynthesis, degradation and function of GABA and Ala during oxygen deprivation and re-aeration is discussed. Finally, a systematic survey of low-oxygen mediated regulation of genes associated with primary metabolism across organs and cell types reveals exciting new avenues for future studies. [ABSTRACT FROM AUTHOR]

Leaves of angiosperms are made up of multiple distinct cell types. While the function of mesophyll cells, guard cells, phloem companion cells and sieve elements are clearly described, this is not the case for the bundle sheath ( BS). To provide insight into the role of the BS in the C3 species Arabidopsis thaliana, we labelled ribosomes in this cell type with a FLAG tag. We then used immunocapture to isolate these ribosomes, followed by sequencing of resident m RNAs. This showed that 5% of genes showed specific splice forms in the BS, and that 15% of genes were preferentially expressed in these cells. The BS translatome strongly implies that the BS plays specific roles in sulfur transport and metabolism, glucosinolate biosynthesis and trehalose metabolism. Much of the C4 cycle is differentially expressed between the C3 BS and the rest of the leaf. Furthermore, the global patterns of transcript residency on BS ribosomes overlap to a greater extent with cells of the root pericycle than any other cell type. This analysis provides the first insight into the molecular function of this cell type in C3 species, and also identifies characteristics of BS cells that are probably ancestral to both C3 and C4 plants. [ABSTRACT FROM AUTHOR]

Loaded into ARGONAUTE(AGO) proteins, eukaryotic micro(mi)RNAs regulate gene expression via cleavage, translational repression, and/or accelerated decay of sequence‐complementary target transcripts. Despite their importance in development, cell identity maintenance and stress responses, how individual miRNAs contribute to spatial gene regulation within the complex cell mosaics formed in tissues/organs has remained inaccessible in any organism to date. We have developed a non‐invasive methodology to examine, at single‐cell‐type resolution, the AGO‐loading and activity patterns of entire miRNA cohorts in intact organs, applied here to the Arabidopsis root tip. A dual miRNAome–targetome analytical interface allowing intuitive data integration/visualization was developed as the basis for in‐depth investigations via single‐cell‐type experimentation. These uncovered an array of so far speculative or hitherto unknown types of spatial miRNA‐mediated gene regulation schemes, including via widespread cell‐to‐cell movement between contiguous layers of distinct identities. This study provides the proof of principle that minimally invasive, genome‐scale analysis of miRNA activities within and between single‐cell types of whole organs is achievable. Synopsis: Spatial coordination of miRNA activity at a genome‐wide level within and across the various cell types of an intact organ remains largely unexplored. The current study tackles this question in the Arabidopsis root tip and offers novel insights into miRNA‐mediated gene regulation in a complex organ. Exhaustive, cell‐type‐specific repertoires of functional miRNAs ("miRNAomes") where acquired via cell‐type‐specific AGO1 immunoprecipitation.Cell‐type‐specific translatomes obtained in WT versus miRNA‐deficient roots allowed identification of cell‐type‐specific repertoires of miRNA target transcripts ("targetomes").miRNAomes and targetomes were then integrated into the miRoot browser, allowing user‐friendly data interrogation.miRoot coupled to experimentation uncovered new modes of plant miRNA action, including via unexpectedly widespread, functional cell‐to‐cell movement of miRNA between root layers. [ABSTRACT FROM AUTHOR]