Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated by MPK3, MPK4 and MPK6. These responses have been mainly analyzed at the transcriptional level, however many splicing factors are direct targets of MAPKs. Here, we studied alternative splicing induced by the PAMP flagellin in Arabidopsis. We identified 506 PAMP-induced differentially alternatively spliced (DAS) genes. Although many DAS genes are targets of nonsense-mediated degradation (NMD), only 19% are potential NMD targets. Importantly, of the 506 PAMP-induced DAS genes, only 89 overlap with the set of 1849 PAMP-induced differentially expressed genes (DEG), indicating that transcriptome analysis does not identify most DAS events. Global DAS analysis of mpk3, mpk4, and mpk6 mutants revealed that MPK4 is a key regulator of PAMP-induced differential splicing, regulating AS of a number of splicing factors and immunity-related protein kinases, such as the calcium-dependent protein kinase CPK28, the cysteine-rich receptor like kinases CRK13 and CRK29 or the FLS2 co-receptor SERK4/BKK1.These data suggest that MAP kinase regulation of splicing factors is a key mechanism in PAMP-induced AS regulation of PTI.

bioRxiv, 511980

DOI: 10.1101/511980

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Whole-genome landscape of Medicago truncatula symbiotic genes.

Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.

Nature Plants, 2018, 4(12):1017-1025

DOI: 10.1038/s41477-018-0286-7

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Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses.

Nuclear speckle RNA binding proteins (NSRs) act as regulators of alternative splicing (AS) and auxin-regulated developmental processes such as lateral root formation in Arabidopsis thaliana. These proteins were shown to interact with specific alternatively spliced mRNA targets and at least with one structured lncRNA, named Alternative Splicing Competitor RNA. Here, we used genome-wide analysis of RNAseq to monitor the NSR global role on multiple tiers of gene expression, including RNA processing and AS. NSRs affect AS of 100s of genes as well as the abundance of lncRNAs particularly in response to auxin. Among them, the FPA floral regulator displayed alternative polyadenylation and differential expression of antisense COOLAIR lncRNAs in nsra/b mutants. This may explains the early flowering phenotype observed in nsra and *nsra/b mutants. GO enrichment analysis of affected lines revealed a novel link of NSRs with the immune response pathway. A RIP-seq approach on an NSRa fusion protein in mutant background identified that lncRNAs are privileged direct targets of NSRs in addition to specific AS mRNAs. The interplay of lncRNAs and AS mRNAs in NSR-containing complexes may control the crosstalk between auxin and the immune response pathway.

Front. Plant Sci., 2018, 9:1209.

DOI: 10.3389/fpls.2018.01209

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Light dynamically regulates growth rate and cellular organisation of the Arabidopsis root meristem.

Large-scale methods and robust algorithms are needed for a quantitative analysis of cells status/geometry in situ. It allows the understanding the cellular mechanisms that direct organ growth in response to internal and environmental cues. Using advanced whole-stack imaging in combination with pattern analysis, we have developed a new approach to investigate root zonation under different dark/light conditions. This method is based on the determination of 3 different parameters: cell length, cell volume and cell proliferation on the cell-layer level. This method allowed to build a precise quantitative 3D cell atlas of the Arabidopsis root tip. Using this approach we showed that the meristematic (proliferation) zone length differs between cell layers. Considering only the rapid increase of cortex cell length to determine the meristematic zone overestimates of the proliferation zone for epidermis/cortex and underestimates it for pericycle. The use of cell volume instead of cell length to define the meristematic zone correlates better with cell proliferation zone.

bioRxiv, 353987

DOI: 10.1101/353987

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Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions.

In Arabidopsis thaliana, HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b) controls resistance to environmental stress and is a determinant of reproductive fitness by influencing seed yield. To understand how HSFA1b achieves this, we surveyed its genome-wide targets (ChIP-seq) and its impact on the transcriptome (RNA-seq) under non-stress (NS), heat stress (HS) in the wild type, and in HSFA1b-overexpressing plants under NS. A total of 952 differentially expressed HSFA1b-targeted genes were identified, of which at least 85 are development associated and were bound predominantly under NS. A further 1780 genes were differentially expressed but not bound by HSFA1b, of which 281 were classified as having development-associated functions. These genes are indirectly regulated through a hierarchical network of 27 transcription factors (TFs). Furthermore, we identified 480 natural antisense non-coding RNA (cis NAT) genes bound by HSFA1b, defining a further mode of indirect regulation. Finally, HSFA1b-targeted genomic features not only harboured heat shock elements, but also MADS box, LEAFY, and G-Box promoter motifs. This revealed that HSFA1b is one of eight TFs that target a common group of stress defence and developmental genes. We propose that HSFA1b transduces environmental cues to many stress tolerance and developmental genes to allow plants to adjust their growth and development continually in a varying environment.

Journal of Experimental Botany 2018, 69(11):2847–2862

DOI: 10.1093/jxb/ery142

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GDP-L-fucose is required for boundary definition in plants

The CUP-SHAPED COTYLEDON (CUC) transcription factors control plant boundary formation, thus allowing the emergence of novel growth axes. While the developmental roles of the CUC genes in different organs and across species are well characterized, upstream and downstream events that contribute to their function are still poorly understood. To identify new players in this network, we performed a suppressor screen of CUC2g-m4, a line overexpressing CUC2 that has highly serrated leaves. We identified a mutation that simplifies leaf shape and affects MURUS1 (MUR1), which is responsible for GDP-L-fucose production. Using detailed morphometric analysis, we show that GDP-L-fucose has an essential role in leaf shape acquisition by sustaining differential growth at the leaf margins. Accordingly, reduced CUC2 expression levels are observed in mur1 leaves. Furthermore, genetic analyses reveal a conserved role for GDP-L-fucose in different developmental contexts where it contributes to organ separation in the same pathway as CUC2. Taken together, our results reveal that GDP-L-fucose is necessary for proper establishment of boundary domains in various developmental contexts.

Journal of Experimental Botany 2017, 68(21-22):5801–5811

DOI: 10.1093/jxb/erx402

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MicroRNAs (miRNAs) and Plant Development

Development in plants is a continuous process during which new tissues and organs are formed all along its life cycle. Development involves the coordination of both time and space of complex cellular processes such as proliferation, expansion and differentiation following endogenous programmes and in response to environmental signals. Since their discovery in 2002, plant microRNAs (miRNAs), a class of small single-stranded regulatory ribonucleic acids (RNAs) have emerged as important nodes in regulatory networks controlling plant development. For instance, miRNAs play important roles for cell fate determination during the patterning of organs and contribute to the regulation of their growth. In addition, miRNAs integrate different signals to regulate the life cycle of plants. Finally, miRNAs appear as molecular links between environmental signals and plant development and may constitute levers to modify plant development in crops.

Key Concepts

  • miRNAs are essential for plant development as mutants affecting miRNA biogenesis or function are embryo lethal or show severe pleiotropic defects.
  • miRNA precursors are mostly produced from independent genetic units and are processed into mature miRNAs via a complex core machinery.
  • miRNAs can have different effects on the expression of their target genes, controlling their spatial pattern, their level of expression or the timing of their expression.
  • miRNAs are regulating many different developmental processes, including pattern formation, morphogenesis and differentiation at all stages of a plant's life.
  • Most of the miRNAs regulating plant development are evolutionary conserved and target evolutionary conserved transcription factors.
  • miRNAs can act non-cell-autonomously, generating a mobile signal that contributes to pattern formation through the regulation of the expression pattern of their targets.
  • miRNAs are integrated into complex regulatory networks and their expression is regulated by both endogenous and exogenous signals.

In: eLS. John Wiley & Sons, Ltd: Chichester.

DOI: 10.1002/9780470015902.a0020106.pub2

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A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture.

Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.

PLoS One, 2015, 10(10):e0138276.

DOI: 10.1371/journal.pone.0138276

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New location of the group

That done! The group move to its final location in the building 630.

Batiment 630

We need know to unpack all the box to reinstall the lab and office.

Lab location

Institute of Plant Sciences Paris-Saclay
Bâtiment 630
rue de Noetzling
91405 Orsay
France
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Institute of Plant Sciences Paris-Saclay

IPS2

It is the end of Institut des Sciences du Végétal (ISV). The unit had to close. The group, with two other from ISV, is joinning the new Institute of Plant Sciences Paris-Saclay (IPS2). We are still in the same location since the final building of IPS2 is not ready to welcome us.

Lab location

Institute of Plant Sciences Paris-Saclay
Bâtiment 23
91198 Gif-sur-Yvette
France
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