Functionnal study of SCR and SHR genes in rice development

Chez les plantes les protéines de la famille GRAS régissent un grand nombre de processus allant du développement racinaire à la transduction de signaux hormonaux. Deux protéines de cette famille de facteurs de transcription, SCR et SHR jouent un rôle essentiel dans le développement racinaire d’Arabidopsis thaliana en régulant la formation des tissus internes. Chez le riz, il existe deux co-orthologues putatifs pour ces deux gènes, OsSCR1, OsSCR2, OsSHR1 et OsSHR2. Nous avons caractérisé la fonction de trois membres de cette famille au cours du développement racinaire et aérien du riz. OsSHR1 et OsSHR2 sont impliqués dans la variation du nombre de couches de cortex et interfèrent aussi dans la formation des cellules bulliformes et du sclerenchyme dans les feuilles. OsSCR2 a un rôle majeur dans le contrôle du nombre de ramifications aériennes. Nos résultats ont aussi permis de démontrer qu’OsSCR2 et OsSHR2 ont des fonctions spécifiques au riz.Summary to be comin

Étude de la fonction des gènes SCR et SHR impliqués dans le développement du riz

Chez les plantes les protéines de la famille GRAS régissent un grand nombre de processus allant du développement racinaire à la transduction de signaux hormonaux. Deux protéines de cette famille de facteurs de transcription, SCR et SHR jouent un rôle essentiel dans le développement racinaire d Arabidopsis thaliana en régulant la formation des tissus internes. Chez le riz, il existe deux co-orthologues putatifs pour ces deux gènes, OsSCR1, OsSCR2, OsSHR1 et OsSHR2. Nous avons caractérisé la fonction de trois membres de cette famille au cours du développement racinaire et aérien du riz. OsSHR1 et OsSHR2 sont impliqués dans la variation du nombre de couches de cortex et interfèrent aussi dans la formation des cellules bulliformes et du sclerenchyme dans les feuilles. OsSCR2 a un rôle majeur dans le contrôle du nombre de ramifications aériennes. Nos résultats ont aussi permis de démontrer qu OsSCR2 et OsSHR2 ont des fonctions spécifiques au riz.Summary to be comingMONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Isolation of nuclei in tagged cell types (intact), rna extraction and ribosomal rna degradation to prepare material for rna-seq

International audienceGene expression is dynamically regulated on many levels, including chromatin accessibility and transcription. In order to study these nuclear regulatory events, we describe our method to purify nuclei with Isolation of Nuclei in TAgged Cell Types (INTACT). As nuclear RNA is low in polyadenylated transcripts and conventional pulldown methods would not capture non-polyadenylated pre-mRNA, we also present our method to remove ribosomal RNA from the total nuclear RNA in preparation for nuclear RNA-Seq

Evolutionary flexibility in flooding response circuitry in angiosperms

Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin accessibility and gene expression at three scales of transcript control in four angiosperms, ranging from a dryland-adapted wild species to a wetland crop. The data define a cohort of conserved submergenceactivated genes with signatures of overlapping cis regulation by four transcription factor families. Syntenic genes are more highly expressed than nonsyntenic genes, yet both can have the cis motifs and chromatin accessibility associated with submergence up-regulation.Whereas the flexible circuitry spans the eudicot-monocot divide, the frequency of specific cis motifs, extent of chromatin accessibility, and degree of submergence activation are more prevalent in the wetland crop and may have adaptive importance.Fil: Reynoso, Mauricio Alberto. Center For Plant Cell Biology Riverside; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnol.conicet - la Plata. Centro de Endocrinología Exp.y Aplicada (i). Grupo Vinculado Cenexa-fcex-unlp; ArgentinaFil: Kajala, Kaisa. Utrecht University; Países Bajos. University of California at Davis; Estados UnidosFil: Bajic, Marko. University of Emory; Estados UnidosFil: West, Donnelly. University of California at Davis; Estados UnidosFil: Pauluzzi, Germain. University of California; Estados UnidosFil: Yao, Andrew I.. University of California at Davis; Estados UnidosFil: Hatch, Kathryn. University of Emory; Estados UnidosFil: Zumstein, Kristina. University of California at Davis; Estados UnidosFil: Woodhouse, Margaret. University of California at Davis; Estados UnidosFil: Rodríguez Medina, Joel. University of California at Davis; Estados UnidosFil: Sinha, Neelima. University of California at Davis; Estados UnidosFil: Brady, Siobhan M.. University of California at Davis; Estados UnidosFil: Deal, Roger. University of Emory; Estados UnidosFil: Bailey Serres, Julia. University of California at Davis; Estados Unidos. Utrecht University; Países Bajo

A plausible mechanism, based upon SHORT-ROOT movement, for regulating the number of cortex cell layers in roots

Formation of specialized cells and tissues at defined times and in specific positions is essential for the development of multicellular organisms. Often this developmental precision is achieved through intercellular signaling networks, which establish patterns of differential gene expression and ultimately the specification of distinct cell fates. Here we address the question of how the SHORT-ROOT (SHR) proteins from Arabidopsis thaliana (AtSHR), Brachypodium distachyon (BdSHR), and Oryza sativa (OsSHR1 and OsSHR2) function in patterning the root ground tissue.We find that all of the SHR proteins function as mobile signals in A. thaliana and all of the SHR homologs physically interact with the AtSHR binding protein, SCARECOW (SCR). Unlike AtSHR, movement of the SHR homologs was not limited to the endodermis. Instead, the SHR proteins moved multiple cell layers and determined the number of cortex, not endodermal, cell layers formed in the root. Our results in A. thaliana are consistent with a mechanism by which the regulated movement of the SHR transcription factor determines the number of cortex cell layers produced in the roots of B. distachyon and O. sativa. These data also provide a new model for ground tissue patterning in A. thaliana in which the ability to form a functional endodermis is spatially limited independently of SHR. (Résumé d'auteur

Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice

: Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience

Nuclear Transcriptomes at High Resolution Using Retooled INTACT

Breakthrough Technologies - Focus IssueInternational audienceIsolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here, we describe transfer of the isolation of nuclei from tagged specific cell types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nuclear-envelope-targeting domain of the nuclear tagging fusion (NTF) protein with an outer nuclear-envelope-anchored domain. This modified NTF was combined with codon-optimized Escherichia coli BirA in a single T-DNA construct. We also developed inexpensive methods for INTACT, T-DNA insertion mapping, and profiling of the complete nuclear transcriptome, including a ribosomal RNA degradation procedure that minimizes pre-ribosomal RNA (pre-rRNA) transcripts. A high-resolution comparison of nuclear and steady-state poly(A)+ transcript populations of seedling root tips confirmed the capture of pre-messenger RNA (pre-mRNA) and exposed distinctions in diversity and abundance of the nuclear and total transcriptomes. This retooled INTACT can enable high-resolution monitoring of the nuclear transcriptome and chromatin in specific cell types of rice and other species