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Small RNA profiling in an Arabidopsis transgenic line overexpressing AtmiR472

ABSTRACT: Virus resistance relies in some plant-viral interactions on the RNA-DEPENDANT RNA POLYMERASE 6 (RDR6), a major actor of RNA silencing that acts at the post-transcriptional level. Here, we demonstrate that RDR6 also plays a role in basal defense and race-specific resistance. RDR6 and the microRNA miR472, which target the mRNAs of disease resistance genes of coiled-coil nucleotide-binding leucine-rich-repeats family (e.g. RPS5), act in cooperation to control post-transcriptionally these immune receptors. Induction of these resistance genes is primed in rdr6- and miR472-elicited mutants and this effect is associated with an enhanced basal and race-specific immunity in these backgrounds.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE53484 | GEO | 2013/12/19

SECONDARY ACCESSION(S): PRJNA232090

REPOSITORIES: GEO

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Small RNA profiling in an Arabidopsis transgenic line overexpressing AtmiR472

Project description:Virus resistance relies in some plant-viral interactions on the RNA-DEPENDANT RNA POLYMERASE 6 (RDR6), a major actor of RNA silencing that acts at the post-transcriptional level. Here, we demonstrate that RDR6 also plays a role in basal defense and race-specific resistance. RDR6 and the microRNA miR472, which target the mRNAs of disease resistance genes of coiled-coil nucleotide-binding leucine-rich-repeats family (e.g. RPS5), act in cooperation to control post-transcriptionally these immune receptors. Induction of these resistance genes is primed in rdr6- and miR472-elicited mutants and this effect is associated with an enhanced basal and race-specific immunity in these backgrounds. Comparison of Col0 WT sRNA with miR472 over-expressor mutant.

2013-12-19 | E-GEOD-53484 | biostudies-arrayexpress

Expression data from HT-1080 cells incubated or not in the presence of laminin111 coiled-coiled recombinant fragment (rLCC111)

Project description:Laminins are large heterotrimeric cross-shaped extracellular matrix (ECM) glycoproteins with terminal globular domains and a coiled-coil region. We have produced for the first time a recombinant laminin coiled-coil domain and studied the transcriptional profile of cells incubated in coiled-coil-coated wells. Cells were incubated in 24w plates, onto coiled-coil-coated wells or control BSA-coated wells (one each), 24h

2011-10-11 | E-GEOD-32896 | biostudies-arrayexpress

Expression data from HT-1080 cells incubated or not in the presence of laminin111 coiled-coiled recombinant fragment (rLCC111)

2011-10-12 | GSE32896 | GEO

The Northern Corn Leaf Blight Resistance Gene, Ht1, Encodes an NLR Immune Receptor

Project description:Northern corn leaf blight (NLB), caused by the fungal pathogen Exserohilum turcicum, results significant yield reductions in infected corn. The first major locus conferring resistance to E. turcicum race 0, Ht1, was identified over 50 years ago, but despite widespread deployment the underlying gene has remained unknown. We employed map-based cloning to identify the Ht1 causal gene, which was found to be a coiled-coil nucleotide-binding, leucine-rich repeat (NLR) gene, termed PH4GP-Ht1. Transgenic testing confirmed that addition of the native PH4GP-Ht1 sequence to the susceptible maize variety PH184C resulted in resistance to E. turcicum race 0. A survey of the maize NAM genomes revealed that susceptible Ht1 alleles had very low to no expression, but overexpression of the susceptible B73 allele did not result in resistant plants, indicating that relatively minor protein sequence variations may underlie the resistance phenotype. Modeling of the PH4GP-Ht1 protein indicated that it has structural homology to the Arabidopsis NLR resistance gene ZAR1, and likely forms a similar homo-pentamer structure following activation. RNA-seq data from an infection time course revealed that one week after inoculation there was a threefold reduction in fungal biomass and a dramatic increase in DEGs when comparing mock to inoculated PH4GP-Ht1 transgenic plants and null plants. These results demonstrate that the NLR PH4GP-Ht1 is the causal gene underlying the NLB resistance phenotype of Ht1.

2022-10-03 | GSE206951 | GEO

RNA-Sequencing analysis of white adipose tissue from wild type mice and Ccdc92 knockout mice

Project description:Multiple independent genome-wide association studies (GWAS) have uncovered specific genetic variants in the Coiled-Coil Domain Containing 92 (CCDC92) locus that are associated with obesity and insulin resistance in humans. However, the biological function of CCDC92 in metabolism remains unclear. We explored the effects of CCDC92 on obesity and insulin resistance by utilizing wild-type (WT) and Ccdc92 knockout (KO) mice. RNA-seq was used to analyze the gene expression profile regulated by CCDC92 in white adipose tissue.

2022-12-12 | GSE191174 | GEO

Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression

Project description:TAZ promotes cell proliferation, development, and tumorigenesis by regulating target gene transcription. However, how TAZ orchestrates the transcriptional responses remains poorly defined. Here we demonstrate that TAZ forms nuclear condensates via liquid-liquid phase separation to compartmentalize its DNA binding co-factor TEAD4, the transcription co-activators BRD4 and MED1 and the transcription elongation factor CDK9 for activation of gene expression. TAZ, but not its paralog YAP, forms phase-separated droplets in vitro and liquid-like nuclear condensates in cells and tissues, and this ability is negatively regulated by Hippo signaling via LATS-mediated phosphorylation and mediated by the coiled-coil domain. Deletion of the TAZ coiled-coil domain or substitution with the YAP coiled-coil domain does not affect the interaction with its partners, but prevents its phase separation and more importantly, its ability to induce expression of TAZ-specific target genes. Thus, our study has identified a novel mechanism for the transcriptional activation by TAZ and demonstrated for the first time that pathway-specific transcription factors also engage the phase separation mechanism for efficient and specific transcription activation.

2019-12-21 | GSE142474 | GEO

Nuclear Envelope Retention of LINC Complexes Is Promoted by SUN-1 Oligomerization in the Caenorhabditis elegans Germ Line

Project description:SUN (Sad1 and UNC-84) and KASH (Klarsicht, ANC-1 and Syne homology) proteins are constituents of the inner and outer nuclear membranes. They interact in the perinuclear space via carboxy-terminal SUN-KASH domains to form the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex thereby bridging the nuclear envelope. LINC complexes sustain numerous biological processes by connecting chromatin with the cytoplasmic force generating machinery. Here we show that the coiled-coil domains of SUN-1 are required for oligomerization and retention of the protein in the nuclear envelope, especially at later stages of female gametogenesis. Consistently, deletion of the coiled coil domain makes SUN-1 sensitive to unilateral force generation across the nuclear membrane. However, absence of this domain does not lead to different expression levels of sun-1 and other known meiotic genes in the mutant compared to wild type. Premature loss of SUN-1 from the nuclear envelope leads to embryonic death due to loss of centrosome-nuclear envelope attachment. However, in contrast to previous notions we can show that the coiled-coil domain is dispensable for functional LINC complex formation, exemplified by successful chromosome sorting and synapsis in meiotic prophase I in their absence.

2016-05-08 | GSE76773 | GEO

Expression data from wild-type and MURC knockout male mouse hearts

Project description:Muscle-restricted coiled-coil protein (MURC)/Cavin-4, which is a component of caveolae, is involved in the pathophysiology of dilated cardiomyopathy and cardiac hypertrophy. We used microarrays to examine the gene expression of mouse hearts perturbed by MURC deficieny.

2019-01-19 | GSE125308 | GEO

Cross-linking of mouse laminin 111

Project description:Laminin, a ~800 kD heterotrimeric protein, is a major functional component of the extracellular matrix, contributing to tissue development and maintenance. We used cross-linking and mass spectrometry to determine the order of subunits in the ~750 Å trimeric coiled-coil oligomerization domain of laminin and to achieve an estimate of the register of the three subunits along the length of the coiled coil.

2016-12-22 | PXD004898 | Pride

Molecular Basis for CPC-Sgo1 Interaction: Implications for Centromere Localisation and Function of the CPCMolecular Basis for CPC-Sgo1 Interaction: Implications for Centromere Localisation and Function of the CPC

Project description:Sgo1 makes multipartite interactions with CPC subunits Previous studies have suggested that the Sgo1-CPC (Chromosomal Passenger Complex) interaction is mediated via the N-terminal coiled-coil of Sgo1 and Borealin. However, our structural data revealed that the very N-terminus of Sgo1 can interact with the BIR domain of Survivin. Together, these studies suggest that multi-partite interactions between Sgo1 and different CPC subunits could facilitate CPC-Sgo1 complex formation. To gain further structural insights, we performed chemical cross-linking of the CPCISB10-280-Sgo11-415 complex using a zero-length cross-linker, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC), followed by mass spectrometry analysis. Cross-linking-mass spectrometry (CLMS) data showed that: (1) consistent with our previous observations, the N-terminal region of Sgo1 (amino acids 1-34) makes extensive contacts with Survivin BIR domain (amino acids 18-89); (2) the N-terminal coiled-coil of Sgo1 (amino acids 10-120) interacts with the CPC triple helical bundle; (3) consistent with previous findings, the N-terminal coiled-coil also contacts the Borealin dimerisation domain; and (4) the Sgo1 region beyond the N-terminal coil-coil region, which is predicted to be unstructured, contacts both Survivin and Borealin with most contacts confined to the Sgo1 central region spanning amino acids (aa) 180-300. Thus, our cross-linking results suggests that Sgo1 interacts with CPC, mainly via two regions, the N-terminal coiled-coil domain and the unstructured central region.

2022-06-29 | PXD028433 | Pride

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