E-GEOD-115951
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-115951 | ExpressionAtlas | 2020-04-15
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-115951-analysis-methods.tsv | Tabular | |||
| E-GEOD-115951-analytics.tsv | Tabular | |||
| E-GEOD-115951-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-115951-configuration.xml | Xml | |||
| E-GEOD-115951-g7_g1-mvaPlot.png | Other |
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Project description:RNA Polymerase II read-through promotes expression of neighboring genes in SAL1-PAP-XRN retrograde signaling
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Project description:Abstract: In plants, the molecular function(s) of the nuclear localised 5’-3’ EXORIBONUCLEASES (XRNs) are unclear, however their activity is reported to have a significant effect on gene expression and SAL1-mediated retrograde signaling. Using Parallel Analysis of RNA Ends (PARE) we document a dramatic increase in uncapped RNA substrates of the XRNs in both sal1 and xrn2xrn3 mutants. We find that a major consequence of reducing SAL1 or XRN activity is RNA Polymerase II (Pol II) 3’ read-through. This occurs at 72% of expressed genes, demonstrating a major genome-wide role for the XRN-torpedo model of transcription termination in Arabidopsis. Read-through is speculated to have a negative effect on transcript abundance, however we do not observe this. Rather, we identify a strong association between read-though and increased transcript abundance of tandemly orientated downstream genes, strongly correlated with the proximity (<1,000bp) and expression of the upstream gene. We observe read-though in the proximity of 903 genes upregulated in the sal1-8 retrograde signaling mutant; thus, this phenomenon may directly account for up to 23% of genes upregulated in sal1-8. Using APX2 and AT5G43770 as exemplars, we genetically uncouple read-through loci from downstream genes to validate the principle of read-through mediated mRNA regulation, potentially providing one mechanism by which an obstensibly post-transcriptional exoribonuclease that targets uncapped RNAs could modulate gene expression.
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Project description:Chloroplast-nuclear retrograde signaling is viewed as a mechanism for inter-organelle communication. Here we show the SAL1-PAP (3′-phosphoadenosine 5′- phosphate) retrograde pathway functions more broadly in guard cells, interacting with abscisic acid (ABA) signaling at least in part via exoribonucleases. Unexpectedly, PAP bypasses the canonical signaling components ABA Insensitive 1 (ABI1) and Open Stomata 1 (OST1) by priming an alternative pathway that restores ABA-responsive gene expression, ROS bursts, ion channel function and stomatal closure in ost1-2. This alternative pathway up-regulates lowly expressed Calcium Dependent Protein Kinases (CDPKs) which have the capacity to activate the key slow anion channel SLAC1 in response to ABA-mediated and ost1-2 independent calcium release. The role of PAP in priming an alternative pathway to bypass components previously considered essential for stomatal closure demonstrates how a chloroplast signal can have broader roles as a secondary messenger to directly intersect with and tune hormone signaling.
2017-03-21 | GSE84997 | GEO
Project description:XRN2 is a conserved 5â??-->3â?? exoribonuclease that complexes with XTB-domain containing proteins. Thus, in Caenorhabditis elegans (C. elegans), the XTBD-protein PAXT-1 stabilizes XRN2 to retain its activity. XRN2 activity is also promoted by 3'(2'),5'-bisphosphate nucleotidase 1 (BPNT1) through its hydrolysis of 3â??-phosphoadenosine-5'-bisphosphate (PAP), an endogenous XRN inhibitor. Here, we find through unbiased screening that loss of bpnt-1 function suppresses lethality caused by paxt-1 deletion. This unexpected finding is explained by XRN2 autoregulation, which occurs through repression of a cryptic promoter activity and destabilization of the xrn-2 transcript. Autoregulation appears to be triggered at different thresholds of XRN2 inactivation, such that more robust XRN2 perturbation, by elimination of both PAXT-1 and BPNT1, is less detrimental to worm viability than absence of PAXT-1 alone. Like more than 15% of C. elegans genes, xrn-2 occurs in an operon, and we identify additional operons under its control, consistent with a broader function of XRN2 in polycistronic gene regulation. Regulation occurs through intercistronic regions that link genes in an operon, but similar mechanisms may allow XRN2 to operate on monocistronic genes in organisms lacking operons. Wild-type C. elegans worms were subjected to mock or xrn-2 RNAi from L1 to L4 stage at 20°C. Total RNA was extracted from the worms, and polyadenylated RNA was analyzed.
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Project description:We report that developmental competition between sympathetic neurons for survival is critically dependent on a sensitization process initiated by target innervation and mediated by a series of feedback loops. Target-derived nerve growth factor (NGF) promoted expression of its receptor TrkA in neurons and prolonged TrkA-mediated signals. NGF also controlled expression of brain derived neurotrophic factor (BDNF) and neurotrophin-4 (NT4), which, through the receptor p75, can kill neighboring neurons with low retrograde NGFâ??TrkA signaling whereas neurons with high NGFâ??TrkA signaling are protected. Perturbation of any of these feedback loops disrupts the dynamics of competition. We suggest that three target-initiated events are essential for rapid and robust competition between neurons: sensitization, paracrine apoptotic signaling, and protection from such effects. Experiment Overall Design: This experiment examine gene expression differences in superior cervical ganglia fro P0 bax null versus NGF-Bax double null animals. The Bax genotype was used in order to prevent the neuronal cell death normally observed in the NGF null animal.
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