scholarly journals PhyB induces intron retention and uORF-mediated translational inhibition of PIF3

2019 ◽  
Author(s):  
Jie Dong ◽  
Haodong Chen ◽  
Xing Wang Deng ◽  
Vivian F. Irish ◽  
Ning Wei
Keyword(s):  
Alternative Splicing ◽  
Protein Degradation ◽  
Intron Retention ◽  
Red Light ◽  
Light Response ◽  
Protein Translation ◽  
Light Cycle ◽  
Light Responses ◽  
E3 Ligases ◽  
Short Day

AbstractThe phytochrome B (phyB) photoreceptor stimulates light responses in plants in part by inactivating repressors of light responses such as phytochrome-interacting factor 3 (PIF3). It has been established that activated phyB inhibits PIF3 by rapid protein degradation and decreased transcription. PIF3 protein degradation has been shown to be mediated by EIN3-BINDING F-BOX PROTEIN (EBF) and LIGHT-RESPONSE BTB (LRB) E3 ligases, the latter simultaneously targeting phyB for degradation. In this study, we show that PIF3 level is additionally regulated by alternative splicing and protein translation. Overaccumulation of photo-activated phyB, which occur in the mutant defective for LRB genes under continuous red light (Rc), induces a specific alternative splicing of PIF3 that results in retention of an intron in the 5’UTR of PIF3 mRNA. In turn, the upstream opening reading frames (uORF) contained within this intron inhibit PIF3 protein synthesis. The phyB-dependent alternative splicing of PIF3 is diurnally regulated under the short-day light cycle. We hypothesize that this reversible regulatory mechanism may be utilized to fine-tune the level of PIF3 protein in light-grown plants, and may contribute to the oscillation of PIF3 protein abundance under the short-day environment.One Sentence SummaryLight down-regulates PIF3 by multiple mechanisms. We show that phyB induces an alternative splicing event that inhibits PIF3 protein translation, and that is regulated by short-day diurnal cycle.

scholarly journals Novel light-regulated genes in Trichoderma atroviride: a dissection by cDNA microarrays

Microbiology ◽  
2006 ◽  
Vol 152 (11) ◽  
pp. 3305-3317 ◽  
Author(s):  
T. Rosales-Saavedra ◽  
E. U. Esquivel-Naranjo ◽  
S. Casas-Flores ◽  
P. Martínez-Hernández ◽  
E. Ibarra-Laclette ◽  
...  
Keyword(s):  
Red Light ◽  
Continuous Light ◽  
Soil Fungus ◽  
Light Response ◽  
Trichoderma Atroviride ◽  
Light Responses ◽  
The Common ◽  
Living Organisms ◽  
Regulated Gene Expression

The influence of light on living organisms is critical, not only because of its importance as the main source of energy for the biosphere, but also due to its capacity to induce changes in the behaviour and morphology of nearly all forms of life. The common soil fungus Trichoderma atroviride responds to blue light in a synchronized manner, in time and space, by forming a ring of green conidia at what had been the colony perimeter at the time of exposure (photoconidiation). A putative complex formed by the BLR-1 and BLR-2 proteins in T. atroviride appears to play an essential role as a sensor and transcriptional regulator in photoconidiation. Expression analyses using microarrays containing 1438 unigenes were carried out in order to identify early light response genes. It was found that 2.8 % of the genes were light responsive: 2 % induced and 0.8 % repressed. Expression analysis in blr deletion mutants allowed the demonstration of the occurrence of two types of light responses, a blr-independent response in addition to the expected blr-dependent one, as well as a new role of the BLR proteins in repression of transcription. Exposure of T. atroviride to continuous light helped to establish that the light-responsive genes are subject to photoadaptation. Finally, evidence is provided of red-light-regulated gene expression and a possible crosstalk between the blue and red light signalling pathways.

scholarly journals An Erythroid-Specific Intron Retention Program Regulates Expression of Selected Genes during Terminal Erythropoiesis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 449-449
Author(s):  
Harold Pimentel ◽  
Marilyn Parra ◽  
Sherry Gee ◽  
Narla Mohandas ◽  
Lior Pachter ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Iron Homeostasis ◽  
Rna Binding ◽  
Conflicts Of Interest ◽  
Intron Retention ◽  
Great Majority ◽  
Protein Translation ◽  
Membrane Properties ◽  
Disease Genes ◽  
Rna Seq

Abstract Erythroid RNAs, like their nonerythroid counterparts, are subject to post-transcriptional processing events that critically impact their coding capacity for the erythroid proteome. Previous studies have shown that differentiating human and mouse erythroblasts execute an extensive and dynamic alternative splicing program involving regulation of numerous alternative exons. Here we report that controlled excision of selected introns is also an important component of the erythroblast alternative splicing program. Intron retention (IR) patterns in differentiating human erythroblasts were determined via RNA-seq analysis of FACS-purified erythroblast populations. Comparison of IR among erythroblast populations and between erythroblasts and other hematopoietic cells suggests that regulation of IR occurs in a differentiation stage- and tissue-specific manner. For example, there was little overlap of intron retention events in erythroblasts with those reported in differentiating granulocytes. Moreover, the IR profile of proerythroblasts differed substantially from that in orthochromatic erythroblasts, with IR generally increasing in the more mature cells that are preparing for enucleation. IR in erythroblasts affected numerous genes functioning in RNA processing, iron homeostasis and heme biosynthesis, protein translation, and membrane properties. Mature erythroblasts exhibited retention of introns in several human disease genes including SF3B1, a splicing factor often mutated in myelodysplasia; TFR2, encoding transferrin receptor 2 that is mutated in a form of hemochromatosis; and FUS, an RNA binding protein implicated in ALS. Inspection of intronic RNA-seq reads in >60 genes with IR revealed that single or multiple introns can be retained within a transcript; however, other introns within the same genes, and indeed the great majority of introns in erythroblast-expressed genes, are efficiently spliced with minimal or no IR. Retained introns may be flanked by either constitutively or alternatively spliced exons, suggesting different regulatory mechanisms. Ongoing studies will explore whether IR in some transcripts might function to down-regulate gene expression by introduction of premature termination codons that induce nonsense-mediated decay, or alternatively, whether IR transcripts could represent a reserve of nearly-completed mRNAs that can be processed in response to appropriate physiological stimuli. In sum, these results suggest that a highly regulated IR program plays an important role in erythroid differentiation. Disclosures No relevant conflicts of interest to declare.

scholarly journals Genome-Wide Analysis of Light-Regulated Alternative Splicing in Artemisia annua L.

2021 ◽  
Vol 12 ◽  
Author(s):  
Tingyu Ma ◽  
Han Gao ◽  
Dong Zhang ◽  
Wei Sun ◽  
Qinggang Yin ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Single Molecule ◽  
Artemisia Annua ◽  
Intron Retention ◽  
Genetic Regulation ◽  
Red Light ◽  
Light Regulation ◽  
Full Length ◽  
Common Mechanism ◽  
Genome Wide

Artemisinin is currently the most effective ingredient in the treatment of malaria, which is thus of great significance to study the genetic regulation of Artemisia annua. Alternative splicing (AS) is a regulatory process that increases the complexity of transcriptome and proteome. The most common mechanism of alternative splicing (AS) in plant is intron retention (IR). However, little is known about whether the IR isoforms produced by light play roles in regulating biosynthetic pathways. In this work we would explore how the level of AS in A. annua responds to light regulation. We obtained a new dataset of AS by analyzing full-length transcripts using both Illumina- and single molecule real-time (SMRT)-based RNA-seq as well as analyzing AS on various tissues. A total of 5,854 IR isoforms were identified, with IR accounting for the highest proportion (48.48%), affirming that IR is the most common mechanism of AS. We found that the number of up-regulated IR isoforms (1534/1378, blue and red light, respectively) was more than twice that of down-regulated (636/682) after treatment of blue or red light. In the artemisinin biosynthetic pathway, 10 genes produced 16 differentially expressed IR isoforms. This work demonstrated that the differential expression of IR isoforms induced by light has the potential to regulate sesquiterpenoid biosynthesis. This study also provides high accuracy full-length transcripts, which can be a valuable genetic resource for further research of A. annua, including areas of development, breeding, and biosynthesis of active compounds.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals Quantitative Trait Loci Controlling Light and Hormone Response in Two Accessions ofArabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 683-696 ◽  
Author(s):  
Justin O Borevitz ◽  
Julin N Maloof ◽  
Jason Lutes ◽  
Tsegaye Dabi ◽  
Joanna L Redfern ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Natural Variation ◽  
Red Light ◽  
Light Response ◽  
Environment Interaction ◽  
Isogenic Line ◽  
Hormone Response ◽  
New Genes ◽  
Trait Loci

AbstractWe have mapped quantitative trait loci (QTL) responsible for natural variation in light and hormone response between the Cape Verde Islands (Cvi) and Landsberg erecta (Ler) accessions of Arabidopsis thaliana using recombinant inbred lines (RILs). Hypocotyl length was measured in four light environments: white, blue, red, and far-red light and in the dark. In addition, white light plus gibberellin (GA) and dark plus the brassinosteroid biosynthesis inhibitor brassinazole (BRZ) were used to detect hormone effects. Twelve QTL were identified that map to loci not previously known to affect light response, as well as loci where candidate genes have been identified from known mutations. Some QTL act in all environments while others show genotype-by-environment interaction. A global threshold was established to identify a significant epistatic interaction between two loci that have few main effects of their own. LIGHT1, a major QTL, has been confirmed in a near isogenic line (NIL) and maps to a new locus with effects in all light environments. The erecta mutation can explain the effect of the HYP2 QTL in the blue, BRZ, and dark environments, but not in far-red. LIGHT2, also confirmed in an NIL, has effects in white and red light and shows interaction with GA. The phenotype and map position of LIGHT2 suggest the photoreceptor PHYB as a candidate gene. Natural variation in light and hormone response thus defines both new genes and known genes that control light response in wild accessions.

Improvement of red light response of Cu2Sn1−xGexS3 solar cells by optimization of CdS buffer layers

2015 ◽  
Vol 118 (15) ◽  
pp. 154502 ◽  
Author(s):  
Mitsutaro Umehara ◽  
Yasuhiko Takeda ◽  
Shin Tajima ◽  
Tomoyoshi Motohiro ◽  
Takenobu Sakai ◽  
...  
Keyword(s):  
Solar Cells ◽  
Red Light ◽  
Light Response ◽  
Buffer Layers

scholarly journals Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Bin Liu ◽  
Shuo Zhao ◽  
Pengli Li ◽  
Yilu Yin ◽  
Qingliang Niu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Light Intensity ◽  
Intron Retention ◽  
Light Stress ◽  
Photosynthetic Photon Flux Density ◽  
Photon Flux ◽  
Photon Flux Density ◽  
Rna Seq ◽  
Multiple Transcripts ◽  
Novel Transcript

AbstractIn plants, alternative splicing (AS) is markedly induced in response to environmental stresses, but it is unclear why plants generate multiple transcripts under stress conditions. In this study, RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities. We identified a novel transcript of the gibberellin (GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8 (CsGA2ox8). Compared with canonical CsGA2ox8.1, the CsGA2ox8.2 isoform presented intron retention between the second and third exons. Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs. Moreover, expression analysis demonstrated that both transcripts were upregulated by increased light intensity, but the expression level of CsGA2ox8.1 increased slowly when the light intensity was >400 µmol·m−2·s−1 PPFD (photosynthetic photon flux density), while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was >200 µmol·m−2·s−1 PPFD. Our findings provide evidence that plants might finely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.

scholarly journals Deep learning-based pupil model predicts time and spectral dependent light responses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Babak Zandi ◽  
Tran Quoc Khanh
Keyword(s):  
Deep Learning ◽  
Time Course ◽  
Light Response ◽  
Absolute Error ◽  
Light Responses ◽  
Temporal Prediction ◽  
Feed Forward Neural Networks ◽  
Self Learning ◽  
Pupil Light Response ◽  
Planckian Locus

AbstractAlthough research has made significant findings in the neurophysiological process behind the pupillary light reflex, the temporal prediction of the pupil diameter triggered by polychromatic or chromatic stimulus spectra is still not possible. State of the art pupil models rested in estimating a static diameter at the equilibrium-state for spectra along the Planckian locus. Neither the temporal receptor-weighting nor the spectral-dependent adaptation behaviour of the afferent pupil control path is mapped in such functions. Here we propose a deep learning-driven concept of a pupil model, which reconstructs the pupil’s time course either from photometric and colourimetric or receptor-based stimulus quantities. By merging feed-forward neural networks with a biomechanical differential equation, we predict the temporal pupil light response with a mean absolute error below 0.1 mm from polychromatic (2007 $$\pm$$ ± 1 K, 4983 $$\pm$$ ± 3 K, 10,138 $$\pm$$ ± 22 K) and chromatic spectra (450 nm, 530 nm, 610 nm, 660 nm) at 100.01 ± 0.25 cd/m2. This non-parametric and self-learning concept could open the door to a generalized description of the pupil behaviour.

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