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Transcript profiling in LTR mutants

ABSTRACT: STN7-dependent phosphorylation of an as yet unknown thylakoid protein triggers the signaling events associated with the long-term acclimatory response (LTR). The LTR-associated signaling events regulate the expression of photosynthesis-related genes on the post-transcriptional level (nucleus), as indicated by transcript profiling in LTR mutants.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE15939 | GEO | 2009/06/01

SECONDARY ACCESSION(S): PRJNA116987

REPOSITORIES: GEO

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Transcript profiling in LTR mutants

Project description:STN7-dependent phosphorylation of an as yet unknown thylakoid protein triggers the signaling events associated with the long-term acclimatory response (LTR). The LTR-associated signaling events regulate the expression of photosynthesis-related genes on the post-transcriptional level (nucleus), as indicated by transcript profiling in LTR mutants. 5 µg of total RNA of two to three biological replicates of the different pools (10 plants each pool) of rosette leaves of 4-week-old Col-0, Wassilewskija, stn7-1, psad1-1, stn7-1 psad1-1, psae1-3 and stn7-1 psae1-3 plants was processed and hybridized to a GeneChip Arabidopsis ATH1 Genome Array using the One-Cycle Target Labeling and Control Reagents according to the manufacturer’s instructions (Affymetrix); psad1 (2 replicates) psad1 stn7 (3 replicates) Col-0 (3 replicates) Ws (2 replicates) psae (2 replicates) psae stn7 (2 replicates) stn7 (3 replicates)

2009-06-01 | E-GEOD-15939 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type and TROL (AT4G01050) knock-out plants

Project description:Here we describe TROL (thylakoid rhodanese-like protein), a nuclear-encoded component of thylakoid membranes that is required for sustaining efficient linear electron flow in vascular plants. Thus, TROL might represent a missing thylakoid membrane linker for the assembly of a ternary complex between FNR, ferredoxin and NADP+. Such a complex is necessary for maintaining photosynthetic redox poise and balancing between several alternative electron-transport pathways of oxygenic photosynthesis. TROL inactivation modulates the expression of 638 nuclear genes, revealing a novel retrograde signaling pathway. Chloroplasts are the major source of NADPH which is exported to the cytosol where it participates in various redox-dependent processes. TROL is most likely the first element in a metabolic signaling pathway which influences the expression of a large set of stress related genes. Among them are O-methyltransferases and anthocyanin 5-aromatic acyltransferase which are highly upregulated. Microarray analysis was performed in order to identify metabolic networks and pathways regulated by the deficient protein TROL. Comparing ATH1 Affymetrix data results, 317 genes were down-regulated and 321 genes were classified as up-regulated, amongst which mostly affected enzymes were catalyses, oxigenases, monooxygenases and reductases involved in the process of photosynthesis.

2009-08-20 | E-MEXP-1783 | biostudies-arrayexpress

Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [RNA-Seq]

Project description:LTR retrotransposons are repetitive DNA elements comprising ~10% of the human genome. However, Whether or how the LTR lncRNAs serve biological functions is largely unknown. Here we show that in primary human erythroblasts, lncRNAs transcribed from the LTR retrotransposons of ERV-9 human endogenous retrovirus regulated transcription of key erythroid genes. Global knock-down of ERV-LTR lncRNAs was performed in the in vitro erythropoiesis system of human CD34 cells, and genome wide RNA-seq was carried out to detect the effect on transcription.

2017-01-07 | GSE93280 | GEO

Comparative quantitative proteomic analysis of Arabidopsis thylakoid membranes from plants grown under low, moderate and high illumination. Effects of stn7 and tap38 mutations.

Project description:Plants grown under different illumination levels undergo a long-term acclimation response (LTR) resulting in differences in their leaf morphology and chloroplast protein composition to maximise their growth. At the proteomic level, LTR involves modulating the stoichiometry of photosynthetic complexes within the thylakoid membrane through de novo synthesis and degradation of specific proteins. The signalling pathways that mediate LTR in relation to light intensity remain largely unknown, however earlier studies demonstrated a key role for the light-harvesting complex II (LHCII) serine-threonine kinase STN7. We explored the effects of mutant strains of Arabidopsis targeting STN7 and its cognate phosphatase TAP38 in the LTR to low, moderate and high illumination, employing label-free quantitative proteomic analysis.

2023-03-30 | PXD037358 | Pride

Long noncoding RNAs transcribed by ERV-9 LTR retrotransposon act in cis to modulate long-range LTR enhancer function [ChIRP-Seq]

Project description:LTR retrotransposons are repetitive DNA elements comprising ~10% of the human genome.However, Whether or how the LTR lncRNAs serve biological functions is largely unknown. Here we show that in primary human erythroblasts, lncRNAs transcribed from the LTR retrotransposons of ERV-9 human endogenous retrovirus regulated transcription of key erythroid genes. Genome wide ChIRP-Seq was carried out to detect the association of ERV-9 lncRNAs with the genomic DNA in the Day 13 erythroid cells from in vitro culture and phenylhydrazine treated Day 5 spleen cells from transgenic mice in vivo.

2017-01-07 | GSE93281 | GEO

Onco-exaptation of an Endogenous Retroviral LTR Drives IRF5 Expression in Hodgkin Lymphoma

Project description:The transcription factor interferon regulatory factor 5 (IRF5) is upregulated in Hodgkin lymphoma (HL) and a key regulator of the aberrant transcriptome characteristic of this disease. Here we show that IRF5 upregulation in HL is driven by transcriptional activation of a normally dormant endogenous retroviral LOR1a long terminal repeat (LTR) upstream of IRF5. Specifically, through screening of RNA-seq libraries, we detected LTR-IRF5 chimeric transcripts in multiple HL cell lines but not in normal B-cell controls. In HL, the LTR was in an open and hypomethylated epigenetic state and we further show the LTR is the site of transcriptional initiation. Among HL cell lines, usage of the LTR promoter strongly correlates with overall levels of IRF5 mRNA and protein, indicating that LTR transcriptional awakening is a major contributor to IRF5 upregulation in HL. Taken together, oncogenic IRF5 overexpression in HL is the result of a specific LTR transcriptional activation. We propose that such LTR derepression is a distinct mechanism of oncogene activation (“onco-exaptation”) and that such a mechanism warrants further investigation in molecular and cancer research.

| EGAS00001001205 | EGA

Research on the mode of action of a novel 2-cyclopropyl-4-aminopyrimidine hydrazine compound (4k) for control of cyanobacteria

Project description:We reported the transcriptomics files of cyanobacteria treated by compound 4k, which exhibited a good algicidal activity. The results revealed that the transcription of genes in the photosynthesis pathways, such as thylakoid and PSI pathway, were affected by 4k, which was validated by the qPCR results. Photosynthesis parameters was further measured and showed that photosynthesis were significantly affected by 4k treatments.

2022-05-31 | GSE194275 | GEO

Trichoderma viride strain:LTR-2

Project description:Trichoderma viride LTR-2 Whole Genome sequencing

| PRJNA266090 | ENA

Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

Project description:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome. Examination of small RNA populations in the sugarcane leaves that show matches against sugarcane LTR-RTs.

2012-04-16 | E-GEOD-35143 | biostudies-arrayexpress

The application of a reverse transcriptase inhibitor suppresses LTR retrotransposon mobilization in plants [RNA-seq]

Project description:Recently developed methods applied to plant material, for example tissue culture during plant transformation, can induce genome instability by activating uncontrolled mobilization of LTR retrotransposons (LTR-TEs), the most abundant class of mobile genetic elements in plant genomes. Here we tested the use of Reverse Transcriptase inhibitors to avoid LTR-TE mobilization in plants. We demonstrated that the application of the drug Tenofovir in systems with high LTR-TE activity, like Arabidopsis and rice, allows generation of plants free from LTR-TE insertions without interfering with their development. We propose the use of Tenofovir as a new tool to both study LTR-TE transposition and to regenerate more genetically stable plant lines from tissue culture.

2023-01-06 | GSE196869 | GEO

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