E-GEOD-114363
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-114363 | ExpressionAtlas | 2020-04-15
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-114363-analysis-methods.tsv | Tabular | |||
| E-GEOD-114363-analytics.tsv | Tabular | |||
| E-GEOD-114363-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-114363-configuration.xml | Xml | |||
| E-GEOD-114363-g2_g1-mvaPlot.png | Other |
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Project description:Discovery of a novel plant eIF4E-binding protein: Conserved Binding of eIF4E 1 (CBE1)
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Project description:Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. However, none of the miRNAs from S. europaea have been identified so far. Results: Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and twelve conserved miRNAs comprising 51 families and 31 novel miRNAs (including 7 miRNA star sequences) belonging to 30 families were identified. Interestingly, about half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs changed significantly in response to salinity. In addition, 53 conserved miRNAs and 13 novel miRNAs were differentially expressed between shoots and roots. Furthermore, a total of 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encode a wide range of proteins, and genes involved in transcription regulation constitute the largest category. Four of them, which encode laccase, F-box family protein, SAC3/GANP family protein, and nadph-cytochrome P450 oxydoreductase, were validated using 5'-RACE. Conclusions: Our results indicate specific miRNAs are tightly regulated by salinity in shoots and/or roots of S. europaea, which play important roles in salt adaptation of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with higher stress tolerance, and genetic modification of biofuel crops with higher biomass and regulatable lignin biosynthesis.
2017-02-09 | GSE62521 | GEO
Project description:Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.
2012-06-28 | GSE24226 | GEO
Project description:Regulation of translation initiation is accomplished in diverse eukaryotes through proteins which bind to the mRNA cap-binding protein, eIF4E, and either prevent its association with eIF4G or form repressive mRNPs which exclude the translation machinery. Such mechanisms in plants, and even the presence of eIF4E-interacting proteins outside of eIF4G (and the plant-specific isoform eIFiso4G, which binds eIFiso4E) which operate in a gene regulatory manner are not known. Here we describe the Conserved Binding of eIF4E 1 (CBE1), a plant-specific protein with an evolutionarily conserved eIF4E binding motif. This protein binds eIF4E or eIFiso4E in vitro to form cap-binding complexes, and is found as a constituent of cap-binding complexes in vivo in an eIF4E-dependent manner. Mutants lacking CBE1 show dysregulation of cell cycle related transcripts, accumulating higher levels relative to wild-type plants of mRNAs encoding proteins involved in mitotic processes. These findings support CBE1 as a plant protein with the capability to form cap-binding complexes with the potential for gene regulatory activity.
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Project description:The binding patterns of some transcription factors have been shown to diverge substantially between closely related species. Here, we show that the binding pattern of the developmental transcription factor Twist is highly conserved across six Drosophila species, revealing strong functional constraints at developmental enhancers. Conserved binding correlates with sequence motifs for Twist and its partners, permitting the de novo discovery of their cooperative binding. It also includes over 10,000 low-occupancy sites near the detection limit, which tend to mark enhancers of later developmental stages. We predict that conservation, dynamic occupancy, and combinatorial regulation will be generally true for developmental enhancers.
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Project description:Profiling of small RNAs identified a total of 359 and 357 conserved; and 490 and 155 novel miRNAs in C. chinense and C. frutescens, respectively. Based on the sequence similarity observed on alignment with already reported plant miRNAs, conserved and novel miRNAs were identified in both the species. The target prediction analysis reveals vital role of miRNAs in regulating genes involved in transcriptions, protein modification, signal transduction and metabolism. Several miRNAs were expressed in a tissue-specific/preferential manner indicating their involvement in tissue/organ development.
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Project description:Discovery of novel and conserved microRNAs in Spirodela polyrhiza by deep sequencing
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Project description:Conserved miRNA discovery in switchgrass
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Project description:Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP
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Project description:Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum. Results: The transcriptome sequencing analysis showed that the enriched pathways of top 3 differentially expressed genes (DEGs) were categorized as carotenoid biosynthesis, plant-pathogen interaction and plant hormone signal transduction in both A1-A9 and A3-A9. The ABA and IAA related factors were differentially expressed in the mutants. Importantly, we found the lower expressed SAUR and elevated expressed GH3, and ABA related genes such as NCED and PP2C maybe relate to reduced growth of the plant height in Ari1327 which is consistent with the higher auxin and ABA content in this mutant. Furthermore, miRNA160 targeted to the auxin response factor (ARF) and miRNA166 (gma-miR166u and gma-miR166h-3p) targeted to ABA responsive element binding factor were related to the mutation in cotton. We have noticed that the cell growth related factors (smg7 targeted by gra-miR482 and 6 novel miRNAs and Pectatelyases targeted by osa-miR159f), the redox reactions related factors (Cytochrome P450 targeted by miR172) and MYB genes targeted by miR828, miR858 and miR159 were also involved in plant height of the cotton mutants. A total of 226 conserved miRNAs representing 32 known miRNA families were obtained, and 38 novel miRNAs corresponding to 23 unique RNA sequences were identified. Total 531 targets for 211 conserved miRNAs were obtained. Using PAREsnip, 27 and 29 miRNA/target conserved interactions were validated in A1-A9 and A3-A9, respectively. Furthermore, miRNA160, miRNA858 and miRNA172 were validated to be up-regulated in A1-A9 but down-regulated in A3-A9, whereas miRNA159 showed the opposite regulation. Conclusions: This comprehensive interaction of the transcriptome and miRNA at tall-culmand dwarf mutant led to the discovery of regulatory mechanisms in plant height. It also provides the basis for in depth analyses of dwarf mutant genes for further breeding of dwarf cotton. Total RNA was purified from stem apexes of three samples at the fifth true leaf stages and sequenced deeply using Illumina HiSeq 2000 system.
2016-07-30 | E-GEOD-71608 | biostudies-arrayexpress