Genome-Wide Investigation and Functional Analysis of RNA Editing Sites in Wheat
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ABSTRACT:
PROVIDER: PRJNA788400 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17215572_1.fastq.gz | Fastqsanger.gz | |||
| SRR17215572_2.fastq.gz | Fastqsanger.gz | |||
| SRR17215573_1.fastq.gz | Fastqsanger.gz | |||
| SRR17215573_2.fastq.gz | Fastqsanger.gz | |||
| SRR17215574_1.fastq.gz | Fastqsanger.gz |
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Project description:The goals of this study were to compare the transcriptome of six genotypes of wheat grown under the normal conditions by RNA-Seq and to study the root architecture in drought sensitive and tolerant genotypes.
2022-03-16 | GSE190755 | GEO
Project description:Studies in epitranscriptomics indicates that RNA is modified by a variety of enzymes. Among these RNA modifications, A-to-I RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA-seq data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNAEditor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affects the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncover that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands are examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, HuR, was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme ADAR compared to the control—suggesting that the presence of RNA editing islands influences HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.
2019-11-30 | GSE141095 | GEO
Project description:Investigation of RNA editing sites within bound regions of RNA-binding proteins
| PRJNA592064 | ENA
Project description:Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10-12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat.
| S-EPMC8916659 | biostudies-literature
Project description:The genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remains incomplete. Deep sequencing, data filtering and validation from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs (74-81% true-positive), all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites were unique to liver. Changes in RNA editing led to corresponding changes in intestinal mRNA and protein levels in 11 genes. We found distinctive polysome profiles for several editing targets and demonstrated nuclear but not cytoplasmic editing of novel exonic sites in intestinal (but not hepatic) apoB RNA. RNA editing was validated using cell-free extracts from wild-type but not Apobec-1 deficient mice. These studies define selective, tissue-specific targets of Apobec-1 dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific. Examination of C-to-U RNA editing in mouse liver and intestine
2014-05-23 | E-GEOD-57910 | biostudies-arrayexpress
Project description:Purpose: RNA editing by ADAR1 is essential for hematopoietic development. The goals of this study were firstly, to identify ADAR1-specific RNA-editing sites by indentifying A-to-I (G) mismatches in RNA-seq data compared to mm9 reference genome in wild type mice that were not edited or reduced in editing frequency in ADAR1E861A editing deficient mice. Secondly, to determine the transcriptional consequence of an absence of ADAR1-mediated A-to-I editing. Methods: Fetal liver mRNA profiles of embryonic day 12.5 wild-type (WT) and ADAR1 editing-deficient (ADAR1E861A) mice were generated by RNA sequencing, in triplicate (biological replicates), using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. A-to-I (G) RNA editing sites were identified as previously described by Ramaswami G. et al., Nature Methods, 2012 using Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA). RNA editing sites were confirmed by Sanger sequencing. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 14,484 transcripts in the fetal livers of WT and ADAR1E861A mice with BWA. RNA-seq data had a goodness of fit (R2) of >0.94 between biological triplicates per genotype. Approximately 4.4% of the transcripts showed differential expression between the WT and ADAR1E861A fetal liver, with a LogFC≥1.5 and p value <0.05. A profound upregulation of interferon stimulated genes were found to be massively upregulated (up to 11 logFC) in ADAR1E861A fetal liver compared to WT. 6,012 A-to-I RNA editing sites were identified when assessing mismatches in RNA-seq data of WT and ADAR1E861A fetal liver. Conclusions: Our study represents the first detailed analysis of fetal liver transcriptomes and A-to-I RNA editing sites, with biologic replicates, generated by RNA-seq technology. A-to-I RNA editing is the essential function of ADAR1 and is required to suppress interferon signaling to endogenous RNA. Fetal liver mRNA profiles of E12.5 wild type (WT) and ADAR E861A mutant mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 200.
2015-07-23 | E-GEOD-58917 | biostudies-arrayexpress
Project description:RNA editing is essential for processing transcripts in plant chloroplasts and mitochondria. Levels of RNA editing vary between lineages, but some hornworts, lycophytes and ferns have an extraordinary abundance of RNA editing. A feature of ‘hyper-editing’ species is the prevalence of RNA editing events which influence translation by affecting start codons and stop codons via C-to-U editing and U-to-C editing respectively. These ‘translationally significant’ RNA editing events may play roles in regulating organelle gene expression. To investigate the importance of translationally significant RNA editing events, we generated DNA and RNA sequence libraries for four Salviniales water ferns: Azolla rubra, Azolla pinnata, Marsilea mutica and Salvinia molesta. We assembled chloroplast genomes, mitochondrial genes and transcriptomes, and identified RNA editing sites and candidate RNA editing factors. We re-analysed sequence data of Azolla filiculoides and conducted a comparative analysis of RNA editing in chloroplasts and mitochondrial transcripts. Estimates of pyrimidine transition rates show that translationally significant RNA editing sites are more conserved than other non-synonymous editing sites, suggesting an emergent role in organelle gene expression that is not selectively neutral. Shotgun proteomics of Marsilea mutica chloroplast thylakoid fractions verified the expected consequences of RNA editing on translation of chloroplast transcripts and implies that mechanisms exist to avoid translation of partially edited transcripts. Start codon editing may be one of those mechanisms.
2025-10-27 | PXD065205 | Pride
Project description:The genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remains incomplete. Deep sequencing, data filtering and validation from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs (74-81% true-positive), all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites were unique to liver. Changes in RNA editing led to corresponding changes in intestinal mRNA and protein levels in 11 genes. We found distinctive polysome profiles for several editing targets and demonstrated nuclear but not cytoplasmic editing of novel exonic sites in intestinal (but not hepatic) apoB RNA. RNA editing was validated using cell-free extracts from wild-type but not Apobec-1 deficient mice. These studies define selective, tissue-specific targets of Apobec-1 dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
2014-05-23 | GSE57910 | GEO
Project description:Background: RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoproteinB (apoB) mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remains incomplete. Results: Deep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs (74-81% Sanger sequenced validated), all within 3’ untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites were unique to liver. Changes in RNA editing led to corresponding changes in intestinal mRNA and protein levels in 11 genes. RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression revealed that a subset of targets identified in wild-type mice were restored in Apobec-1 deficient mouse intestine and liver following Apobec-1 rescue. We found distinctive polysome profiles for several RNA editing targets and demonstrated novel exonic editing sites in nuclear preparations from intestine (but not hepatic) apoB RNA. RNA editing was validated using cell-free extracts from wild-type but not Apobec-1 deficient mice, demonstrating that Apobec-1 is required. Conclusions: These studies define selective, tissue-specific targets of Apobec-1 dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
2014-06-02 | PXD001007 | Pride
Project description:Prime editing is a novel genome editing technology using fusion proteins of Cas9-nickase and reverse transcriptase, that holds promise to correct a wide variety of genetic defects.
We succeeded in efficient prime editing and functional recovery of disease-causing mutations in patient-derived liver and intestinal stem cell organoids. Whole genome sequencing of did not detect off-target mutations or a mutational signature induced by prime editing.
| EGAS00001004611 | EGA