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Genome-Wide Investigation and Functional Analysis of RNA Editing Sites in Wheat

ABSTRACT: Genome-Wide Investigation and Functional Analysis of RNA Editing Sites in Wheat

PROVIDER: PRJNA788400 | ENA |

REPOSITORIES: ENA

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			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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Genome-Wide Investigation and Functional Analysis of RNA Editing Sites in Wheat

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

Investigation of RNA editing sites within bound regions of RNA-binding proteins

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

Investigation of RNA editing sites within bound regions of RNA-binding proteins

Project description:Investigation of RNA editing sites within bound regions of RNA-binding proteins

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Genome-wide investigation and functional analysis of RNA editing sites in wheat.

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.

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METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers

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Genome-wide identification and functional analysis of Apobec-1 mediated C-to-U RNA editing in mouse small intestine and liver

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

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Project description:METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [ChIP-Seq]

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METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [CRISPR screen_H358]

Project description:METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [CRISPR screen_H358]

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METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [RNA-Seq_shKD]

Project description:METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [RNA-Seq_shKD]

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METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [CRISPR screen_22Rv1]

Project description:METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers [CRISPR screen_22Rv1]