The dynamic epitranscriptome: A to I editing modulates genetic information

Tajaddod, Mansoureh; Jantsch, Michael F.; Licht, Konstantin

doi:10.1007/s00412-015-0526-9

Cited by 35 publications

(21 citation statements)

References 132 publications

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“…Another post-transcriptional modification, A-to-I RNA editing 49 , commonly occurs in introns, UTRs, and Alu elements. It plays an important role in splicing and regulating innate immunity 50,51 and is associated with epilepsy, autism, neurodegenerative diseases, and cancer 52 . NGS detects A-to-I editing as a nucleotide variant in cDNA sequences (A-to-G).…”

Section: Modification Detectionmentioning

confidence: 99%

Nanopore native RNA sequencing of a human poly(A) transcriptome

Workman

Tang

et al. 2018

Preprint

188

349

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High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not carried forward in cDNA. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads. These native RNA reads had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes from nanopore RNA data. Together, these nanopore-based techniques are poised to deliver new insights into RNA biology.

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Section: Modification Detectionmentioning

confidence: 99%

Nanopore native RNA sequencing of a human poly(A) transcriptome

Workman

Tang

et al. 2018

Preprint

188

349

View full text Add to dashboard Cite

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“…Construction and characterization of ADAR and/or apobec as recognition elements of RNA chips for detection of base mutations could illuminate for instance which specific target organ or group of tissues bear the mutation and when, comparing eventually mutation analysis under physiological and toxicological conditions. It could also compare genomic and RNA templates, investigating evolutionary and functional aspects of exon (coding) versus intron (non-coding) RNA editing or how fast a non-silent base mutation can occur and drastically affect the proteome repertoire [ 96 , 97 ]. A cytidine deaminase edits C to U to permit proper folding and functionality of RNA in archaean bacteria such as Methanopyrus kandleri [ 98 ].…”

Section: Biosensing Expression Of Tissue-specific Rna Mutationsmentioning

confidence: 99%

Genotyping and Bio-Sensing Chemosensory Proteins in Insects

Liu

Arnaúd

Offmann

et al. 2017

Sensors

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Genotyping is the process of determining differences in the genetic make-up of an individual and comparing it to that of another individual. Focus on the family of chemosensory proteins (CSPs) in insects reveals differences at the genomic level across various strains and biotypes, but none at the level of individuals, which could be extremely useful in the biotyping of insect pest species necessary for the agricultural, medical and veterinary industries. Proposed methods of genotyping CSPs include not only restriction enzymatic cleavage and amplification of cleaved polymorphic sequences, but also detection of retroposons in some specific regions of the insect chromosome. Design of biosensors using CSPs addresses tissue-specific RNA mutations in a particular subtype of the protein, which could be used as a marker of specific physiological conditions. Additionally, we refer to the binding properties of CSP proteins tuned to lipids and xenobiotic insecticides for the development of a new generation of biosensor chips, monitoring lipid blood concentration and chemical environmental pollution.

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“…However, rather than permanent DNA mutations or reversible RNA modifications, RNA editing has its own limited lifespan and results in more permanent modification [102]. Adenosine-to-inosine RNA editing (A-to-I editing), also called I, is catalysed by adenosine deaminases acting on RNA (ADARs) [101,103,104]. Recently, 1741 I sites have been reported in CD regions of transcripts from RNA-seq data of different human tissues [105].…”

Section: And Umentioning

confidence: 99%

Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation

2020

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RNA modifications can be added or removed by a variety of enzymes that catalyse the necessary reactions, and these modifications play roles in essential molecular mechanisms. The prevalent modifications on mRNA include N6-methyladenosine (m 6 A), N1-methyladenosine (m 1 A), 5-methylcytosine (m 5 C), 5-hydroxymethylcytosine (hm 5 C), pseudouridine (Ψ), inosine (I), uridine (U) and ribosemethylation (2'-O-Me). Most of these modifications contribute to pre-mRNA splicing, nuclear export, transcript stability and translation initiation in eukaryotic cells. By participating in various physiological processes, RNA modifications also have regulatory roles in the pathogenesis of tumour and non-tumour diseases. We discussed the physiological roles of RNA modifications and associated these roles with disease pathogenesis. Functioning as the bridge between transcription and translation, RNA modifications are vital for the progression of numerous diseases and can even regulate the fate of cancer cells.

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The dynamic epitranscriptome: A to I editing modulates genetic information

Cited by 35 publications

References 132 publications

Nanopore native RNA sequencing of a human poly(A) transcriptome

Nanopore native RNA sequencing of a human poly(A) transcriptome

Genotyping and Bio-Sensing Chemosensory Proteins in Insects

Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation

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