Transcriptome‐Wide Identification of Pseudouridine Modifications Using Pseudo‐seq

Carlile, Thomas M.; Rojas-Durán, María F.; Gilbert, Wendy V.

doi:10.1002/0471142727.mb0425s112

Cited by 22 publications

(20 citation statements)

References 28 publications

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“…Pus1 is a member of the TruA family that typically pseudouridylates tRNA but was also recently found to act on rRNA, snRNA, and mRNA (Schwartz et al, 2014a ; Carlile et al, 2015 ). Mutations of Pus1 in human lead to mitochondrial myopathy and sideroblastic anemia (Bykhovskaya et al, 2004 ; Fernandez-Vizarra et al, 2007 ; Bergmann et al, 2010 ).…”

Section: Pseudouridine (ψ)mentioning

confidence: 99%

The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders

Angelova

Dimitrova

Dinges

et al. 2018

Front. Bioeng. Biotechnol.

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Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.

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Section: Pseudouridine (ψ)mentioning

confidence: 99%

The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders

Angelova

Dimitrova

Dinges

et al. 2018

Front. Bioeng. Biotechnol.

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“…m6A is found preferentially at the consensus motif DRACH (D=A, G or U; R=A or G; H=A, C or U) and is highly enriched near mRNA stop codons 12,13 . Pseudouridine is another well characterised modification, occurring via an isomerisation of uracil catalysed by enzymes of the pseudouridine synthase (PUS) family and the dyskerin pseudouridine synthase 1 (DKC1) enzyme 14 . It is the most abundant internal PTM present in RNAs, including the highly conserved transcriptional regulator 7SK RNA 15 .…”

Section: Introductionmentioning

confidence: 99%

RNA modifications detection by comparative Nanopore direct RNA sequencing

Léger

Pandolfini

et al. 2019

Preprint

144

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RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. To date, over 150 naturally occurring PTMs have been identified, however the overwhelming majority of their functions remain elusive. In recent years, a small number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing (DRS) technology has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework to evaluate the presence of modifications in DRS data. To do so, we compare an RNA sample of interest against a non-modified control sample. Our strategy does not require a training set and allows the use of replicates to model biological variability. Here, we demonstrate the ability of Nanocompore to detect RNA modifications at single-molecule resolution in human polyA+ RNAs, as well as in targeted non-coding RNAs. Our results correlate well with orthogonal methods, confirm previous observations on the distribution of N6-methyladenosine sites and provide novel insights into the distribution of RNA modifications in the coding and non-coding transcriptomes. The latest version of Nanocompore can be obtained at https://github.com/tleonardi/nanocompore.

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“…In contrast, detection of pseudouridine must, so far, entirely rely on chemical treatment for the generation of RT-stops, as the nucleoside itself leaves no exploitable RT-signature. To this end, several labs have performed mapping experiments using soluble carbodiimide ( N -Cyclohexyl- N ’-(2-morpholinoethyl)carbodiimide metho- p -toluenesulfonate, usually abbreviated as CMCT) [3,54,55,56,57,58], an agent developed by Bakin and Ofengand [59] for mapping of pseudouridine in ribosomal RNA. A promising variant used a “clickable” derivative, which was conjugated with an affinity tag for the enrichment of derivatized, pseudouridine containing RNA [60,61].…”

Section: Exploiting Specific Chemical Reactivity Of Modified Nuclementioning

confidence: 99%

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

Motorin

Helm

2019

Genes

108

106

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New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell’s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use the term “epitranscriptome”. Due to the high rate of newly published mapping techniques, a significant number of chemically distinct RNA modifications have become amenable to mapping, albeit with variegated accuracy and precision, depending on the nature of the technique. This review gives a brief overview of known techniques, and how they were applied to modification calling.

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Transcriptome‐Wide Identification of Pseudouridine Modifications Using Pseudo‐seq

Cited by 22 publications

References 28 publications

The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders

The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders

RNA modifications detection by comparative Nanopore direct RNA sequencing

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

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