Pseudouridylation meets next-generation sequencing (Q38770274)

6 September 2017

Pseudouridylation meets next-generation sequencing (English)

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6 September 2017

1

Maryam Zaringhalam

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author name string

F Nina Papavasiliou

series ordinal

2

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6 September 2017

8 March 2016

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6 September 2017

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6 September 2017

107

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6 September 2017

63-72

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Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure

6 September 2017

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Clustering of pseudouridine residues around the peptidyltransferase center of yeast cytoplasmic and mitochondrial ribosomes.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

A pseudouridine residue in the spliceosome core is part of the filamentous growth program in yeast.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite-multisubstrate RNA:Psi-synthase also acting on tRNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudo-Seq: Genome-Wide Detection of Pseudouridine Modifications in RNA.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

A method for counting PCR template molecules with application to next-generation sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudouridine in RNA: what, where, how, and why

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Some results of the applications of ion-exchange chromatography to nucleic acid chemistry.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

rRNA modifications and ribosome function

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Unusual base pairing during the decoding of a stop codon by the ribosome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Counting individual DNA molecules by the stochastic attachment of diverse labels

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

The nucleotide sequen of human tRNAGly(anticodon GCC)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

InterPro in 2011: new developments in the family and domain prediction database

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Converting nonsense codons into sense codons by targeted pseudouridylation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Nop58p is a common component of the box C+D snoRNPs that is required for snoRNA stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

MODOMICS: a database of RNA modification pathways--2013 update

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

7 January 2021

Dissecting dyskeratosis

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudouridylation goes regulatory

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

A telomerase component is defective in the human disease dyskeratosis congenita

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Investigation of Overhauser effects between pseudouridine and water protons in RNA helices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Dyskeratosis congenita and cancer in mice deficient in ribosomal RNA modification

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Pseudouridine: still mysterious, but never a fake (uridine)!

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

An improved direct RNA sequence method; its application to Vicia faba 5.8S ribosomal RNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure of Schizosaccharomyces pombe ribosomal RNAs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Characterization of the yeast transcriptome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Functions and mechanisms of spliceosomal small nuclear RNA pseudouridylation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Psi35 in the branch site recognition region of U2 small nuclear RNA is important for pre-mRNA splicing in Saccharomyces cerevisiae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2016.03.001

10.1016/J.YMETH.2016.03.001

7 January 2021

Identifiers

DOI

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6 September 2017

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PubMed ID

26968262