DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo (Q33901950)

29 July 2017

title

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo (English)

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29 July 2017

5

Jonathan S Weissman

1 reference

29 July 2017

Meghan Zubradt

1

1 reference

29 July 2017

Paromita Gupta

2

1 reference

29 July 2017

Sitara Persad

3

1 reference

29 July 2017

Alan M Lambowitz

4

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29 July 2017

Silvi Rouskin

6

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29 July 2017

publication date

7 November 2016

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29 July 2017

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29 July 2017

volume

14

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29 July 2017

issue

1

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29 July 2017

page(s)

75-82

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RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs

29 July 2017

cites work

1 reference

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A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

5 July 2018

1 reference

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Detection of RNA-Protein Interactions in Living Cells with SHAPE.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Systematic imaging reveals features and changing localization of mRNAs in Drosophila development

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Structural imprints in vivo decode RNA regulatory mechanisms

5 July 2018

1 reference

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The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

5 July 2018

1 reference

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Rational experiment design for sequencing-based RNA structure mapping

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

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

5 July 2018

1 reference

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Single-molecule correlated chemical probing of RNA.

5 July 2018

1 reference

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Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).

5 July 2018

1 reference

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Insights into RNA structure and function from genome-wide studies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Landscape and variation of RNA secondary structure across the human transcriptome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Comparative analysis of RNA sequencing methods for degraded or low-input samples

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

5 July 2018

ViennaRNA Package 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

The structure of the eukaryotic ribosome at 3.0 Å resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Dimerization of oskar 3' UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Conserved RNA structures in the non-canonical Hac1/Xbp1 intron

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

VARNA: Interactive drawing and editing of the RNA secondary structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Coding-sequence determinants of gene expression in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Accurate SHAPE-directed RNA structure determination

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Messenger RNA targeting to endoplasmic reticulum stress signalling sites.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Control of mammalian translation by mRNA structure near caps

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

gurken and the I factor retrotransposon RNAs share common localization signals and machinery

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Targeted mRNA degradation by deadenylation-independent decapping.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Use of dimethyl sulfate to probe RNA structure in vivo

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

On the fidelity of DNA replication: manganese mutagenesis in vitro.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

bicoid mRNA localization signal: phylogenetic conservation of function and RNA secondary structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5508988

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

5 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.4057

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FNMETH.4057

Structural elements required for the localization of ASH1 mRNA and of a green fluorescent protein reporter particle in vivo

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27819661

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NMETH.4057

1 reference

Dimensions Publication ID

29 July 2017

0 references

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29 July 2017

1 reference