(Q38211391)

31 August 2017

Insights into RNA structure and function from genome-wide studies (English)

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31 August 2017

3

Jennifer A Doudna

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31 August 2017

Stefanie A Mortimer

1

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PubMed ID

24821474

31 August 2017

Mary Anne Kidwell

series ordinal

2

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31 August 2017

13 May 2014

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31 August 2017

Nature Reviews Genetics

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31 August 2017

15

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31 August 2017

7

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31 August 2017

469-479

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https://scigraph.springernature.com/pub.10.1038/nrg3681

31 August 2017

0 references

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21 January 2018

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RNA structure and the mechanisms of alternative splicing.

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Regulation of translation via mRNA structure in prokaryotes and eukaryotes

21 January 2018

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mRNA localization: gene expression in the spatial dimension

21 January 2018

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The highways and byways of mRNA decay

21 January 2018

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The genetic code as expressed through relationships between mRNA structure and protein function

21 January 2018

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RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

21 January 2018

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Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding

21 January 2018

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Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly

21 January 2018

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Advances in RNA structure analysis by chemical probing

21 January 2018

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Vienna RNA secondary structure server

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Mfold web server for nucleic acid folding and hybridization prediction

21 January 2018

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Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

21 January 2018

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Structural inference of native and partially folded RNA by high-throughput contact mapping

21 January 2018

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

21 January 2018

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Widespread purifying selection on RNA structure in mammals

21 January 2018

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RNA design rules from a massive open laboratory

21 January 2018

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Genome-wide measurement of RNA secondary structure in yeast

21 January 2018

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Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis

21 January 2018

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

21 January 2018

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Global analysis of RNA secondary structure in two metazoans.

21 January 2018

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Regulatory impact of RNA secondary structure across the Arabidopsis transcriptome

21 January 2018

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Genome-wide measurement of RNA folding energies

21 January 2018

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

21 January 2018

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

21 January 2018

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Landscape and variation of RNA secondary structure across the human transcriptome

21 January 2018

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Understanding the transcriptome through RNA structure

21 January 2018

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Widespread selection for local RNA secondary structure in coding regions of bacterial genes

21 January 2018

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Architecture and secondary structure of an entire HIV-1 RNA genome

21 January 2018

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

21 January 2018

1 reference

Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol

21 January 2018

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A periodic pattern of mRNA secondary structure created by the genetic code

21 January 2018

1 reference

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

21 January 2018

1 reference

Coding-sequence determinants of gene expression in Escherichia coli

21 January 2018

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Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites

21 January 2018

1 reference

A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes

21 January 2018

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Efficient translation initiation dictates codon usage at gene start

21 January 2018

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Causes and effects of N-terminal codon bias in bacterial genes

21 January 2018

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Translation efficiency is determined by both codon bias and folding energy

21 January 2018

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A pause for thought along the co-translational folding pathway

21 January 2018

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Rate-limiting steps in yeast protein translation

21 January 2018

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Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs

21 January 2018

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Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells

21 January 2018

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Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure.

21 January 2018

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Following translation by single ribosomes one codon at a time.

21 January 2018

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Monitoring cotranslational protein folding in mammalian cells at codon resolution

21 January 2018

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Strong association between mRNA folding strength and protein abundance in S. cerevisiae

21 January 2018

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Global analysis of protein expression in yeast

21 January 2018

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Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

21 January 2018

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A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

21 January 2018

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Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae

21 January 2018

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Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

21 January 2018

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Subcellular mRNA localization in animal cells and why it matters

21 January 2018

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Cis-acting determinants of asymmetric, cytoplasmic RNA transport

21 January 2018

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The signal sequence coding region promotes nuclear export of mRNA

21 January 2018

1 reference

Egalitarian is a selective RNA-binding protein linking mRNA localization signals to the dynein motor

21 January 2018

1 reference

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

21 January 2018

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Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance

21 January 2018

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Bacterial RNA thermometers: molecular zippers and switches

21 January 2018

1 reference

Molecular basis for temperature sensing by an RNA thermometer

21 January 2018

1 reference

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

21 January 2018

1 reference

Arabidopsis mRNA secondary structure correlates with protein function and domains.

21 January 2018

1 reference

Genomic expression programs in the response of yeast cells to environmental changes

21 January 2018

1 reference

The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation

21 January 2018

1 reference

The response of mammalian cells to double-stranded RNA

21 January 2018

1 reference

The role of site accessibility in microRNA target recognition

21 January 2018

1 reference

SHAPE-directed discovery of potent shRNA inhibitors of HIV-1.

21 January 2018

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MicroRNAs: target recognition and regulatory functions

21 January 2018

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Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

21 January 2018

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Computational analysis of miRNA targets in plants: current status and challenges

21 January 2018

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Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome

21 January 2018

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Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends

21 January 2018

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A link between RNA metabolism and silencing affecting Arabidopsis development.

21 January 2018

1 reference

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

21 January 2018

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starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

21 January 2018

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starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data

21 January 2018

1 reference

Use of dimethyl sulfate to probe RNA structure in vivo

21 January 2018

1 reference

RNA SHAPE analysis in living cells

21 January 2018

1 reference

The cellular environment stabilizes adenine riboswitch RNA structure

21 January 2018

1 reference

Determination of in vivo RNA structure in low-abundance transcripts.

21 January 2018

1 reference

DMS footprinting of structured RNAs and RNA-protein complexes

21 January 2018

1 reference

Disease-associated mutations that alter the RNA structural ensemble

21 January 2018

1 reference

Free State Conformational Sampling of the SAM-I Riboswitch Aptamer Domain

21 January 2018

1 reference

An unusual topological structure of the HIV-1 Rev response element

21 January 2018

1 reference

A two-dimensional mutate-and-map strategy for non-coding RNA structure

21 January 2018

1 reference

Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility

21 January 2018

1 reference

Structure and function of long noncoding RNAs in epigenetic regulation

21 January 2018

1 reference

Rise of the RNA machines: exploring the structure of long non-coding RNAs

21 January 2018

1 reference

Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency

21 January 2018

1 reference

Modeling and automation of sequencing-based characterization of RNA structure

21 January 2018

1 reference

Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution

21 January 2018

1 reference

The dynamic landscapes of RNA architecture

21 January 2018

1 reference

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

31 March 2020

1 reference

Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants.

31 March 2020

1 reference

Universally increased mRNA stability downstream of the translation initiation site in eukaryotes and prokaryotes

31 March 2020

1 reference

Asymmetric sorting of ash1p in yeast results from inhibition of translation by localization elements in the mRNA

31 March 2020

1 reference

Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes--GMUCT 2.0.

31 March 2020

1 reference

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

31 March 2020

1 reference

Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133-278)

31 March 2020

1 reference

Molecular mechanisms of RNA interference

31 March 2020

1 reference

12 December 2020

Translational control during heat shock

1 reference

12 December 2020

Probing RNA structure with chemical reagents and enzymes

1 reference

12 December 2020

Ribosome pausing and stacking during translation of a eukaryotic mRNA.

1 reference

12 December 2020

Identifiers

DOI

10.1038/NRG3681

1 reference

PubMed ID

24821474

Dimensions Publication ID

31 August 2017

0 references

1 reference

PubMed ID

24821474