Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes (Q40067843)

17 September 2017

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes (English)

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17 September 2017

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Carlos L Araya

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William Greenleaf

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object named as

William J Greenleaf

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17 September 2017

1

Jason D Buenrostro

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17 September 2017

Curtis J Layton

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17 September 2017

Howard Y Chang

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17 September 2017

Michael P Snyder

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13 April 2014

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562-568

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describes a project that uses

17 September 2017

ImageJ

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11 June 2022

https://www.ebi.ac.uk/europepmc/webservices/rest/PMC4414031/fullTextXML

inferred from PubMed Central ID database lookup

exact match

https://scigraph.springernature.com/pub.10.1038/nbt.2880

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cites work

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

1 reference

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

22 September 2017

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A compendium of RNA-binding motifs for decoding gene regulation.

22 September 2017

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Epistasis among adaptive mutations in deer mouse hemoglobin.

22 September 2017

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Systematic reconstruction of RNA functional motifs with high-throughput microfluidics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

22 September 2017

1 reference

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Programmable single-cell mammalian biocomputers

22 September 2017

1 reference

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Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

22 September 2017

1 reference

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Modular regulatory principles of large non-coding RNAs

22 September 2017

1 reference

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Counting absolute numbers of molecules using unique molecular identifiers

22 September 2017

1 reference

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Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing

22 September 2017

1 reference

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Understanding the transcriptome through RNA structure

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

22 September 2017

1 reference

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Genome-wide identification of polycomb-associated RNAs by RIP-seq

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

A screen for RNA-binding proteins in yeast indicates dual functions for many enzymes.

22 September 2017

1 reference

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High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing

22 September 2017

1 reference

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Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins

22 September 2017

1 reference

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Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae

22 September 2017

1 reference

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Genome-wide measurement of RNA secondary structure in yeast

22 September 2017

1 reference

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Long noncoding RNA as modular scaffold of histone modification complexes

22 September 2017

1 reference

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An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

22 September 2017

1 reference

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Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

22 September 2017

1 reference

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Unbiased RNA-protein interaction screen by quantitative proteomics.

22 September 2017

1 reference

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Accurate whole human genome sequencing using reversible terminator chemistry

22 September 2017

1 reference

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HITS-CLIP yields genome-wide insights into brain alternative RNA processing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Single-molecule fluorescence resonance energy transfer assays reveal heterogeneous folding ensembles in a simple RNA stem-loop

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Direct observation of hierarchical folding in single riboswitch aptamers

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

RNA regulons: coordination of post-transcriptional events

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Darwinian evolution can follow only very few mutational paths to fitter proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Localization of ASH1 mRNA particles in living yeast

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Mutations that increase the affinity of a translational repressor for RNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

RNA binding site of R17 coat protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Hidden specificity in an apparently nonspecific RNA-binding protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Rapid construction of empirical RNA fitness landscapes

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Real-time tRNA transit on single translating ribosomes at codon resolution

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

The role of epistasis in protein evolution.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Epistasis as the primary factor in molecular evolution

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Sequence-specific interaction of R17 coat protein with its ribonucleic acid binding site

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4414031

Crystal structure of an RNA bacteriophage coat protein–operator complex

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24727714

12 December 2020

inferred from PubMed ID database lookup

Measuring the thermodynamics of RNA secondary structure formation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24727714

12 December 2020

inferred from PubMed ID database lookup

Interaction of R17 coat protein with synthetic variants of its ribonucleic acid binding site

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24727714

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1038/NBT.2880

1 reference

17 September 2017

1 reference

17 September 2017

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