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RNA Remodeling Proteins

Overview of attention for book
Cover of 'RNA Remodeling Proteins'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Key Points to Consider When Studying RNA Remodeling by Proteins
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    Chapter 2 Happy Birthday: 25 Years of DEAD-Box Proteins.
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    Chapter 3 In Vivo Cross-Linking Followed by PolyA Enrichment to Identify Yeast mRNA Binding Proteins.
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    Chapter 4 Dynamics of the spb4 interactome monitored by affinity purification.
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    Chapter 5 Using EMOTE to Map the Exact 5′-Ends of Processed RNA on a Transcriptome-Wide Scale
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    Chapter 6 Cellular Localization of RNA Degradation and Processing Components in Escherichia coli
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    Chapter 7 Recombineering Applications for the Mutational Analysis of Bacterial RNA-Binding Proteins and Their Sites of Action
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    Chapter 8 Determination of RNA Chaperone Activity Using an Escherichia coli Mutant
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    Chapter 9 Biochemical Characterization of G4 Quadruplex Telomerase RNA Unwinding by the RNA Helicase RHAU
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    Chapter 10 ATPase Site Configuration of the RNA Helicase DbpA Probed by ENDOR Spectroscopy
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    Chapter 11 Bioinformatics and Biochemical Methods to Study the Structural and Functional Elements of DEAD-Box RNA Helicases
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    Chapter 12 Measuring Helicase Inhibition of the DEAD-Box Protein Dbp2 by Yra1.
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    Chapter 13 A FRET-Based, Continuous Assay for the Helicase Activity of DEAD-Box Proteins
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    Chapter 14 A Fluorescence-Based Screening Assay for Identification of Hepatitis C Virus NS3 Helicase Inhibitors and Characterization of Their Inhibitory Mechanism
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    Chapter 15 Mechanisms of HCV NS3 Helicase Monitored by Optical Tweezers
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    Chapter 16 Constructing a Magnetic Tweezers to Monitor RNA Translocation at the Single-Molecule Level
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    Chapter 17 Probing RNA Translocases with DNA
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    Chapter 18 Monitoring RNA Unwinding by the Transcription Termination Factor Rho from Mycobacterium tuberculosis
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    Chapter 19 Characterization of the mechanisms of transcription termination by the helicase sen1.
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    Chapter 20 Characterization of TRAP-Mediated Regulation of the B. subtilis trp Operon Using In Vitro Transcription and Transcriptional Reporter Fusions In Vivo
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    Chapter 21 Single-Molecule FRET Characterization of RNA Remodeling Induced by an Antitermination Protein
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    Chapter 22 Fluorescence Reporters for Hfq Oligomerization and RNA Annealing
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    Chapter 23 Fluorescence anisotropy-based salt-titration approach to characterize protein-nucleic Acid interactions.
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    Chapter 24 Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting.
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    Chapter 25 Purification of Eukaryotic Exoribonucleases Following Heterologous Expression in Bacteria and Analysis of Their Biochemical Properties by In Vitro Enzymatic Assays
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    Chapter 26 Tips and Tricks to Probe the RNA-Degrading Activities of Hyperthermophilic Archaeal β-CASP Ribonucleases.
Attention for Chapter 24: Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting.
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Chapter title
Probing Hfq:RNA Interactions with Hydroxyl Radical and RNase Footprinting.
Chapter number 24
Book title
RNA Remodeling Proteins
Published in
Methods in molecular biology, January 2015
DOI 10.1007/978-1-4939-2214-7_24
Pubmed ID
25579599
Book ISBNs
978-1-4939-2213-0, 978-1-4939-2214-7
Authors

Ellis MJ, Trussler RS, Ross JA, Haniford DB, Michael J. Ellis, Ryan S. Trussler, Joseph A. Ross, David B. Haniford

Abstract

RNA footprinting and structure probing techniques are used to characterize the interaction between RNA-binding proteins and RNAs in vitro. Hydroxyl radical footprinting results in the identification of protein binding site(s) in an RNA. Ribonuclease (RNase) structure probing is a complementary technique that also provides information about protein binding sites, as well as RNA structure and possible protein-directed RNA remodeling. Here we provide a comprehensive protocol for studying the interaction between Hfq and an mRNA or sRNA of interest using a combination of RNase A, T1, and V1 as well as hydroxyl radical footprinting techniques. Detailed protocols for in vitro synthesis of (32)P-labeled RNA; formation of Hfq:RNA binary complex(es), RNase, and hydroxyl radical footprinting; preparation and running of sequencing gels; and data analysis are provided.

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X Demographics

X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
 Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 9 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 9 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 2 22%
Student > Ph. D. Student 1 11%
Unspecified 1 11%
Student > Bachelor 1 11%
Student > Doctoral Student 1 11%
Other 0 0%
Unknown 3 33%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 3 33%
Agricultural and Biological Sciences 2 22%
Unspecified 1 11%
Unknown 3 33%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 13 January 2015.
All research outputs
#18,389,490
of 22,778,347 outputs
Outputs from Methods in molecular biology
#7,875
of 13,093 outputs
Outputs of similar age
#256,766
of 353,651 outputs
Outputs of similar age from Methods in molecular biology
#481
of 1,007 outputs
Altmetric has tracked 22,778,347 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,093 research outputs from this source. They receive a mean Attention Score of 3.3. This one is in the 24th percentile – i.e., 24% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 353,651 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 16th percentile – i.e., 16% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 1,007 others from the same source and published within six weeks on either side of this one. This one is in the 36th percentile – i.e., 36% of its contemporaries scored the same or lower than it.

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