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UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts

Overview of attention for article published in Plant Methods, November 2016
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Title
UV crosslinked mRNA-binding proteins captured from leaf mesophyll protoplasts
Published in
Plant Methods, November 2016
DOI 10.1186/s13007-016-0142-6
Pubmed ID
Authors

Zhicheng Zhang, Kurt Boonen, Piero Ferrari, Liliane Schoofs, Ewald Janssens, Vera van Noort, Filip Rolland, Koen Geuten

Abstract

The complexity of RNA regulation is one of the current frontiers in animal and plant molecular biology research. RNA-binding proteins (RBPs) are characteristically involved in post-transcriptional gene regulation through interaction with RNA. Recently, the mRNA-bound proteome of mammalian cell lines has been successfully cataloged using a new method called interactome capture. This method relies on UV crosslinking of proteins to RNA, purifying the mRNA using complementary oligo-dT beads and identifying the crosslinked proteins using mass spectrometry. We describe here an optimized system of mRNA interactome capture for Arabidopsis thaliana leaf mesophyll protoplasts, a cell type often used in functional cellular assays. We established the conditions for optimal protein yield, namely the amount of starting tissue, the duration of UV irradiation and the effect of UV intensity. We demonstrated high efficiency mRNA-protein pull-down by oligo-d(T)25 bead capture. Proteins annotated to have RNA-binding capacity were overrepresented in the obtained medium scale mRNA-bound proteome, indicating the specificity of the method and providing in vivo UV crosslinking experimental evidence for several candidate RBPs from leaf mesophyll protoplasts. The described method, applied to plant cells, allows identifying proteins as having the capacity to bind mRNA directly. The method can now be scaled and applied to other plant cell types and species to contribute to the comprehensive description of the RBP proteome of plants.

Twitter Demographics

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

Mendeley readers

The data shown below were compiled from readership statistics for 59 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 59 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 19%
Student > Ph. D. Student 10 17%
Student > Master 8 14%
Student > Bachelor 8 14%
Student > Doctoral Student 6 10%
Other 8 14%
Unknown 8 14%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 27 46%
Agricultural and Biological Sciences 21 36%
Engineering 2 3%
Computer Science 1 2%
Unknown 8 14%

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 03 November 2016.
All research outputs
#4,623,350
of 8,614,521 outputs
Outputs from Plant Methods
#215
of 310 outputs
Outputs of similar age
#136,599
of 247,037 outputs
Outputs of similar age from Plant Methods
#5
of 6 outputs
Altmetric has tracked 8,614,521 research outputs across all sources so far. This one is in the 27th percentile – i.e., 27% of other outputs scored the same or lower than it.
So far Altmetric has tracked 310 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.5. This one is in the 19th percentile – i.e., 19% 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 247,037 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 35th percentile – i.e., 35% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 6 others from the same source and published within six weeks on either side of this one.