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An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue

Overview of attention for article published in Biological Procedures Online, August 2017
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  • Among the highest-scoring outputs from this source (#33 of 130)
  • Good Attention Score compared to outputs of the same age (70th percentile)

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10 tweeters

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10 Dimensions

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30 Mendeley
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Title
An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue
Published in
Biological Procedures Online, August 2017
DOI 10.1186/s12575-017-0059-0
Pubmed ID
Authors

Sarah-Anne David, Benoît Piégu, Christelle Hennequet-Antier, Maëlle Pannetier, Tiphaine Aguirre-Lavin, Sabine Crochet, Thierry Bordeau, Nathalie Couroussé, Aurélien Brionne, Yves Bigot, Anne Collin, Vincent Coustham

Abstract

Genomic loci associated with histone marks are typically analyzed by immunoprecipitation of the chromatin followed by quantitative-PCR (ChIP-qPCR) or high throughput sequencing (ChIP-seq). Chromatin can be either cross-linked (X-ChIP) or used in the native state (N-ChIP). Cross-linking of DNA and proteins helps stabilizing their interactions before analysis. Despite X-ChIP is the most commonly used method, muscle tissue fixation is known to be relatively inefficient. Moreover, no protocol described a simple and reliable preparation of skeletal muscle chromatin of sufficient quality for subsequent high-throughput sequencing. Here we aimed to set-up and compare both chromatin preparation methods for a genome-wide analysis of H3K27me3, a broad-peak histone mark, using chicken P. major muscle tissue. Fixed and unfixed chromatin were prepared from chicken muscle tissues (Pectoralis major). Chromatin fixation, shearing by sonication or digestion and immunoprecipitation performed equivalently. High-quality Illumina reads were obtained (q30 > 93%). The bioinformatic analysis of the data was performed using epic, a tool based on SICER, and MACS2. Forty millions of reads were analyzed for both X-ChIP-seq and N-ChIP-seq experiments. Surprisingly, H3K27me3 X-ChIP-seq analysis led to the identification of only 2000 enriched regions compared to about 15,000 regions identified in the case of N-ChIP-seq. N-ChIP-seq peaks were more consistent between replicates compared to X-ChIP-seq. Higher N-ChIP-seq enrichments were confirmed by ChIP-qPCR at the PAX5 and SOX2 loci known to be enriched for H3K27me3 in myotubes and at the loci of common regions of enrichment identified in this study. Our findings suggest that the preparation of muscle chromatin for ChIP-seq in cross-linked conditions can compromise the systematic analysis of broad histone marks. Therefore, native chromatin preparation should be preferred to cross-linking when a ChIP experiment has to be performed on skeletal muscle tissue, particularly when a broad source signal is considered.

Twitter Demographics

The data shown below were collected from the profiles of 10 tweeters 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 30 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 30 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 10 33%
Researcher 7 23%
Student > Bachelor 3 10%
Student > Postgraduate 2 7%
Student > Master 2 7%
Other 2 7%
Unknown 4 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 13 43%
Agricultural and Biological Sciences 7 23%
Computer Science 2 7%
Medicine and Dentistry 2 7%
Psychology 1 3%
Other 1 3%
Unknown 4 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 25 September 2017.
All research outputs
#4,357,067
of 16,639,069 outputs
Outputs from Biological Procedures Online
#33
of 130 outputs
Outputs of similar age
#80,819
of 275,997 outputs
Outputs of similar age from Biological Procedures Online
#1
of 1 outputs
Altmetric has tracked 16,639,069 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 130 research outputs from this source. They receive a mean Attention Score of 3.6. This one has gotten more attention than average, scoring higher than 74% of its peers.
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 275,997 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 70% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them