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Links between DNA methylation and nucleosome occupancy in the human genome

Overview of attention for article published in Epigenetics & Chromatin, April 2017
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (80th percentile)

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19 tweeters

Citations

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24 Dimensions

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71 Mendeley
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Title
Links between DNA methylation and nucleosome occupancy in the human genome
Published in
Epigenetics & Chromatin, April 2017
DOI 10.1186/s13072-017-0125-5
Pubmed ID
Authors

Clayton K. Collings, John N. Anderson

Abstract

DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome. The results demonstrated that increasing methylated CpG density is correlated with nucleosome occupancy in the total genome and within nearly all subgenomic regions. Features with elevated methylated CpG density such as exons, SINE-Alu sequences, H3K36-trimethylated peaks, and methylated CpG islands are among the highest nucleosome occupied elements in the genome, while some of the lowest occupancies are displayed by unmethylated CpG islands and unmethylated transcription factor binding sites. Additionally, outside of CpG islands, the density of CpGs within nucleosomes was shown to be important for the nucleosomal location of DNA methylation with low CpG frequencies favoring linker methylation and high CpG frequencies favoring core particle methylation. Prominent exceptions to the correlations between methylated CpG density and nucleosome occupancy include CpG islands marked by H3K27me3 and CpG-poor heterochromatin marked by H3K9me3, and these modifications, along with DNA methylation, distinguish the major silencing mechanisms of the human epigenome. Thus, the relationship between DNA methylation and nucleosome occupancy is influenced by the density of methylated CpG dinucleotides and by other epigenomic components in chromatin.

Twitter Demographics

The data shown below were collected from the profiles of 19 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 71 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 1%
Italy 1 1%
Unknown 69 97%

Demographic breakdown

Readers by professional status Count As %
Researcher 21 30%
Student > Ph. D. Student 15 21%
Student > Master 8 11%
Student > Doctoral Student 5 7%
Student > Bachelor 4 6%
Other 6 8%
Unknown 12 17%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 29 41%
Agricultural and Biological Sciences 16 23%
Chemistry 4 6%
Computer Science 3 4%
Medicine and Dentistry 2 3%
Other 4 6%
Unknown 13 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 10. 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 06 October 2017.
All research outputs
#1,943,228
of 15,094,393 outputs
Outputs from Epigenetics & Chromatin
#93
of 443 outputs
Outputs of similar age
#51,816
of 265,914 outputs
Outputs of similar age from Epigenetics & Chromatin
#1
of 1 outputs
Altmetric has tracked 15,094,393 research outputs across all sources so far. Compared to these this one has done well and is in the 86th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 443 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.6. This one has done well, scoring higher than 78% 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 265,914 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 80% 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