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Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

Overview of attention for article published in Genome Research, May 2014
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (90th percentile)

Mentioned by

twitter
18 tweeters
patent
1 patent
wikipedia
3 Wikipedia pages

Citations

dimensions_citation
59 Dimensions

Readers on

mendeley
155 Mendeley
citeulike
4 CiteULike
Title
Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
Published in
Genome Research, May 2014
DOI 10.1101/gr.164418.113
Pubmed ID
Authors

Vladimir B. Teif, Daria A. Beshnova, Yevhen Vainshtein, Caroline Marth, Jan-Philipp Mallm, Thomas Höfer, Karsten Rippe

Abstract

During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type-specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors depends on their genomic context. The mostly unmethylated CpG islands have reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides are preferentially associated with nucleosomes. In contrast, outside of CpG islands most CpGs are methylated, and the average methylation density oscillates so that it is highest in the linker region between nucleosomes. Outside CpG islands, binding of TET1, an enzyme that converts 5mC to 5hmC, is associated with labile, MNase-sensitive nucleosomes. Such nucleosomes are poised for eviction in ESCs and become stably bound in differentiated cells where the TET1 and 5hmC levels go down. This process regulates a class of CTCF binding sites outside CpG islands that are occupied by CTCF in ESCs but lose the protein during differentiation. We rationalize this cell type-dependent targeting of CTCF with a quantitative biophysical model of competitive binding with the histone octamer, depending on the TET1, 5hmC, and 5mC state.

Twitter Demographics

The data shown below were collected from the profiles of 18 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 155 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 3%
United Kingdom 3 2%
Germany 2 1%
France 2 1%
Canada 2 1%
Bulgaria 1 <1%
Japan 1 <1%
China 1 <1%
Unknown 138 89%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 58 37%
Researcher 51 33%
Student > Master 11 7%
Student > Bachelor 8 5%
Professor > Associate Professor 6 4%
Other 21 14%
Readers by discipline Count As %
Agricultural and Biological Sciences 85 55%
Biochemistry, Genetics and Molecular Biology 36 23%
Computer Science 5 3%
Unspecified 5 3%
Neuroscience 4 3%
Other 20 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. 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 31 July 2018.
All research outputs
#893,946
of 11,676,441 outputs
Outputs from Genome Research
#768
of 3,278 outputs
Outputs of similar age
#18,135
of 188,036 outputs
Outputs of similar age from Genome Research
#29
of 41 outputs
Altmetric has tracked 11,676,441 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,278 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 13.6. This one has done well, scoring higher than 76% 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 188,036 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 90% of its contemporaries.
We're also able to compare this research output to 41 others from the same source and published within six weeks on either side of this one. This one is in the 29th percentile – i.e., 29% of its contemporaries scored the same or lower than it.