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Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

Overview of attention for article published in Genome Biology, August 2012
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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 (95th percentile)
  • High Attention Score compared to outputs of the same age and source (80th percentile)

Mentioned by

blogs
2 blogs
twitter
20 X users
facebook
1 Facebook page
wikipedia
2 Wikipedia pages

Citations

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206 Dimensions

Readers on

mendeley
236 Mendeley
citeulike
1 CiteULike
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Title
Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase
Published in
Genome Biology, August 2012
DOI 10.1186/gb-2012-13-8-r69
Pubmed ID
Authors

Eun-Ang Raiber, Dario Beraldi, Gabriella Ficz, Heather E Burgess, Miguel R Branco, Pierre Murat, David Oxley, Michael J Booth, Wolf Reik, Shankar Balasubramanian

Abstract

ABSTRACT: BACKGROUND: Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the methylation landscape is dynamically reprogrammed in part through active demethylation. Recent advances have identified key players involved in active demethylation pathways, including oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) by the TET enzymes, and excision of 5fC by the base excision repair enzyme thymine DNA glycosylase (TDG). Here, we provide the first genome-wide map of 5fC in mouse embryonic stem (ES) cells and evaluate potential roles for 5fC in differentiation. RESULTS: Our method exploits the unique reactivity of 5fC for pulldown and high-throughput sequencing. Genome-wide mapping revealed 5fC enrichment in CpG islands (CGIs) of promoters and exons. CGI promoters in which 5fC was relatively more enriched than 5mC or 5hmC corresponded to transcriptionally active genes. Accordingly, 5fC-rich promoters had elevated H3K4me3 levels, associated with active transcription, and were frequently bound by RNA polymerase II. TDG down-regulation led to 5fC accumulation in CGIs in ES cells, which correlates with increased methylation in these genomic regions during differentiation of ES cells in wild-type and TDG knockout contexts. CONCLUSIONS: Collectively, our data suggest that 5fC plays a role in epigenetic reprogramming within specific genomic regions, which is controlled in part by TDG-mediated excision. Notably, 5fC excision in ES cells is necessary for the correct establishment of CGI methylation patterns during differentiation and hence for appropriate patterns of gene expression during development.

X Demographics

X Demographics

The data shown below were collected from the profiles of 20 X users 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 236 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 3 1%
Germany 2 <1%
Brazil 2 <1%
Japan 2 <1%
Netherlands 1 <1%
Spain 1 <1%
Portugal 1 <1%
United States 1 <1%
Luxembourg 1 <1%
Other 0 0%
Unknown 222 94%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 62 26%
Researcher 59 25%
Student > Master 30 13%
Student > Bachelor 12 5%
Professor 12 5%
Other 34 14%
Unknown 27 11%
Readers by discipline Count As %
Agricultural and Biological Sciences 95 40%
Biochemistry, Genetics and Molecular Biology 49 21%
Chemistry 38 16%
Medicine and Dentistry 7 3%
Arts and Humanities 4 2%
Other 13 6%
Unknown 30 13%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 27. 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 June 2022.
All research outputs
#1,436,260
of 25,373,627 outputs
Outputs from Genome Biology
#1,144
of 4,467 outputs
Outputs of similar age
#8,384
of 187,104 outputs
Outputs of similar age from Genome Biology
#8
of 41 outputs
Altmetric has tracked 25,373,627 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,467 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. 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 187,104 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 95% 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 has done well, scoring higher than 80% of its contemporaries.