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In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine

Overview of attention for article published in Genome Biology (Online Edition), June 2016
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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 (91st percentile)

Mentioned by

blogs
1 blog
twitter
24 tweeters

Citations

dimensions_citation
53 Dimensions

Readers on

mendeley
115 Mendeley
citeulike
2 CiteULike
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Title
In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine
Published in
Genome Biology (Online Edition), June 2016
DOI 10.1186/s13059-016-1001-5
Pubmed ID
Authors

Mario Iurlaro, Gordon R. McInroy, Heather E. Burgess, Wendy Dean, Eun-Ang Raiber, Martin Bachman, Dario Beraldi, Shankar Balasubramanian, Wolf Reik

Abstract

Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair. These modified bases are stable and detectable in the genome, suggesting that they could have epigenetic functions in their own right. However, functional investigation of the genome-wide distribution of 5fC has been restricted to cell culture-based systems, while its in vivo profile remains unknown. Here, we describe the first analysis of the in vivo genome-wide profile of 5fC across a range of tissues from both wild-type and Tdg-deficient E11.5 mouse embryos. Changes in the formylation profile of cytosine upon depletion of TDG suggest TET/TDG-mediated active demethylation occurs preferentially at intron-exon boundaries and reveals a major role for TDG in shaping 5fC distribution at CpG islands. Moreover, we find that active enhancer regions specifically exhibit high levels of 5fC, resulting in characteristic tissue-diagnostic patterns, which suggest a role in embryonic development. The tissue-specific distribution of 5fC can be regulated by the collective contribution of TET-mediated oxidation and excision by TDG. The in vivo profile of 5fC during embryonic development resembles that of embryonic stem cells, sharing key features including enrichment of 5fC in enhancer and intragenic regions. Additionally, by investigating mouse embryo 5fC profiles in a tissue-specific manner, we identify targeted enrichment at active enhancers involved in tissue development.

Twitter Demographics

The data shown below were collected from the profiles of 24 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 115 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 3 3%
Portugal 1 <1%
Belgium 1 <1%
Unknown 110 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 37 32%
Researcher 27 23%
Student > Master 20 17%
Student > Postgraduate 6 5%
Professor 4 3%
Other 12 10%
Unknown 9 8%
Readers by discipline Count As %
Agricultural and Biological Sciences 42 37%
Biochemistry, Genetics and Molecular Biology 33 29%
Chemistry 14 12%
Medicine and Dentistry 5 4%
Arts and Humanities 2 2%
Other 8 7%
Unknown 11 10%

Attention Score in Context

This research output has an Altmetric Attention Score of 20. 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 28 October 2017.
All research outputs
#1,046,795
of 16,035,941 outputs
Outputs from Genome Biology (Online Edition)
#1,051
of 3,428 outputs
Outputs of similar age
#23,717
of 264,576 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 2 outputs
Altmetric has tracked 16,035,941 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,428 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 25.8. This one has gotten more attention than average, scoring higher than 69% 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 264,576 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 91% of its contemporaries.
We're also able to compare this research output to 2 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