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The frequent evolutionary birth and death of functional promoters in mouse and human

Overview of attention for article published in Genome Research, August 2015
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (97th percentile)
  • High Attention Score compared to outputs of the same age and source (97th percentile)

Mentioned by

news
5 news outlets
twitter
43 tweeters

Readers on

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102 Mendeley
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4 CiteULike
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Title
The frequent evolutionary birth and death of functional promoters in mouse and human
Published in
Genome Research, August 2015
DOI 10.1101/gr.190546.115
Pubmed ID
Authors

Robert S Young, Yosihide Hayashizaki, Robin Andersson, Albin Sandelin, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, FANTOM Consortium, Wendy A Bickmore, Alistair R Forrest, Martin S Taylor, Young, Robert S, Hayashizaki, Yosihide, Andersson, Robin, Sandelin, Albin, Kawaji, Hideya, Itoh, Masayoshi, Lassmann, Timo, Carninci, Piero, , , Bickmore, Wendy A, Forrest, Alistair R, Taylor, Martin S, Robert S. Young, Yoshihide Hayashizaki, The FANTOM Consortium, Wendy A. Bickmore, Alistair R. Forrest, Martin S. Taylor

Abstract

Promoters are central to the regulation of gene expression. Changes in gene regulation are thought to underlie much of the adaptive diversification between species and phenotypic variation within populations. In contrast to earlier work emphasizing the importance of enhancer evolution and subtle sequence changes at promoters, we show that dramatic changes such as the complete gain and loss (collectively turnover) of functional promoters are common. Using quantitative measures of transcription initiation in both humans and mice across 52 matched tissues we discriminate promoter sequence gains from losses and resolve the lineage of changes. We also identify expression divergence and functional turnover between orthologous promoters, finding only the latter is associated with local sequence changes. Promoter turnover has occurred at the majority (>56%) of protein-coding genes since humans and mice diverged. Tissue-restricted promoters are the most evolutionarily volatile where retrotransposition is an important, but not the sole source of innovation. There is considerable heterogeneity of turnover rates between promoters in different tissues, but the consistency of these in both lineages suggests the same biological systems are similarly inclined to transcriptional rewiring. The genes affected by promoter turnover show evidence of adaptive evolution. In mice, promoters are primarily lost through deletion of the promoter containing sequence; whereas in humans, many promoters appear to be gradually decaying with weak transcriptional output and relaxed selective constraint. Our results suggest that promoter gain and loss is an important process in the evolutionary rewiring of gene regulation and may be a significant source of phenotypic diversification.

Twitter Demographics

The data shown below were collected from the profiles of 43 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 102 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 3%
Germany 2 2%
Australia 1 <1%
France 1 <1%
United Kingdom 1 <1%
Denmark 1 <1%
China 1 <1%
Japan 1 <1%
Norway 1 <1%
Other 2 2%
Unknown 88 86%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 32 31%
Researcher 27 26%
Student > Master 14 14%
Student > Bachelor 9 9%
Student > Doctoral Student 5 5%
Other 15 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 76 75%
Biochemistry, Genetics and Molecular Biology 16 16%
Computer Science 4 4%
Medicine and Dentistry 2 2%
Pharmacology, Toxicology and Pharmaceutical Science 1 <1%
Other 3 3%

Attention Score in Context

This research output has an Altmetric Attention Score of 66. 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 05 June 2017.
All research outputs
#138,522
of 8,320,311 outputs
Outputs from Genome Research
#79
of 2,369 outputs
Outputs of similar age
#5,274
of 230,936 outputs
Outputs of similar age from Genome Research
#1
of 46 outputs
Altmetric has tracked 8,320,311 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 98th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,369 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 13.0. This one has done particularly well, scoring higher than 96% 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 230,936 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 97% of its contemporaries.
We're also able to compare this research output to 46 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 97% of its contemporaries.