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DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

Overview of attention for article published in Nature Genetics, June 2013
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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 (98th percentile)
  • High Attention Score compared to outputs of the same age and source (83rd percentile)

Citations

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110 Dimensions

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mendeley
441 Mendeley
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9 CiteULike
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Title
DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements
Published in
Nature Genetics, June 2013
DOI 10.1038/ng.2677
Pubmed ID
Authors

Tim R Mercer, Stacey L Edwards, Michael B Clark, Shane J Neph, Hao Wang, Andrew B Stergachis, Sam John, Richard Sandstrom, Guoliang Li, Kuljeet S Sandhu, Yijun Ruan, Lars K Nielsen, John S Mattick, John A Stamatoyannopoulos

Abstract

The precise splicing of genes confers an enormous transcriptional complexity to the human genome. The majority of gene splicing occurs cotranscriptionally, permitting epigenetic modifications to affect splicing outcomes. Here we show that select exonic regions are demarcated within the three-dimensional structure of the human genome. We identify a subset of exons that exhibit DNase I hypersensitivity and are accompanied by 'phantom' signals in chromatin immunoprecipitation and sequencing (ChIP-seq) that result from cross-linking with proximal promoter- or enhancer-bound factors. The capture of structural features by ChIP-seq is confirmed by chromatin interaction analysis that resolves local intragenic loops that fold exons close to cognate promoters while excluding intervening intronic sequences. These interactions of exons with promoters and enhancers are enriched for alternative splicing events, an effect reflected in cell type-specific periexonic DNase I hypersensitivity patterns. Collectively, our results connect local genome topography, chromatin structure and cis-regulatory landscapes with the generation of human transcriptional complexity by cotranscriptional splicing.

X Demographics

X Demographics

The data shown below were collected from the profiles of 30 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 441 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 12 3%
United Kingdom 4 <1%
Spain 3 <1%
Switzerland 2 <1%
Netherlands 2 <1%
Australia 2 <1%
Denmark 2 <1%
Finland 1 <1%
Germany 1 <1%
Other 4 <1%
Unknown 408 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 138 31%
Researcher 124 28%
Student > Master 34 8%
Professor 32 7%
Professor > Associate Professor 24 5%
Other 56 13%
Unknown 33 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 256 58%
Biochemistry, Genetics and Molecular Biology 105 24%
Medicine and Dentistry 13 3%
Computer Science 12 3%
Chemistry 5 1%
Other 14 3%
Unknown 36 8%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 87. 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 April 2019.
All research outputs
#455,870
of 24,133,587 outputs
Outputs from Nature Genetics
#956
of 7,367 outputs
Outputs of similar age
#3,296
of 200,489 outputs
Outputs of similar age from Nature Genetics
#13
of 72 outputs
Altmetric has tracked 24,133,587 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 7,367 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 42.4. This one has done well, scoring higher than 87% 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 200,489 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 98% of its contemporaries.
We're also able to compare this research output to 72 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 83% of its contemporaries.