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Short DNA sequence patterns accurately identify broadly active human enhancers

Overview of attention for article published in BMC Genomics, July 2017
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Title
Short DNA sequence patterns accurately identify broadly active human enhancers
Published in
BMC Genomics, July 2017
DOI 10.1186/s12864-017-3934-9
Pubmed ID
Authors

Laura L. Colbran, Ling Chen, John A. Capra

Abstract

Enhancers are DNA regulatory elements that influence gene expression. There is substantial diversity in enhancers' activity patterns: some enhancers drive expression in a single cellular context, while others are active across many. Sequence characteristics, such as transcription factor (TF) binding motifs, influence the activity patterns of regulatory sequences; however, the regulatory logic through which specific sequences drive enhancer activity patterns is poorly understood. Recent analysis of Drosophila enhancers suggested that short dinucleotide repeat motifs (DRMs) are general enhancer sequence features that drive broad regulatory activity. However, it is not known whether the regulatory role of DRMs is conserved across species. We performed a comprehensive analysis of the relationship between short DNA sequence patterns, including DRMs, and human enhancer activity in 38,538 enhancers across 411 different contexts. In a machine-learning framework, the occurrence patterns of short sequence motifs accurately predicted broadly active human enhancers. However, DRMs alone were weakly predictive of broad enhancer activity in humans and showed different enrichment patterns than in Drosophila. In general, GC-rich sequence motifs were significantly associated with broad enhancer activity, and consistent with this enrichment, broadly active human TFs recognize GC-rich motifs. Our results reveal the importance of specific sequence motifs in broadly active human enhancers, demonstrate the lack of evolutionary conservation of the role of DRMs, and provide a computational framework for investigating the logic of enhancer sequences.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 30 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Italy 1 3%
Canada 1 3%
Unknown 28 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 30%
Researcher 5 17%
Student > Bachelor 4 13%
Professor 3 10%
Student > Doctoral Student 2 7%
Other 5 17%
Unknown 2 7%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 14 47%
Agricultural and Biological Sciences 10 33%
Computer Science 2 7%
Physics and Astronomy 1 3%
Neuroscience 1 3%
Other 0 0%
Unknown 2 7%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 22 August 2017.
All research outputs
#7,249,544
of 11,642,880 outputs
Outputs from BMC Genomics
#4,464
of 6,953 outputs
Outputs of similar age
#151,777
of 265,073 outputs
Outputs of similar age from BMC Genomics
#74
of 93 outputs
Altmetric has tracked 11,642,880 research outputs across all sources so far. This one is in the 23rd percentile – i.e., 23% of other outputs scored the same or lower than it.
So far Altmetric has tracked 6,953 research outputs from this source. They receive a mean Attention Score of 4.2. This one is in the 27th percentile – i.e., 27% of its peers scored the same or lower than it.
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 265,073 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 33rd percentile – i.e., 33% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 93 others from the same source and published within six weeks on either side of this one. This one is in the 16th percentile – i.e., 16% of its contemporaries scored the same or lower than it.