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DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements

Overview of attention for article published in Epigenetics & Chromatin, January 2015
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Among the highest-scoring outputs from this source (#21 of 180)
  • High Attention Score compared to outputs of the same age (88th percentile)
  • Above-average Attention Score compared to outputs of the same age and source (55th percentile)

Mentioned by

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1 news outlet
twitter
8 tweeters

Citations

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36 Dimensions

Readers on

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55 Mendeley
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Title
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements
Published in
Epigenetics & Chromatin, January 2015
DOI 10.1186/1756-8935-8-8
Pubmed ID
Authors

Matthew S Wilken, Joseph A Brzezinski, Anna La Torre, Kyle Siebenthall, Robert Thurman, Peter Sabo, Richard S Sandstrom, Jeff Vierstra, Theresa K Canfield, R Hansen, Michael A Bender, John Stamatoyannopoulos, Thomas A Reh

Abstract

The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied this approach to the mouse CNS, including developing and mature neural retina, whole brain, and two well-characterized brain regions, the cerebellum and the cerebral cortex. For the various regions and developmental stages of the CNS that we analyzed, there were approximately the same number of DHSs; however, there were many DHSs unique to each CNS region and developmental stage. Many of the DHSs are likely to mark enhancers that are specific to the specific CNS region and developmental stage. We validated the DNase I mapping approach for identification of CNS enhancers using the existing VISTA Browser database and with in vivo and in vitro electroporation of the retina. Analysis of transcription factor consensus sites within the DHSs shows distinct region-specific profiles of transcriptional regulators particular to each region. Clustering developmentally dynamic DHSs in the retina revealed enrichment of developmental stage-specific transcriptional regulators. Additionally, we found reporter gene activity in the retina driven from several previously uncharacterized regulatory elements surrounding the neurodevelopmental gene Otx2. Identification of DHSs shared between mouse and human showed region-specific differences in the evolution of cis-regulatory elements. Overall, our results demonstrate the potential of genome-wide DNase I mapping to cis-regulatory questions regarding the regional diversity within the CNS. These data represent an extensive catalogue of potential cis-regulatory elements within the CNS that display region and temporal specificity, as well as a set of DHSs common to CNS tissues. Further examination of evolutionary conservation of DHSs between CNS regions and different species may reveal important cis-regulatory elements in the evolution of the mammalian CNS.

Twitter Demographics

The data shown below were collected from the profiles of 8 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 55 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 2%
United States 1 2%
France 1 2%
Unknown 52 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 19 35%
Researcher 10 18%
Student > Master 6 11%
Student > Bachelor 5 9%
Professor 4 7%
Other 6 11%
Unknown 5 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 26 47%
Biochemistry, Genetics and Molecular Biology 11 20%
Neuroscience 6 11%
Unspecified 2 4%
Physics and Astronomy 1 2%
Other 3 5%
Unknown 6 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. 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 03 June 2015.
All research outputs
#373,011
of 5,181,074 outputs
Outputs from Epigenetics & Chromatin
#21
of 180 outputs
Outputs of similar age
#18,078
of 152,505 outputs
Outputs of similar age from Epigenetics & Chromatin
#4
of 9 outputs
Altmetric has tracked 5,181,074 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 180 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.1. This one has done well, scoring higher than 88% 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 152,505 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 88% of its contemporaries.
We're also able to compare this research output to 9 others from the same source and published within six weeks on either side of this one. This one has scored higher than 5 of them.