| Title |
The accessible chromatin landscape of the human genome
|
|---|---|
| Published in |
Nature, September 2012
|
| DOI | 10.1038/nature11232 |
| Pubmed ID | |
| Authors |
Robert E. Thurman, Eric Rynes, Richard Humbert, Jeff Vierstra, Matthew T. Maurano, Eric Haugen, Nathan C. Sheffield, Andrew B. Stergachis, Hao Wang, Benjamin Vernot, Kavita Garg, Sam John, Richard Sandstrom, Daniel Bates, Lisa Boatman, Theresa K. Canfield, Morgan Diegel, Douglas Dunn, Abigail K. Ebersol, Tristan Frum, Erika Giste, Audra K. Johnson, Ericka M. Johnson, Tanya Kutyavin, Bryan Lajoie, Bum-Kyu Lee, Kristen Lee, Darin London, Dimitra Lotakis, Shane Neph, Fidencio Neri, Eric D. Nguyen, Hongzhu Qu, Alex P. Reynolds, Vaughn Roach, Alexias Safi, Minerva E. Sanchez, Amartya Sanyal, Anthony Shafer, Jeremy M. Simon, Lingyun Song, Shinny Vong, Molly Weaver, Yongqi Yan, Zhancheng Zhang, Zhuzhu Zhang, Boris Lenhard, Muneesh Tewari, Michael O. Dorschner, R. Scott Hansen, Patrick A. Navas, George Stamatoyannopoulos, Vishwanath R. Iyer, Jason D. Lieb, Shamil R. Sunyaev, Joshua M. Akey, Peter J. Sabo, Rajinder Kaul, Terrence S. Furey, Job Dekker, Gregory E. Crawford, John A. Stamatoyannopoulos |
| Abstract |
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation. |
X Demographics
The data shown below were collected from the profiles of 23 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 7 | 30% |
| Canada | 2 | 9% |
| Austria | 1 | 4% |
| Japan | 1 | 4% |
| Slovenia | 1 | 4% |
| United Kingdom | 1 | 4% |
| Sao Tome and Principe | 1 | 4% |
| Unknown | 9 | 39% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 12 | 52% |
| Members of the public | 10 | 43% |
| Practitioners (doctors, other healthcare professionals) | 1 | 4% |
Mendeley readers
The data shown below were compiled from readership statistics for 3,267 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 87 | 3% |
| United Kingdom | 34 | 1% |
| Germany | 25 | <1% |
| Spain | 17 | <1% |
| Canada | 9 | <1% |
| Brazil | 8 | <1% |
| France | 7 | <1% |
| Denmark | 7 | <1% |
| Italy | 6 | <1% |
| Other | 78 | 2% |
| Unknown | 2989 | 91% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 950 | 29% |
| Researcher | 746 | 23% |
| Student > Master | 315 | 10% |
| Student > Bachelor | 246 | 8% |
| Student > Doctoral Student | 161 | 5% |
| Other | 505 | 15% |
| Unknown | 344 | 11% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 1475 | 45% |
| Biochemistry, Genetics and Molecular Biology | 831 | 25% |
| Medicine and Dentistry | 178 | 5% |
| Computer Science | 119 | 4% |
| Neuroscience | 51 | 2% |
| Other | 210 | 6% |
| Unknown | 403 | 12% |
Attention Score in Context
This research output has an Altmetric Attention Score of 136. 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 06 February 2024.
All research outputs
#310,301
of 25,837,817 outputs
Outputs from Nature
#16,672
of 98,779 outputs
Outputs of similar age
#1,489
of 189,385 outputs
Outputs of similar age from Nature
#186
of 994 outputs
Altmetric has tracked 25,837,817 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 98,779 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 102.5. This one has done well, scoring higher than 83% 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 189,385 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 99% of its contemporaries.
We're also able to compare this research output to 994 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 81% of its contemporaries.