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New tools for making sense of the human genome
DOI: 10.1038/nmeth888
DOI: 10.1038/nmeth890
New procedures for mapping the regions responsible for controlling gene expression across the entire human genome are described in two papers in the July issue of Nature Methods. The resulting understanding should help researchers understand the genetic problems leading to various diseases.
The challenge since the completion of the human genome sequence has been to make sense of the millions of letters that compose our genetic blueprint. In addition to genes, the genome also contains regulatory regions, which control gene expression. Locating all of these regulatory regions and comparing their activity in different situations—such as disease and healthy cells¾will be crucial to understanding how genes are controlled and how problems in this control lead to disease.
As a tool for such investigations, the groups of Francis Collins, and John Stamatoyannopoulos, have revamped a 25-year-old method to bring it up to the task of analyzing the human genome. The old method uses an enzyme called DNase to distinguish active regulatory regions from the rest of the genome. It works well, but only on small regions of DNA, and it cannot be applied to the entire genome. These two groups have now modified the technique to incorporate microarrays, allowing them to map regulatory regions in 1% of the human genome.
The portion of the human genome studied in these papers was limited to the ‘pilot’ regions chosen by the Encyclopedia of DNA Elements (ENCODE) project, an ambitious collaborative effort launched by NHGRI to map all functional elements in the genome. But as Jason Lieb points out in the accompanying News and Views, “Although these studies focus on only 1% of the human genome, it is reasonable to expect that genome-wide detection will soon become routine.”
Author contact:
Francis Collins (National Human Genome Research Institute, NIH, Bethesda, MD, USA)
Tel: +1 301 496 0844; Email: [email protected]
John Stamatoyannopoulos (University of Washington, Seattle, WA, USA)
Tel: +1 206 267 1098; Email: [email protected]
Jason Lieb (University of North Carolina, Chapel Hill, NC, USA) News and Views author
Tel: +1 919 843 3228; Email: [email protected]
Other papers to be published in the July issue of Nature Methods:
Monitoring dynamic protein interactions with photoquenching FRET
DOI: 10.1038/NMETH889
Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins
DOI: 10.1038/NMETH892
Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software
DOI: 10.1038/NMETH891
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