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Caught in the act! Fast, cheap, high-resolution, easy way to tell which genes a cell is using

caught catA new technique promises to provide huge amounts of information about which genes in a cell are hard at work and which are sleeping.  This, in turn,could pay off in dozens of different ways.

From my news release on the advance, which was just published in Nature Methods:

Genes are recipes for the production of proteins, which do almost all the work in every living cell. The biological field of genomics focuses on describing which genes an organism has. The newer field of epigenomics aims to discern which genes are actually used by various tissues within an organism — or, in the case of disease, misused... Virtually every cell in a person’s body contains essentially the same genes. Yet cells from different tissues — liver, skin, muscle, blood — do very different things because they use different genes, as do otherwise identical cells in different biochemical environments, developmental stages or states of health.

Geneticists Howard Chang, MD, PhD, and Will Greenleaf, PhD, of Stanford have teamed up to produce a method of mapping the epigenome - the on/off status of each of the 22,000-odd genes in virtually every human cell - in as little as 10 hours, using off-the-shelf instrumentation and easily available reagents, and requiring only the amount of cells that can be obtained in a single blood draw or needle biopsy.

That's a major leap. Current epigenome-mapping methods are costly, time-consuming and difficult - and understandably so. The real estate occupied by the roughly 22,000 protein-coding genes in a human cell's genome is dwarfed by the vast stretches of regulatory DNA regions that control the timing of, and degree to which, these genes are "switched on" (engaged in the production of proteins) or "shut down" (prevented in one way or another from being actively put to use use in protein generation.)

All the DNA in a human cell - which if stretched out would be about six feet long - is scrunched into the cell's nucleus, which measures about 1/50,000 inch in diameter, Greenleaf told me. This is like bunching up a telephone line that stretches from New York City to Los Angeles and stuffing it into a two-bedroom house, he said.

Chang told me that as advance word of their new study's publication has leaked out, dozens of labs around the world are already putting the new method to work in research applications. The technique's speed, low cost, tiny sample-size requirement and ease of use also radically reduce the barriers to widespread and even clinical use. Remember: Which genes a tissue is using, and to what extent, tells a ton about that tissue's health status.

Previously: Night of the living dead gene: Pseudogene wakes up, puts chill on inflammation, Red light, green light: Simultaneous stop and go signals on stem cells' genes may enable fast activation, provide aging clock and New job description for RNA, oldest professional molecule
Photo by Mel B.

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