Editors' Choice

Science  20 Apr 2012:
Vol. 336, Issue 6079, pp. 277
  1. Genetics

    Exons Encode Enhancers

    1. Beverly A. Purnell

    Transcription factor binding to enhancer elements is critical for proper gene regulation. Enhancers are often found in noncoding sequences in close proximity to the gene that they regulate and sometimes even on another chromosome; however, whether they are also found in exons, the coding regions of DNA, is unclear. Birnbaum et al. analyzed 25 mouse and human enhancer-associated ChIP-seq data sets in order to identify enhancer peaks that overlap exons and found regulatory transcription factor binding to exonic regions. In fact, in mice, roughly 7% of enhancer peaks overlapped coding exons. Mutation of these elements in zebrafish and mouse enhancer assays showed that although exonic sequences are necessary, they are not sufficient for full enhancer function. Absence of an exon-encoded enhancer, however, did have functional consequences. Thus, exonic sequences may function in the regulation of nearby genes. Moreover, phenotypes seen in genetic knockout animals may be the result of not only the lack of expression of the deleted gene but also alterations in the expression of genes that are regulated by enhancers in the deleted exons.

    Genome Res. 22, 10.1101/gr.133546.111 (2012).

  2. Climate Science

    The Sun's Push

    1. H. Jesse Smith

    Unraveling the influence of the Sun on Earth's climate depends on having accurate chronologies of the variability of both climate and solar activity. Cosmic rays produced by stellar explosions interact with elements in the atmosphere and on the land to make the radionuclides 14C and 10Be, both of which can be measured in order to construct a record of their fluxes at Earth's surface. That record, in turn, can be reinterpreted as a chronicle of solar activity, because the magnetic field of the Sun helps to control the intensity of cosmic rays that penetrate to Earth's surface. Steinhilber et al. present a high-resolution 10Be data set derived from an Antarctic ice core and combine it with existing 10Be and 14C records, as well as data from a Chinese stalagmite, to provide a 9400-year-long history of solar activity, in order to determine the solar imprint on the Asian monsoon during that interval. Whereas solar forcing generally drives the monsoon, periods during which the two show little coherence indicate that other factors, such as volcanoes and greenhouse gases, also are important.

    CREDIT: ISTOCKPHOTO.COM

    Proc. Natl. Acad. Sci. U.S.A. 109, 10.1073/pnas.1118965109 (2012).

  3. Chemistry

    A Clean Sense

    1. Marc S. Lavine

    A primary goal in designing better sensors is to find ways to enhance sensitivity without sacrificing selectivity. Nanoscale materials such as carbon nanotubes should offer an easy route to better sensitivity because of their exceptionally high surface area–to–volume ratio and because their electronic properties are strongly affected by changes in their local environment. Thus, it should be possible to measure exposure to gases that bind to the nanotube surface through changes in electrical conductivity. However, the nanotube surface can easily be altered by low levels of contaminants or by incomplete recovery after an initial sensing cycle, thus changing the electronic properties in an undesired way. Chen et al. show that continuous illumination of single-walled carbon nanotubes by ultraviolet (UV) light leads to a cleaning of the nanotube surface. Detection of dry gases such as NO in an air stream was enhanced, but active sensor material degraded because of the formation of ozone. Detection of NO2 and NH3 in a nitrogen stream reached limits of a few parts per trillion (ppt), and for NO a sub-ppt amount was observed—an improvement of two to three orders of magnitude over other nanoscale devices. The UV light is also responsible for removing the detected gases from the nanotube surface, which enhances the rate at which the sensors can be cycled, but at the risk of increasing the detection limits.

    Sci. Rep. 2, 10.1038/srep00343 (2012).

  4. Plant Sciences

    Toxic Lichens

    1. Caroline Ash
    CREDIT: JOUKO RIKKINEN

    Fungi and green algae can form symbioses called lichens—several involve cyanobacteria as the photosynthetic accessory. Nostoc, a filamentous cyanobacterium, is a common partner forming what are known as cyanolichens. Unfortunately, Nostoc, in common with fresh water bloom–forming cyanobacteria, can produce cyclic peptide toxins such as microcystins and nodularins, which target mammalian phosphatases and may be carcinogens. Kaasalainen et al. have discovered that many cyanolichens contain these toxins too, and have detected over 50 chemical variants of microcystins. The signature gene is mcyE, whose product is required for the synthesis of a variant amino acid; the bond between this amino acid and D-glutamate is essential for microcystin toxicity. But mcyE does not seem to be affected by the horizontal gene transfer that is rife among the cyanobacteria, and this amino acid is a constant in the otherwise variable peptide sequence of the toxin. So lichens with identical mcyE can have very different microcystin compositions. Being trapped in a relationship with a fungus tends to lead to local population bottlenecks, which may have been instrumental in the evolution of this surprising diversity of toxins.

    Proc. Natl. Acad. Sci. U.S.A. 109, 10.1073/pnas.1200279109 (2012).