Chromatin techniques
Assessing histone biology with SILAC
There is great interest in understanding how histone post-translational modifications regulate biological processes. Vermeulen et al. now use a combination of SILAC (stable isotope labeling by amino acids in cell culture), high accuracy mass spectrometry, and a new statistical procedure to monitor differences in transcription factor binding to methylated or nonmethylated histone H3 peptides.
Vermeulen, M. et al. Cell 131, 58–69 (2007).
RNA interference
MicroRNAs need accessible targets
It is still not fully understood how microRNAs recognize their mRNA targets. Sequence complementarity at key positions is an important feature, and Kertesz et al. now show that accessibility of the binding site on the mRNA is equally crucial. They demonstrate that the total energy balance between unwinding an mRNA and binding the microRNA is an important feature in determining the overall silencing efficacy of the microRNA.
Kertesz, M. et al. Nat. Genet. 39, 1278–1284 (2007).
Chemical biology
Promiscuous glycosyltransferases
The synthesis of glycosylated natural products would be made easier with glycosyltransferase enzymes that accept diverse sugar substrates. Williams et al. describe a fluorescence-based assay to screen for increased glycosyltransferase catalytic efficiency and substrate promiscuity via directed evolution. They evolved a 'universal' glycosyltransferase with broad activity.
Williams, G.J. et al. Nat. Chem. Biol. 3, 657–662 (2007).
Imaging and visualization
Imaging nitrogen fixation
Using a technique called multi-isotope imaging mass spectrometry (MIMS), Lechene et al. monitored nitrogen fixation by symbiotic bacteria in the gills of marine shipworms. They followed the incorporation of 15N from nitrogen gas fixed by the bacterium Teredinibacter turnerae by bombarding shipworm gill tissue with a primary cesium ion beam to produce secondary cyanide ions, thus mapping the distribution of 15N and the normal isotope 14N. The technique may be useful in other microbial ecology studies.
Lechene, C.P. et al. Science 317, 1563–1566 (2007).
Gene regulation
Assessing genomic ultraconservation
Sequences with 100% identity between human, mouse and rat (>200 nt), so-called ultraconserved elements, are thought to represent genomic regions of great functional relevance. Ahituv et al. now show that deletion of four such elements in mouse had no discernible effects on the animals. Although alternative explanations are possible, the observation suggests that not all ultraconserved elements are indispensable in mammals.
Ahituv, N. et al. PLoS Biol. 5, e234 (2007).
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News in brief. Nat Methods 4, 883 (2007). https://doi.org/10.1038/nmeth1107-883
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DOI: https://doi.org/10.1038/nmeth1107-883