Genomics

Genome-wide map of the sixth base

Although 5-hyrdoxymethyl-cytosine (5hmC) is thought to be important for genome function in certain cells, a lack of tools has made profiling difficult. Xu et al. used a 5hmC-specific antibody for methylated DNA immunoprecipitation (MeDIP) and found distinct genome-wide 5hmC patterns in the mouse. The researchers saw 5hmC enrichment in gene bodies rather than at promoters and in intergenic regions. They also uncovered a role for the ten-eleven translocation (Tet) family of 5mC hydroxylases.

Xu, Y. et al. Mol. Cell. advance online publication (20 April 2011).

Stem cells

An eye in the Petri dish

Eiraku et al. report the formation of a primitive eye structure starting from a three-dimensional culture of mouse embryonic stem cells. The group grew embryonic stem cell aggregates on Matrigel and added factors that promote their differentiation toward retinal lineages. Under these conditions the cellular aggregates spontaneously formed hemispheral epithelial vesicles and progressively formed a structure reminiscent of the embryonic optic cup seen in vivo.

Eiraku, M. et al. Nature 472, 51–56 (2011).

Molecular engineering

Evolving RNA polymerase ribozymes

Wochner et al. describe the evolution of an RNA polymerase ribozyme capable of synthesizing up to 95-nucleotide RNA strands, much longer than the capabilities of natural ribozymes. They used water-in-oil emulsion technology with microbead display, linking ribozyme genes to multiple copies of the corresponding ribozyme; this allowed them to select ribozymes based on primer-extension capability.

Wochner, A. et al. Science 332, 209–212 (2011).

Imaging

High-throughput subcellular imaging of worms

High-resolution in vivo time-lapse assays in whole Caenorhabditis elegans worms require immobilizing the worms before imaging. Rohde et al. developed a system that allows doing this in a high-throughput manner using multiwell plates. They built an array of individually addressable cooling elements that fit into multiwell plates, and sequentially cooled down and imaged each worm using inverted epi-fluorescence microscopy. They used this technology to perform laser microsurgery of single neurons in vivo.

Rohde, C.B. et al. Nat. Commun. 2, 271 (2011).

Molecular biology

A cellular system for epitope-tagged PrP

Goold et al. introduce an epitope tag into the cellular prion protein, PrPC, expressed in a neuroblastoma cell line in which endogenous PrP has been knocked down by RNA interference; the tagged PrPC supports prion replication and allows for the generation of infectious misfolded PrPSc. This approach allowed Goold et al. to distinguish newly formed PrPSc from inoculum-derived PrPSc; they observed very rapid infection of cells and found that prion conversion occurs primarily at the plasma membrane.

Goold, R. et al. Nat. Commun. 2, 281 (2011).