Expressible molecular colonies

Carrying out polymerase chain reaction in a gel layer generates a 2-D pattern of DNA colonies comprising pure genetic clones. Here we demonstrate that transcription, translation and protein folding can be performed in the same gel. The resulting nucleoprotein colonies mimic living cells by serving as compartments in which the synthesized RNAs and proteins co-localize with their templates. Yet, due to the absence of penetration barriers, such a molecular colony display allows cloned genes to be directly tested for the encoded functions. Now, the results imply that virtually any manipulations with genes and their expression products can be accomplished in vitro

Gateways to the FANTOM5 promoter level mammalian expression atlas

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users

Spontaneous rearrangements in RNA sequences

AbstractThe ability of RNAs to spontaneously rearrange their sequences under physiological conditions is demonstrated using the molecular colony technique, which allows single RNA molecules to be detected provided that they are amplifiable by the replicase of bacteriophage Qβ. The rearrangements are Mg2+-dependent, sequence-non-specific, and occur both in trans and in cis at a rate of 10−9 h−1 per site. The results suggest that the mechanism of spontaneous RNA rearrangements differs from the transesterification reactions earlier observed in the presence of Qβ replicase, and have a number of biologically important implications