Genome evolution

Genomic signatures of germline gene expression McVicker, G. & Green, P. Genome Res. 4 Aug 2010 (doi:10.1101/gr.106666.110)

Features that influence genome evolution, such as nucleotide substitutions, crossovers and transposon insertions, are observed at different frequencies in transcribed and non-transcribed regions of the human genome. McVicker and Green examined correlations between these features and gene expression in human germline and somatic tissues to discern whether these differences are the result of selection or an influence of germline transcription on their rate of occurrence. Their data suggest that germline transcription is important and should be studied further to understand the uneven distribution of genomic changes.

Disease models

Production of p53 gene knockout rats by homologous recombination in embryonic stem cells Tong, C. et al. Nature 12 Aug 2010 (doi:10.1038/nature09368)

The generation of gene knockouts through homologous recombination in embryonic stem (ES) cells has been invaluable, but until recently germline-competent rat ES cell lines could not be established. These authors previously developed germline-competent rat ES cell lines, and they have now generated knockout rats for the Tp53 tumour suppressor gene using gene targeting through homologous recombination in these cells. The creation of further models using this approach will be important for studying human disease.

Functional genomics

Massive turnover of functional sequence in human and other mammalian genomes Meader, S. J., Ponting, C. P. & Lunter, G. Genome Res. 6 Aug 2010 (doi:10.1101/gr.108795.110)

How much of a genome is under functional constraint? The authors addressed this question by comparing the number of indels shared between closely related pairs of animals. This analysis revealed a high rate of functional sequence turnover and showed that up to 10% of the human genome (most of it non-coding) is under functional constraint. This fraction is lower in invertebrates, suggesting that organismal complexity correlates with the proportion of sequence that is constrained and not with the size of the protein-coding genome.

Transcription

Active RNA polymerases: mobile or immobile molecular machines? Papantonis, A. et al. PLoS Biol. 8, e1000419

This work shows that RNA polymerases do not track along their DNA template, as is traditionally believed, but rather reel in their DNA template while remaining immobile within a transcription factory. This conclusion was reached by carrying out chromosome conformation capture and RNA fluorescence in situ hybridization (FISH) on two human genes that are activated simultaneously by tumour necrosis factor-α: different parts of the two nascent transcripts come into proximity depending on the timing of their transcription, despite being produced at physically distant loci.