Genomics

Complete genomes

Despite advances in high-throughput sequencing, the number of completely sequenced human genomes is still small. A new technique and business model by the company Complete Genomics promises to change that. Their technology involves the assembly of fragmented DNA into nanoballs that are arrayed and sequenced using combinatorial probe-anchor ligation chemistry. The low cost of consumables and efficient parallelization allow Complete Genomics to project that their company will sequence hundreds of individuals in the near future.

Drmanac, R. et al. Science advance online publication 5 November 2009.

Proteomics

The human protein-DNA interactome

Although the DNA targets of key transcription factors have been intensively studied, the targets of the broader set of DNA-binding proteins are largely unknown. Hu et al. used a bioinformatics approach to predict human proteins likely to interact with a set of 460 diverse DNA motifs. They then used a protein microarray containing the 4,191 known and predicted DNA binding proteins to characterize the human protein-DNA 'interactome'; they identified a large number of known and previously unknown protein-DNA interactions.

Hu, S. et al. Cell 139, 610–622 (2009).

Bioinformatics

Correcting gene function annotations

Homology-based methods to annotate gene function are subject to misannotations that can propagate through databases; thus, they are very important to correct. Hsiao et al. describe an algorithm for policing gene annotations. The algorithm looks for genes with poor genomic correlations with their network neighbors, which are likely to represent errors. Hsiao et al. applied their approach to identify misannotations in Bacillus subtilis.

Hsiao, T.-L. et al. Nat. Chem. Biol. 6, 34–40 (2010).

Stem cells

The fate of stem cells

There is high interest in understanding what happens, on a systems level, to stem cells upon perturbation. Lu et al. follow changes in histone acetylation, chromatin-bound RNA polymerase II, mRNA and nuclear protein levels in mouse embryonic stem cells after downregulation of the pluripotency factor Nanog. They find that this single perturbation has widespread repercussions across the epigenetic, transcriptional and translational systems.

Lu, R. et al. Nature 462, 358–362 (2009).

Genomics

Dancing in the rain

When looking for variation in the human genome, researchers are often interested in just a specific subsection. But how best to enrich for such a region? Scientists from the company RainDance Technologies present a microdroplet-based technology in which each target region is amplified in a singleplex reaction within the confines of a microdroplet. This allows efficient amplification of target regions with uniform coverage, high accuracy and reproducibility.

Tewhey, R. et al. Nat. Biotechnol. 27, 1025–1031 (2009).