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This Week in Genome Research: Mar 20, 2013

In the online edition of Genome Research, the University of Oxford's Gerton Lunter leads an international team retracing the origin, evolution, and functional consequences of small insertions and deletions in the human genome. With a collection of some 1.6 million such indels that they assembled with genome sequence data for 179 individuals from three populations, the researchers explored everything from the instigators and incidence of insertions and deletions to the sites in the genome that are most prone to indel-related mutagenesis.

The microbes that make up the human microbiome seem to exhibit substantial intra-species diversity, according to a study by researchers from the US and China. The team cultured microbial microcolonies using a gel microdroplet scheme that made it possible to cultivate hundreds or thousands of identical microbial cells. In addition to showing that the gel microdroplet approach produced sequences that jibe with single-cell sequence data, the investigators used the technique to uncover genomic diversity in two human microbiome members: Streptococcus oralis, from the mouth microbiome community, and Enterococcus faecium, from the gut microbiome.

Manolis Kellis and co-authors from the Massachusetts Institute of Technology and the Broad Institute describe a massively parallel reporter assay that they used to systematically study regulatory motifs falling within thousands of predicted enhancer sequences in the human genome. Using this assay, they examined 2,104 potential enhancers in two human cell lines, along with another 3,314 engineered enhancer variants. "Our results suggest a general strategy for deciphering cis-regulatory elements by systematic large-scale experimental manipulation," they write, "and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to generate and test predictive models of gene expression."