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This Week in Genome Research: Jul 22, 2015

Long noncoding RNAs play a key role in regulating gene expression in embryonic stem cells, researchers from Cold Spring Harbor Laboratory and Isis Pharmaceuticals report in Genome Research. The researchers turned to high-depth poly(A)+ RNA sequencing of mouse embryonic stem and neural progenitor cells to uncover differentially regulated lncRNA. They found that lncRNAs tend to be enriched in the nucleus, and noted that two such nuclear lncRNAs — Platr14 and Firre — are involved in the ESC gene expression program.

A team of German researchers presents an algorithm it designed, dubbed Q, for ChIP-seq peak calling. This method, which is based on saturation analysis of positions within candidate peaks, estimates fragment length from the data, and, the researchers say, out-performs other approaches based on irreproducible discovery rate analysis, motif identification, resolution, and running time.  The researchers also say Q better resolves individual peaks like double RNAPII and H3K4me3 peaks surrounding transcription start sites and note it is freely available under an open-source license.

Finally, researchers in the UK report on the population structure of the equine infectious disease strangles, which is caused by Streptococcus equi. As they write in Genome Research, the researchers performed whole-genome sequencing on S. equi strains collected from around the world, finding low levels of variation as well as evidence of a global population replacement in the 19th or early 20th century. Strangles, the researchers note, is marked by an acute infection phase that's followed by long-term carriage of the pathogen. Isolates from post-acute phase infections were enriched for mutations that streamlined their metabolism and made the bugs less virulent. The researchers also uncovered loci that may be needed for full S. equi virulence that could be exploited to develop a vaccine.