In Nature this week, the International Brachypodium Initiative describes the genome sequence of Brachypodium distachyon, a wild grass. The team used whole-genome shotgun sequencing and deep Illumina sequencing to analyze small RNA populations and found that, much like in Arabidopsis, the small RNA reads were most dense in regions of high repeat density. The consortium also suggests that their genome sequence, along with the grass’ rapid life cycle and ease of cultivation, will help Brachypodium to become a model system for the development of novel energy sources and food crops.
A team of German researchers describes human host factors critical for influenza A virus replication in Nature this week. By performing a genome-wide RNA interference screen, the team deciphered 287 human host cell genes that influence the virus’ replication. Then, by performing an independent assay, the team confirmed 168 hits ― or 59 percent ― that inhibit either the endemic H1N1 or the pandemic swine-origin influenza A viral strains. They found that a subset of the common hits was also essential for H5N1 (avian flu) replication. The researchers also describe their discovery that a small molecule inhibitor of CDC-like kinase 1 abates flu virus replication by more than two orders of magnitude ― a finding they demonstrated with virus-infected cyclin-dependent kinase inhibitor 1B (Cdkn1b) mice.
In another Nature research article, an international consortium describes the first ancient human genome sequence. The team obtained DNA from approximately 4,000-year-old permafrost-preserved hair from a male individual of the first known culture to have settled in Greenland. The researchers report that they were able to recover and sequence 79 percent of the diploid genome, and identified 352,151 single nucleotide polymorphisms ― of which 6.8 percent had not been previously reported. In a functional assessment of the SNPs, the team assigned possible phenotypic characteristics to the individual. By comparing the SNPs with those of contemporary populations, the team suggests they’ve elucidated evidence of a Palaeo-Eskimo migration from Siberia into the New World 5,500 years ago. "We can show that this individual was neither a direct relative of Inuits or Native Americans," says senior author Eske Willerslev at Scientific American, where his colleague Morten Rasmussen adds, "their closest living relatives are [a population] in Siberia now."
In Nature’s advance online publication this week, Christian Popp at the Babraham Institute in Cambridge, UK, and colleagues write that the genome-wide erasure of DNA methylation in the mouse germ cell line is affected by cytidine deaminase AID deficiency. Popp and his colleagues deduce that AID plays a critical role in epigenetic reprogramming, and potentially functions in restricting the inheritance of epimutations in mammals. The team profiled genome-wide methylations by using unbiased bisulphate next-generation sequencing in wild-type and AID-deficient mouse primordial germ cells. They found that AID-deficient PGCs were up to three times more methlated than the wild-type PGCs throughout the genome.