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This Week in Nucleic Acids Research: Mar 6, 2013

George Church and company have cooked up a scheme for harnessing components of the bacterial "clustered interspersed short palindromic repeat" and "CRISPR-associated" system — normally used in adaptive immunity — to aid in genome engineering efforts using the budding yeast Saccharomyces cerevisiae. As they report in the online edition of Nucleic Acids Research, the researchers relied on RNA-guided endonuclease activity offered by components from the type II CRISPR-Cas system. Using a Cas9 gene together with a designer guide RNA, they found that they could target double-stranded DNA breaks in the yeast genome, ratcheting up rates of homologous recombination with donor oligos.

Negative strand genomes generated during hepatitis C virus replication appear impervious to RNA interference by short hairpin RNAs active against the original HCV genome, according to a study by a Stanford University team. After narrowing in on short hairpin RNAs with activity against conserved bits of the RNA-based HCV genome, researchers designed corresponding shRNAs aimed at the virus's "antigenome." Their results suggest such negative strand targets are not vulnerable the shRNAs — a realization that study authors study say should "provide new insights into HCV biology and have important implications for the design of more effective and safer anti-viral RNAi strategies seeking to target HCV and other viruses with similar replicative strategies."

Finally, a group from China and the US describes a methylation sequencing method it used to compare 5-hydroxymethylcytosine profiles in mouse embryonic stem cells with those in neural progenitor cells. The strategy — known as hydroxylated DNA immunoprecipitation sequencing, or hMeDIP-seq — allows for simultaneous analyses of several barcoded DNA samples that are handled in a single hMeDIP reaction, the researchers note, offering what they call a "cost-effective and user-friendly strategy for direct genome-wide comparison of DNA hydroxymethylation across multiple samples."