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This Week in Nucleic Acids Research: Dec 24, 2014

University of Texas at Dallas researchers present a scheme in Nucleic Acids Research for limiting how long an introduced gene product remains in a cell. Their approach builds on the CRISPR-Cas9 system, but adds a self-cleaving mechanism that destroys the message. "As the messenger RNAs are transcribed and then translated the protein Cas9 in complex with the gRNA returns to the plasmid and creates DSB, effectively disrupting its function and destroying the delivery mechanism," the researchers write. They note that their approach could be used for "trace-free delivery for potential applications in protection of genetic material intellectual property."

A duo from the National Center for Biotechnology Information describes their model for identifying causal non-coding SNPs from ChIP-seq data. They used the changes to ChIP-seq intensity that take place in response to allelic changes as a way to gauge the possible roles of the non-coding SNPs. By applying their approach to HepG2 enhancers, the researchers found nearly 5,000 enhancer SNPs that could affect enhancer function after such allelic changes. These enhancer SNPs, they added, were overexpressed at the binding sites of certain liver transcription factors.

Another set of National Center for Biotechnology Information researchers provide an update on the RefSeq prokaryotic genome dataset in Nucleic Acids Research. In the past year, they note that some 10,000 microbial genome assemblies have been publicly released, and the RefSeq prokaryotic genome dataset now contains more than 28,000 genomes representing more than 5,000 species. They also write that they've made improvements to analysis and visualization tools as well as to the data processing pipeline.