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This Week in Nucleic Acids Research: Oct 17, 2012

This post has been updated to clarify the type of cancer studied by the Hong Kong and Shanghai group.

In an online advance access study in Nucleic Acids Research, investigators from Hong Kong and Shanghai report on a computational method for using transcriptional data to piece together the nature of the regulatory networks that control gene expression. The team tested the strategy — which relied on a dynamic cascaded method, or DCM — first using simulations and then with data from samples of the liver cancer hepatocellular carcinoma. The latter analysis uncovered patterns that were consistent with other functional and network studies of liver cancer progression. And, study authors say, "it was shown that the modularity and network rewiring in the [hepatocellular carcinoma] networks can clearly characterize the dynamic patterns of [hepatocellular carcinoma] progression."

New England Biolabs researcher Richard Roberts and colleagues from NEB and Pacific Biosciences used PacBio's RS system to resequence six bacterial genomes in another early access Nucleic Acids Research study. The single-molecule, real-time sequencing strategy made it possible to simultaneously get genome and methylome information from these sequences, which represented Geobacter metallireducens, Chromohalobacter salexigens, Vibrio breoganii, and Bacillus cereus, along with two sub-species of Campylobacter jejuni. In the process, the group not only identified new cytosine and adenosine methylation sites in the bacterial genomes, but also the methyltransferase enzymes mediating these epigenetic marks.

Hundreds of conserved, non-coding DNA elements have been independently jettisoned in multiple mammalian lineages during evolution, according to a study by Stanford University researchers Michael Hiller, Bruce Schaar, and Gill Bejerano. By aligning and comparing sequences from 44 genomes, the trio tracked down more than 600 conserved, non-coding DNA elements that have vanished from at least two mammalian lineages, including almost three-dozen otherwise conserved elements that have been lost from the human lineage. "Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes," the Stanford team writes, adding that "experiments are necessary to test if these independently lost [conserved, non-coding DNA elements] are associated with parallel phenotype changes in mammals."

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.