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This Week in Genome Biology: Aug 12, 2009

In Genome Biology this week, research led by Katharine Webb at the Institute of Developmental Genetics in Neuherberg, Germany, showed that there are specific transcriptional networks that influence addiction. Using a model of a mutant zebrafish that doesn't respond to amphetamines, they combined microarray analysis with qPCR and in situ hybridization to identify and validate specific brain areas that responded to amphetamine in wild-type siblings. The genes affected that they found to be enriched were transcription factors involved in brain development, and the areas of the brain that responded to the drug included domains of ongoing adult neurogenesis. A minireview from Jean Lud Cadet delves further into how "addictive drugs hijack the human brain's 'reward' systems."

In other work, Tim Strom was senior author on a paper looking at SNPs in a second sequenced breed of bovine, the Fleckvieh bull. 24 gigabases of sequence reads at an average 7.4 fold depth revealed 2.44 million SNPs, a good majority of which were unknown, and 115,000 small indels. "This work provides the first single cattle genome by next-generation sequencing," they say, adding that the research will be a "valuable resource for the construction of high density oligonucleotide arrays in the context of genome-wide association studies."

In a minireview, Jeffrey Wilusz examines the literature of herpesvirus biology and cellular mRNA decay/surveillance mechanisms. "Increasing evidence suggests that viruses have evolved ways of interfacing with the cellular RNA decay machinery that aid their survival and replication," he writes, including degrading host mRNA to give the virus a competitive advantage when it comes to propagating itself. Wilusz, who is at Colorado State University, explains recent findings that show that during herpesvirus infection associated with Kaposi's sarcoma – the most common tumor in people with AIDS – mRNA degradation is linked to "hyperadenylation of transcripts and a relocalization of cytoplasmic poly(A)-binding proteins to the nucleus."

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.