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This Week in Genome Biology: Nov 5, 2009

In Genome Biology this week, scientists at the Shanghai Institutes for Biological Sciences have studied how after gene duplication, splicing enhancers and silencers can affect the generation of new splicing isoforms and therefore, new gene functions. Using a computational approach, they found that these enhancers and silencers diverge especially fast shortly after gene duplication and that this divergence "results in exon splicing state transitions, and that the proportion of paralogous exon pairs with different splicing states also increases over time, consistent with previous predictions."

In other work, researchers at the RIKEN Yokohama Institute show that knocking down a swath of transcription factors in differentiating human THP-1 cells proves that they're interdependent. Using a matrix RNAi system to knock down the 78 transcription factor genes in monocytic THP-1 cells and then using qPCR to monitor gene expression changes, they identified 876 cases "where knockdown of one transcription factor significantly affected the expression of another." Using expression profiling data from the FANTOM4 study, they could classify these genes into three groups: pro-differentiative (229), anti-differentiative (76), or neither (571).

Case Western Reserve University's Thomas LaFramboise is senior author on work that reports a "highly sensitive and configurable method" for finding rare CNVs in SNP array data. In the paper, they applied their method to hundreds of samples and were able to not only detect known CNVs, but also previously unreported ones.

In collaborative work between scientists at the University of California, San Diego, and Virginia Commonwealth University, scientists led by first author Tom Conrad found that when growing E. coli is subjected to lactate minimal media, the bacteria shows a range of genetic adaptations. Whole genome resequencing of 11 adapted strains found that in 7 of these there was an 82 base-pair deletion in the rph-pyrE operon. This mutation, they write in the abstract, "conferred ~15% increase to the growth rate when experimentally introduced to the wild-type background and resulted in a ~30% increase to growth rate when introduced to a background already harbouring two adaptive mutations."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.