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This Week in Genome Research: Sep 21, 2011

In a paper published online in advance in Genome Research this week, the University of Washington's James Thomas and Sean Schneider report what they call "a striking correlation across vertebrate genomes between the number of LTR retroelements and the number of host tandem ZF [zinc finger] genes," which, they add, is "not explained by covariation in other genomic features." In addition, the UW duo shows that "recently active LTR retroelements are correlated with recent tandem ZF gene duplicates across vertebrates," and report on their investigation of 34 duplicate human KZNF gene pairs, the results of which the authors say "support a host-pathogen model for tandem ZF gene evolution, in which new LTR retroelement challenges drive duplication and divergence of host tandem ZF genes."

In another Genome Research advance online article, the European Bioinformatics Institute's Judith Zaugg and Nicholas Luscomb present "a qualitative model for nucleosome-positioning in Saccharomyces cerevisiae that helps explain important properties of gene expression," which, when applied to integrated public data sets, showed them that promoter-bound nucelosomes in yeast "assume one of four discrete configurations that determine the active and silent transcriptional states of a gene, but not its expression level."

Tel Aviv University's Chaim Linhar et al. this week report on a pair of cis-regulatory motifs in promoter sequences that they say are conserved among, and unique to, all members of the Caenorhabditis genus. "Our data suggest that this motif pair may function in germline development, oogenesis and early embryogenesis," the Tel Aviv team writes.

Elsewhere, the University of California, Santa Cruz's Benedict Paten et al. report in a Genome Research paper recently published online in advance on the Assemblathon 1 competition, "which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies." As a result of this competition, Paten and his colleagues say "it is possible to assemble the genome to a high level of coverage and accuracy, and that large differences exist between the assemblies, suggesting room for further improvements in current methods."

The Scan

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.

Tumor Microenvironment Immune Score Provides Immunotherapy Response, Prognostic Insights

Using multiple in situ analyses and RNA sequence data, researchers in eBioMedicine have developed a score associated with immunotherapy response or survival.

CRISPR-Based Method for Finding Cancer-Associated Exosomal MicroRNAs in Blood

A team from China presents in ACS Sensors a liposome-mediated membrane fusion strategy for detecting miRNAs carried in exosomes in the blood with a CRISPR-mediated reporter system.

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.