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This Week in Genome Research: Nov 16, 2011

Researchers at the University of North Carolina, Chapel Hill, report in a paper published online in advance in Genome Research that the "tumor-specific retargeting of an oncogenic transcription factor chimera results in dysregulation of chromatin and transcription." More specifically, the team reports its generation of an experimental system in which they addressed "questions regarding the genomic mechanisms by which chimeric transcription factors cause cancer" using EWS-FLI and its parental transcription factor, FLI1. The Chapel Hill team shows that, "through chimerism, EWS-FLI acquired the ability to alter chromatin."

Tel Aviv University's Chaim Linhart and his colleagues report on a pair of cis-regulatory motifs in promoter sequences in C. elegans that "exhibits extraordinary genomic traits," they write. "The motif pair constitutes a nearly combinatorial sequence configuration," Linhart et al. say, adding that this pair "may function in germline development, oogenesis, and early embryogenesis."

In another paper published online in advance in Genome Research this week, the European Bioinformatics Institute's Judith Zaugg and Nicholas Luscombe present a model for nucleosome positioning in S. cerevisiae, which the authors say "helps explain important properties of gene expression." Using publicly available data, the team unearthed evidence to suggest "DNA-binding transcription factors, together with chromatin-remodeling enzymes, are primarily responsible for the nucleosome architecture" in the yeast. "Our model for promoter nucleosome architecture reconciles genome-scale findings with molecular studies; in doing so, we establish principles for nucleosome positioning and gene expression that apply not only to individual genes, but across the entire genome," Zaugg and Luscombe write.

The Scan

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.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.