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This Week in Genome Research: Sep 5, 2013

Recombination has a more pronounced effect on common variation in the human genome than on rare forms of variation, according to a study by researchers in the US and Switzerland. In its effort to assess spontaneous mutations in relation to genomic context, a University of Michigan-lead team focused on very rare variants found in population sequence data representing 202 genes from more than 14,000 individuals. Results from the analysis suggest rare variants in the human lineage have arisen more recently than common variants, more often coinciding with sequence features such as local guanine and cytosine nucleotide content than with recombination rates or recombination hotspot status.

A German research group used chromatin immunoprecipitation and sequencing to look at how hand and foot malformation-associated mutations in HOXD13 affect the transcription factor's binding patterns across the genome in chicken mesenchymal stem cells. Results of the researchers' analysis indicate that the limb malformation-linked missense mutation slightly alters the binding motif recognized by HOXD13 — a shift that they verified through follow-up gene expression profiling and functional assays.

An international team led by investigators at the University of Michigan and Princeton University looked at cell lineage-specific gene expression, with the help of a machine learning-based computational method that considers expression profiles as well as functional genomic information in tissue samples. To demonstrate the feasibility of this approach, investigators employed it in an analysis of cell types affected by chronic kidney disease, demonstrating that transcripts expressed in a cell lineage-specific manner are especially apt to contribute to that condition.