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This Week in Genome Biology: May 21, 2014

University of California, Los Angeles, cell and developmental biology researcher Matteo Pellegrini and colleagues used bisulfite sequencing to track cross-generation DNA methylation marks in two parental mouse strains and their hybrid offspring. Based on DNA methylation patterns in liver samples from eight of the parental or hybrid mice, the team determined that at least a subset of between-strain methylation differences in mice are heritable. It also saw hundreds of sites with sex-specific methylation, including some at loci with distinct expression patterns in male and female mice. In addition, the analysis highlighted genes and microRNAs that appear prone to imprinting — the process by which one allele is preferentially expressed over the other.

A Washington University in St. Louis-led team considered the clusters of bacteria present within human microbial communities at various body sites using a community class classification scheme. With 16S ribosomal RNA gene sequence data and metagenomic sequences generated with samples from more than 200 individuals tested for the Human Microbiome Project, the researchers identified clusters of human-associated microbes that tend to appear together at different sites in the body and looked at how stable these grouping are over time. These included three enterotypes already described in stool samples, along with community classes present at 17 other locales in the human body.

Chromatin collections dappled along the genome in leukemia cells can provide clues for more accurately classifying the disease, according to a study by researchers at McGill University. With the help of an approach called chromosome conformation capture carbon copy, or 5C, the investigators profiled chromatin patterns in and around HOXA genes in multiple leukemia cell lines and modeled their findings using a machine classifier known as 3D-SP. The resulting chromatin patterns made it possible to distinguish between different leukemia sub-types, the study's authors say, including forms of the disease with or without gene fusions involving the histone methyltransferase gene MLL.