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This Week in Cell: Jan 30, 2013

Researchers with Harvard University's FAS Center for Systems Biology report on changes to the human gut microbiome associated with the use of xenobiotics. The team followed human gut microbiomes in three individuals taking xenobiotic compounds over nine months, using a combination of 16S ribosomal RNA sequencing, microbial community gene expression experiments, and flow cytometry to test the individuals' fecal samples. The analyses revealed shifts in the gut microbiome composition, physiological features, and gene expression profiles, even after fairly brief xenobiotic exposures, with drug-exposed gut bugs showing elevated expression of resistance, stress response, and drug metabolism-related genes. "These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics," researchers write, "and suggest that attempts at personalized medicine should consider inter-individual variations in the active human gut microbiome."

Our sister publication GenomeWeb Daily News has more on this study here.

In another Cell study, the National Cancer Institute's André Nussenzweig and colleagues from the US and Spain describe sites in the genome that are particularly prone to DNA damage in replicating B cells. The group identified these recurrent sites — dubbed "early replication fragile sites," or ERFSs — through a series of ChIP-seq, Repli-seq, RNA-seq, and other experiments in mouse B cells. Their subsequent experiments suggest that the ERFSs overlap with sites with pronounced gene expression or elevated repetitive element contents. But they also seem to coincide with many places in the human genome where recurrent amplifications or deletions have been documented in diffuse large B-cell lymphoma, prompting speculation that the sites are a key player in lymphomagenesis-related rearrangements in mammalian cells.

An American-led team takes a look at chromatin organization across the genome in a set of assorted human tissue types and stem cell lines. The researchers turned to ChIP-seq to map genome-wide chromatin patterns, defining the position of various histone modifications in 29 tissue or cell types. Together, the information offers clues to the chromatin state transitions and regulatory features characterizing cells from various lineages, developmental phases, or cellular contexts. The study also considers chromatin organization relative to other features in the cell, including nuclear architecture.