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This Week in Nature: Jul 28, 2011

In a paper published online in advance in Nature this week, the University of British Columbia's Marco Marra and his colleagues report sequencing tumor and matched normal DNA from 13 diffuse large B-cell lymphoma cases and one follicular lymphoma case and analyzing RNA-seq data for these and an additional 113 non-Hodgkin lymphomas. In their analysis, Marra et al. found that "genes with roles in histone modification were frequent targets of somatic mutation," and, as a result, suggest that their study "suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis."

Researchers at the John Innes Centre this week use mathematical models, ChIP data, and the results of an FLC:GUS reporter assay to show that the quantitative nature of vernalization in plants "is generated by H3K27me3-mediated FLC silencing in the warm in a subpopulation of cells whose number depends on the length of the prior cold." Further, the John Innes team proposes a switching mechanism "involving the local nucleation of an opposing histone modification," which it says is "likely to be widely relevant in epigenetic reprogramming."

Investigators at the Okinawa Institute of Science and Technology Promotion Corporation in Japan report their sequencing of the approximately 420-megabase genome of the Acropora digitifera coral. In its molecular phylogenetic analysis, the Okinawa Institute team found that the Acropora digitifera coral and the sea anemone Nematostella vectensis "diverged … considerably earlier than the time over which modern corals are represented in the fossil record." Overall, the team suggests its coral genome work "provides a platform for understanding the molecular basis of symbiosis and responses to environmental changes."

In a recent Nature Biotechnology opinion piece, investigators at the Johns Hopkins Bloomberg School of Public Health, along with their colleague at Brown University, acknowledge that "RNA sequencing technology provides various advantages over DNA microarrays," though they caution that "the euphoria surrounding the technology has led many … to discount the influence of biological variability, forgetting perhaps that unwanted variability in gene expression measurements is not due only to measurement error." That "gene expression is a stochastic process," they authors say, should be taken into account when reporting RNA-seq results.