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This Week in Nature: Apr 8, 2010

In Nature this week, an international research team reports their examination of the alterations in chromatin structure that coincide with pluripotency and genome activation. Using a zebrafish model, the team mapped the location of the repressive H3K27me3 and the activating H3k4me3 histone molecules. While neither were detected before the maternal-zygotic transition, more than 80 percent of the genes were marked by H3K4me3 after genome activation. The team also found several inactive genes that are uniquely marked by H3K4me3. "Moreover, H3K4me3 marks could form in the absence of both sequence-specific transcriptional activators and stable association of RNA polymerase II, as indicated by the analysis of an inducible transgene," the authors write, adding that their results "indicate that bivalent and monovalent domains might poise embryonic genes for activation and that the chromatin profile associated with pluripotency is established during the maternal-zygotic transition."

In an advance, online publication of Nature this week, researchers at the University of Massachusetts Medical School and the University of Manchester, UK, report their eluciations of the miRNA-mediated "integration of haemodynamics and Vegf signaling during angiogenesis." In focusing on aortic arch blood vessels — "known to remodel in response to blood flow" — and by using two-photon imaging of zebrafish embryos, the team ascertained that the sprouting of vessels requires a flow-induced genetic pathway in which klf2a, a zinc finger transcription factor, is activated. The miR-126, they write, "promotes angiogenesis by repressing spred1 and pik3r2, which normally inhibit Vegf signaling." They observed that, in the absence of flow and Klf2a, a reduction in miR-126 expression allows the upregulation of spred1 and pik3r2, consequenty preventing Vegf-induced angiogenesis.

Researchers in Canada and France report the transfer of carbohydrate-active enzymes — absent in the human genome — from marine bacteria to the gut microbiota of a Japanese population. They also describe the first polyphyranases from Zobellia galactanivorans, a member of the marine bacteriodetes. Genes coding for these porphyranases, and similarly for agarases, the authors show, are frequent in a Japanese population but absent in metagenome data from individuals of North American ancestry — a finding they attribute to the high seaweed content in the Japanese diet. "This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes [carbohydrate-active enzymes] were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes," the team writes.

Also in Nature this week, Yijun Chen at the China Pharmaceutical University in Jiangsu responds to the journal's March 4 editorial which outlined the BGI's practice of hiring non-PhD staff members for sequencing projects. The sequencing work that post-baccalaureate technicians perform at the BGI, Chen continues, "cannot measure up to the standards of advanced education or creativity demanded by a formal PhD program." The author suggests that the BGI's practice is a response to political and social demand — the Chinese government is subsidizing institutions that hire new graduates that currently flood the job market, Chen points out — "rather than a genuine scheme to train future scientists."

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.