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This Week in PNAS: Jun 15, 2010

In PNAS this week, researchers from California report their approach to imaging glycans to enable visualization in the enveloping layer during the early stages of zebrafish embryogenesis. The researchers microinjected the embryos with azidosugars at the one-cell stage and detected the metabolically labeled glycans with copper-free click chemistry. "These studies yield insight into the biosynthesis and dynamics of glycans in the enveloping layer during embryogenesis and provide a platform for imaging other biomolecular targets by microinjection of appropriately functionalized biosynthetic precursors," the authors write.

Also in PNAS this week, a team of researchers from China describe a method for constructing ultra high-density linkage maps composed of high-quality SNPs based on low-coverage sequences of recombinant inbred lines. Bar-coded, multiplexed sequence approaches based on next-gen technologies usually generate low-coverage sequences that are filled with errors, the author write. But by making maximum use of SNP information found in the entire population, identifying high-quality SNPs, and genotyping lines in the mapping population using the high-quality SNPs, "a quantitative trait locus for grain width (GW5) was localized to its presumed genomic region in a bin of 200 kb, confirming the accuracy and quality of the map," the researchers write.

Researchers from New York, the UK, and Japan report their detailed structural analysis of chicken kinetochores. The team combined genetic manipulations with deconvolution and super-resolution fluorescence microscopy for the analysis and observed "robust amounts of H3K9me3, but only low levels of H3K4me2, between CENP-A subdomains in unfolded interphase prekinetochores." Based on their data, the researchers suggest mitotic kinetochores are more stable than interphase prekinetochores, reflecting mitotic kinetochore maturation. "Based on our results we propose a new model for inner centromeric chromatin architecture in which chromatin is folded as a layered boustrophedon, with planar sinusoids containing interspersed CENP-A–rich and H3-rich subdomains oriented toward the outer kinetochore," the authors write.

A team of researchers from New York and Texas report their findings that "Rad6-Rad18 mediated monoubiquitylation of proliferating cell nuclear antigen at lys 164 plays a crucial role in promoting the access of translesion synthesis DNA polymerases to PCNA in the replication fork stalled at a lesion site." The authors observed that C-terminal truncations of hPolη that contain the PIP1 domain but lack the UBZ and PIP2 domains promote efficient TLS opposite a cis-syn TT dimer and confer a high degree of UV resistance to XPV cells. This, they write, "provides unambiguous evidence that the binding of PCNA via its PIP domain is essential as well as sufficient for providing hPolη the ability to carry out TLS in human cells."

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.