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This Week in PNAS: Apr 7, 2009

In the current issue of PNAS, plant biologists show that SET7, a known histone methyltransferase, is involved in regulating the stability of DNA methyltransferase (DNMT1), which has a role in regulating cytosine DNA methylation in mammalian cells. SET7 interacts with DNMT1, they found, and overexpression of SET7 leads to decreased DNMT1 levels, while knockdown of SET7 stabilizes DNMT1.

In the early online edition, work led by MIT's Gregory Stephanopoulos developed a model that correlated mRNA and metabolic flux data. In quantifying 5,764 mRNAs, 54 metabolites, and 83 experimental 13C-based reaction fluxes in yeast cultures under stress in the absence or presence of global regulator Gcn4p, they were able to improve the model by adding protein-protein interaction data. "As a first step in linking metabolic control and genetic regulatory networks, this model underscores the importance of integrating diverse data types in large-scale cellular models," they write in the abstract.

Also in early online, biologists at the Weizmann Institute of Science studied the mRNAs of integral membrane proteins. They found that codons of very hydrophobic amino acids are composed of 50 percent uracils, but that even though this is evolutionarily conserved, they saw that the trend actually minimizes usage of U-rich codons. "Taken together, the results suggest that U-richness is an evolutionarily ancient feature of mRNAs encoding integral membrane proteins, which might serve as a physiologically relevant distinctive signature to this group of mRNAs," they say.

Finally, a collaboration between Affy, Genentech, and Stanford's Genome Technology Center has developed a high-throughput, high-accuracy, array-based resequencing method to find rare disease-related alleles. The method creates, according to the abstract, a "fully multiplexed high-throughput pipeline that results in high-quality data. The pipeline consists of target amplification from genomic DNA, followed by allele enrichment to generate pools of purified variant (or nonvariant) DNA and ends with interrogation of purified DNA on resequencing arrays." A story in our sister publication BioArray News has the full scoop.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.