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This Week in PLoS: Dec 9, 2008

A study in PLoS Genetics used genotype and gene expression data from 89 African-American samples to study the relationship between local gene expression and genetic ancestry. Surprisingly, the researchers found that only about 12 percent of difference in gene expression is due to cis-acting variants. Daniel MacArthur thinks this doesn't bode well for personal genomics: considering that the other 88 percent must be trans-variants, it will not only be even more difficult to describe genetic pathways involved in many complex diseases, but, "making de novo predictions about the effect of a novel sequence variant on distant genes will be immensely more challenging," he writes at Genetic Future.

Another paper in PLoS Genetics studied lactic acidosis in a tumor's microenvironment, which directly affects how the tumor grows. Looking at breast cancer gene expression data sets, scientists found that lactic acidosis response was associated with good survival rates and that "may relate to the role of lactic acidosis in directing energy generation toward aerobic respiration and utilization of other energy sources via inhibition of glycolysis," they say in the abstract.

In PLoS Biology, Cold Spring Harbor's Rob Martienssen used chromatin immunoprecipitation and DNA methylation profiling to map histone modifications in a cell suspension culture of Arabidopsis. While some genes show an increase in DNA methylation, some transposable elements undergo significant loss of DNA methylation and transcriptional activation. Plus, after sequencing siRNA, transposable elements activated in culture have increased levels of 21-nucleotide siRNA, suggesting that RNAi plays a role in epigenetic restructuring for plants grown in cell culture.

Two studies look at TB resistance. In one published in PLoS One, researchers used a high-content peptide microarray with 61 M. tuberculosis proteins to perform antibody profiling of a total of 7446 individual peptide epitopes. They found that the difference between TB+ and TB- can be found not in specific TB serum proteins, but in "peptide epitope 'hotspots' at different locations within the same protein," they say in the abstract. In another study in PLoS Pathogens, scientists used gene expression profiling to study the susceptibility to tuberculosis, finding that CCL1 is one gene involved in susceptibility to TB.


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.