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Genomics In The Journals: Feb 2, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, an international group led by investigators in Finland reports on 11 new loci linked to blood metabolite levels.

For the genome-wide association study, researchers genotyped more than 8,300 unrelated individuals from Finland and 561 twin pairs at nearly eight million SNPs and profiled levels of hundreds of metabolites in their blood samples using nuclear magnetic resonance and other methods. The search led to 31 sites in the genome that corresponded to metabolite features, including 11 new variants and variants influencing lipid levels or levels of type 2 diabetes-related amino acids. Information from identical and non-identical twins participating in the study, meanwhile, indicated that the metabolite-linked loci explain much of the inherited variability seen in metabolite levels.

"SNPs at the 31 loci associated with individual metabolites account for a greater proportion of the genetic component of trait variance … than is typically observed for conventional serum metabolic phenotypes," senior author Samuli Ripatti, a researcher affiliated with the University of Helsinki and the Wellcome Trust Sanger Institute, and co-authors wrote. "The identification of such associations may provide substantial insight into cardiometabolic disorders."

German researchers have found evidence of horizontal gene transfer involving plastid genomes in plants from distinct species. As they report in the early, online edition of the Proceedings of the National Academy of Sciences, the researchers used transgenic plants with fluorescence and drug resistance markers in their chloroplast genomes to investigate whether HGT is behind a phenomenon known as "chloroplast capture" in plants from different species that became grafted to one another.

As they demonstrated in plants from the cultivated tobacco plant species and from related woody and herbaceous species in the same genus, chloroplast genomes from one species can move into and replace those normally found in another species, in some cases persisting in subsequent generations. The process occurs even in the absence of mixing between the plants' nuclear genomes, the team noted.

"[W]e do not know how chloroplasts manage to get from one cell to the other," Max Planck Institute of Molecular Plant Physiology researcher Ralph Bock, the study's senior author, said in a statement. "But … the discovery of this process offers a new explanation for important evolutionary processes and opens up new possibilities for plant breeders."

Researchers from the National Institutes of Health and Johns Hopkins University used microarrays to track DNA methylation patterns of some 14,500 genes in a cognition-related brain region known as the prefrontal cortex during human development and aging — work that they describe online in the American Journal of Human Genetics.

Based on findings from more than 100 post-mortem brain tissue samples ranging in age from 14 weeks gestation to around 90 years old, the researchers saw swings in the nature and extent of DNA methylation across the human lifespan, with the most rapid changes happening between prenatal and post-natal development. Between prenatal and post-natal development, for instance, the results point to a shift from predominantly demethylated promoters to promoters that are much more methylated. The work also offers clues to sex-related differences in DNA methylation, genetic variants influencing the epigenetic marks, and the gene expression consequences of methylation in the PFC. Data from the study is available through an online resource dubbed BrainCloudMethyl.

A study in Genome Research takes a closer look at the contributions that gene expression patterns and timing make to human cognition. Researchers from China, Germany, and Australia used a combination of microarray analyses and RNA-sequencing to gauge gene expression patterns in two brain regions — a motor control region called the cerebellum and the more recently evolved prefrontal cortex — in post-natal brain samples from dozens of humans, chimps, and macaques of different ages. Some of the most pronounced development-related expression differences they found were for co-expressed genes involved in forming synaptic connections within the brain, particularly in the PFC. Expression of these genes reached a peak in chimps and macaques before one year of age — years earlier than in humans, who showed the most pronounced expression of these genes at around five years old.

"Our findings suggest that the human brain remains extremely plastic and susceptible to environmental input during the first five years of life," senior author Philipp Khaitovich, a researcher affiliated with the Chinese Academy of Sciences and the Max Planck Institute for Evolutionary Anthropology, said in a statement, adding that the work "uncovers one of the important mechanisms potentially involved in evolution of human cognition."

Meanwhile, in the print edition of Genome Research this month, a special cancer genomics issue brings together studies on everything from cancer genomes, exomes, and epigenetics to cancer detection, diagnosis, and treatment strategies.

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.

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