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Genomics In The Journals: Mar 17, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Investigators from the UK, France, Switzerland, and Mexico unraveled the genetics behind the naked neck trait in chickens. Through fine mapping and targeted sequencing experiments on Transylvanian Naked Neck chickens, they found a culprit insertion in a transcriptional regulator that ramps up the expression of a gene called BMP12. The vitamin A metabolite retinoic acid boosts related BMP signaling, particularly in neck skin, stifling feather growth. Those involved in the study, published in PLoS Biology, say the findings offer insights into a trait that has turned up in several bird species through convergent evolution and provide clues for those interested in breeding other nude-necked birds — a potential advantage for fowl in sweltering settings.

In Nature, researchers from Rockefeller, New York, and Princeton Universities describe some of the genetics underlying foraging behavior in Caenorhabditis elegans. From their quantitative trait locus experiments using C. elegans strains known for different feeding behaviors — as well as worms produced through crosses of these strains — the group concluded that the worm's foraging preferences spring from several genes. One of these, a G-protein-coupled catecholamine receptor gene called tyra-3, resembles a sensory receptor found in vertebrates, they noted, hinting at shared strategies for sensing environmental stimuli across species.

"These results indicate that genetic variation and environmental cues converge on common circuits to regulate behavior, and suggest that catecholamines have an ancient role in regulating behavioral decisions," senior author Cornelia Bargmann, a neural circuits and behavior researcher at Rockefeller, and co-authors wrote.

Members of the Genetic Risk Prediction Studies (GRIPS) Group published a statement online in PLoS Medicine outlining their checklist of recommendations for reporting findings from genetic risk prediction studies. The guidelines, hammered out during a two-day workshop sponsored by the Human Genome Epidemiology Network, are intended to help improve the transparency of the these studies, the international group emphasized — from study design and analysis methods to interpretation.

"With increasing numbers of discovered genetic markers that can be used in future genetic risk prediction studies, it is crucial to enhance the quality of the reporting of these studies," the team wrote, "since valid interpretation could be compromised by the lack of reporting of key information."

The GRIPS Statement will also appear in several other journals, including the European Journal of Human Genetics, Genetics in Medicine, and Genome Medicine.

Swiss researchers reported in the early, online edition of Science that they have come closer to understanding the kinetics of mammalian gene transcription. The group did single-cell real-time imaging of messenger RNA synthesis in mouse fibroblast cells that were designed to express a luciferase reporter gene under the control of various artificial promoters, circadian regulatory sequences, or endogenous loci. They then used mathematical modeling to look at the timing of transcription at different sites in the genome.

"Our analysis demonstrated that bursting kinetics are highly gene-specific," senior author Felix Naef, a researcher with the Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, and co-authors noted, "reflecting refractory periods during which genes stay inactive for a certain time before switching on again."

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

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

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.