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Genomics in the Journals: Mar 7, 2013

NEW YORK (GenomeWeb News) – Mutations in an obesity-associated gene called FTO can contribute to melanoma risk through a pathway that appears independent of body mass index, according to a Nature Genetics article by members of an international melanoma consortium known as GenoMEL. With the help of imputed genotype information, the group conducted a multi-phase association study starting with nearly 1,400 European or Israeli individuals with melanoma and more than 3,500 unaffected controls from Europe.

The search uncovered melanoma-associated variants in FTO, which investigators subsequently verified using data from tens of thousands of cases and controls from Europe, the US, and Australia.

The apparent risk locus for melanoma falls in a different FTO intron than known BMI-related SNPs, which largely cluster in intron 1 of the gene, researchers reported, and appear to be independent from the obesity-linked loci. As such, authors of the study argued that these findings might prove useful for those studying cancer genetics and for obesity researchers.

"[T]his is to our knowledge the first study to identify and replicate an association with SNPs in FTO not related to body mass index," corresponding author Mark Iles, with the Leeds Cancer Research UK Centre, and his GenoMEL co-authors wrote. They added that "[t]his suggests FTO's function may be broader than the existing paradigm that FTO variants influence multiple traits through their associations with BMI and obesity."


University of Georgia researchers turned to transposon-mediated mutagenesis and deep sequencing to assess the function of genes across the genome in a hydrogenotrophic methanogenic archaea species called Methanococcus maripaludis — work that they presented in the early, online version of the Proceedings of the National Academy of Sciences this week.

The team made tens of thousands of M. maripaludis mutants, starting from a bug in the S2 strain that was transformed with a Tn5-derived transposon. By sequencing and mapping transposon insertion sites within these mutants back to the M. maripaludis genome, the investigators got a glimpse at some of the genes that are apparently indispensable or beneficial for the bug's growth. So far, that includes 526 genes — nearly a third of the known genes encoded in the M. maripaludis genome — though study authors say additional work is needed to verify and expand on these results.

"[T]hese results provide fresh insights into numerous metabolic and molecular pathways of these unique prokaryotes," senior author William Whitman, a University of Georgia microbiologist, and his colleagues wrote, noting that "classifications of essentiality are hypotheses about the nature of specific genes."

"Definitive assignments of essentiality require detailed analysis of each gene," they added, "which is not possible in a global survey of the genome."


A team of researchers from the UK and Canada has used mass spectrometry-based analyses of collagen peptides as part of its analysis of ancient giant camel fossil fragments found on Nunavut's Ellesmere Island.

As they explained in Nature Communications, the researchers used a matrix-assisted laser desorption/ionization, or MALDI, mass spec to study collagen samples nabbed from 30 or so bone fragments going back to the mid-Pliocene period roughly 3.5 million years ago when the Arctic was far warmer than it is today.

Comparisons with collagen peptide fingerprints from more than three dozen terrestrial mammal species indicated that the ancient camel-like creature shared collagen patterns with both dromedary camels living today and with an even older giant camel called Paracamelus that once roamed the Yukon and other parts of the world — findings supported by bone preservation, mineralization, and other analyses included in the study.

"[O]ur research shows that the Paracamelus lineage inhabited northern North America for millions of years and the simplest explanation for this pattern would be that Paracamelus originated there," Canadian Museum of Nature paleobiology researcher Natalia Rybczynski, co-first author on the study, said in a statement, adding that "some specializations seen in modern camels, such as their wide flat feet, large eyes and humps for fat may be adaptations derived from living in a polar environment."


Exome sequencing and linkage analyses helped to uncover neurodegenerative disease-related mutations within sequences that encode prion-like domains of certain proteins. A St. Jude Children's Research Hospital and University of Pennsylvania-led team, which published its findings in Nature, began by testing individuals from two families affected by multi-system proteinopathy, an inherited condition that leads to degeneration in muscle, motor neuron, brain, or bone tissue.

When they sorted through protein-coding sequences and linkage data for the families, the researchers saw disease-associated mutations in sequences coding for a heterogeneous nuclear ribonucleoprotein called hnRNPA2B1 in one of the families. In the other family, multi-system proteinopathy segregated with mutations to another heterogeneous nuclear ribonucleoprotein gene, hnRNPA1. Their follow-up work unearthed hnRNPA1 mutations in a third family that was affected not by multi-system proteinopathy, but by amyotrophic lateral sclerosis.

In each case, the offending mutations fell within hnRNPA2B1 or hnRNPA1 sequences coding for so-called prion-like domains — parts of the proteins that resemble yeast prions. Such domains are predicted to appear in hundreds of human proteins, researchers noted, especially those capable of binding RNA.

Results of the study suggest that mutations to such domains might contribute to disease by coercing such proteins to clump together excessively, authors of the study suggested. "Wild-type hnRNPA2 … and hnRNPA1 show an intrinsic tendency to assemble into self-seeding fibrils," they explained, "which is exacerbated by the disease mutations."


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

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