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This Week in Genome Biology : Jul 20, 2011

In Genome Biology this week, a trio of investigators in Sweden reports its use of "genome-wide strain-specific SNP data from 64 strains of budding yeast to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation." By incorporating phylogenetic and population genetic data into their analyses, the researchers observed "a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet, or tertiary structure," as they write in a paper published online in advance this week.

In another paper published online in advance this week, French researchers report that the previously unannotated miR-642a-3p is highly adipocyte-specific, and that miR-30 is a key regulator of human adipogenesis. By inhibiting the miR-30 family, the team found adipogenesis was blocked whereas by over-expressing miR-30a and miR-30d, the process was stimulated. "We additionally showed that both miR-30a and miR-30d target the transcription factor RUNX2, and stimulate adipogenesis via the modulation of this major regulator of osteogenesis," the authors write.

A team led by investigators at BGI in Shenzhen reports a genome sequence and global sequence variation map for the Chinese rhesus macaque in a recent Genome Biology paper published online. The BGI-led team sequenced the macaque genome at 11.56-fold coverage, identifying 2.56 million homozygous and 2.94 million heterozygous SNPs. Further, the team detected "125,150 structural variations, of which 123,610 were deletions," the authors write, adding that they also "annotated 5,187 and 962 non-synonymous SNPs to the macaque orthologs of human disease and drug-target genes, respectively."

In comparatively analyzing genome-wide DNA methylation profiles of three human embryonic stem cell lines by combining bisulfite sequencing and RNA-seq data, researchers at the University of California, Los Angeles, found that "heavily methylated non-CG sites are strongly conserved especially when found within the motif TACAG," they write in Genome Biology. "They are enriched in splice sites and are more methylated than other non-CG sites in genes." Further, the UCLA researchers add that they "identified variations in methylation levels at binding sites and found that for several transcription factors the correlation between the methylation at binding sites and gene expression is generally stronger than in the neighboring sequences."

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.