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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

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.