In a paper published online in advance in Genome Research this week, researchers at Erasmus MC in Rotterdam show that the human pigmentation-associated SNP HERC2 rs12913832 functions as an enhancer, regulating OCA2 transcription. Overall, the team shows that "allelic variation of a common non-coding SNP located in a distal regulatory element not only disrupts the regulatory potential of this element but also affects its interaction with the relevant promoter," providing what it calls "key mechanistic insight that allele-dependent differences in chromatin-loop formation results in differences in allelic gene expression that affects common phenotypic traits."
Researchers in Spain this week present an analysis of the excess of deletions over insertions in mammalian genomes, through which they found that "the only mammalian branch with a strong deletional bias is the rodent ancestral branch."
Harvard University's Alexander Schier and his colleagues present results from a "time series of RNA-seq experiments at eight stages during early zebrafish development," through which they "reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci." Altogether, Schier et al. identified 1,133 non-coding multi-exonic transcripts expressed during embryogenesis, including lincRNAs, intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs, they write.
Children's Hospital Boston's Kenneth Mandl and his colleagues report in a Genome Research paper published online in advance an estimate of the number of variants that might qualify for disclosure to research participants based on published recommendations for the return of results, extrapolated to genome scale. "We find that the total number of variants meeting the threshold for recommended disclosure ranges from 3955 [to] 12,579 in the most conservative estimate to 6,998 [to] 17,189 in an estimate including variants with variable disease expressivity," Mandl et al. write, adding that as researchers continue to validate disease-associated variants at the rate they have in the last four years, "the total number ... will grow 37 [percent] over the next 4 yr. [years]," further complicating the ethical dilemma they describe.