In a PLoS One paper published this week, Stanford University School of Medicine's Atul Butte and his colleagues show that "non-synonymous and synonymous coding SNPs show similar likelihood and effect size of human disease association." By surveying more than 20,000 disease-SNP associations from 2,113 GWAS papers, Butte et al. found that "the likelihood of disease association was positively associated with the effect size across different types of SNPs" and that SNPs in the 3' UTRs "might be under-investigated." The team suggests that sSNPS are "just as likely to be involved in disease mechanisms" as nsSNPs, and therefore, "should also be examined with functional studies," the authors write.
Researchers from Chicago describe ExprTarget, a novel method for human microRNA target predictions. ExprTarget, the authors write, integrates the miRanda, PicTar, and TargetScan methods with HapMap miRNA and mRNA data sets, and therefore, it "greatly improves miRNA target prediction relative to the individual prediction algorithms in terms of sensitivity and specificity." ExprTargetDB, a database of human miRNA target predictions, is now available online.
In another paper appearing in PLoS One this week, researchers at the University of York in the UK and the Spanish National Cancer Research Centre report that mammalian SIRT1-ΔExon8, an alternative isoform of the stress-tolerance coordinator, is a result of alternative splicing that occurs in an auto-regulatory loop with p53, "whereby SIRT1-ΔExon8 can regulate p53, while in reciprocal p53 can influence SIRT1 splice variation." The authors suggest that their results "reveal a new level of inter-dependency between p53 and SIRT1" and assert that functions previously attributed to SIRT1 could be associated with its isoforms.
An international public-private research collaboration reports a method for the "genome-wide identification of targets and function of individual microRNAs in mouse embryonic stem cells" in PLoS Genetics this week. The team introduced miR-295 to Dicer1-null murine ESCs and then performed transcriptome profiling via microarrays and "a biochemical approach to isolate mRNA targets associated with the Argonaute2 protein of the RISC effector, followed by RNA-sequencing." The researchers conclude that their resulting data suggest that "miR-294 may promote pluripotency by regulating a subset of c-Myc target genes and upregulating pluripotency-associated genes such as Lin28."