In early online publication at Genome Research, a group of researchers led by McGill’s Tomi Pastinen and Elin Grundberg carried out a cell-type specific eQTL study of primary human osteoblasts, or bone cells, and combined it with publicly available GWAS data for bone mineral density. They were able to study the top 2,000 BMD-associated SNPs to determine their cis-regulatory effects. They write in the abstract: “Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies.”
Also in early online, scientists at Japan's National Cancer Center Research Institute used sys bio tools to find that whether active or stalled RNA polymerase II affects promoter CpG islands. Using MeDIP and microarrays, they found 5,510 and 521 genes with promoter CpG islands resistant and susceptible, respectively, to DNA methylation in prostate cancer cell lines. Using ChIP-chip, they found that the presence alone of RNA pol II made the DNA resistant to methylation.
Brigham & Women's Hospital and Harvard Medical School's Martha Bulyk was lead author on a paper that designed the "first method for distinguishing between direct and indirect TF-DNA interactions, integrating in vivo TF binding data, in vivo nucleosome occupancy data, and motifs from in vitro protein binding microarray experiments." Using her method on yeast ChIP-chip data, she showed that only 48 percent of the binding interactions can be explained by direct binding, 16 percent by indirect binding – where a protein also interacts with the TF – while 36 percent are left unexplained.
Finally, in the August issue of the journal, Johns Hopkins scientists have devised an "ultrasensitive and reliable nanotechnology assay, MS-qFRET, for detection and quantification of DNA methylation." Their method uses bisulfite DNA, PCR, and quantum dots that can determine the methylation status from FRET. Key features, they say, are low background noise, high resolution, and high sensitivity; it can also be used on clinical samples for early diagnosis, prognostic application, and monitoring of therapeutics.