In Nucleic Acids Research this week, researchers in Germany report on four DNA-binding regions in the Tr domain on the Res subunit of the Type III restriction endonuclease EcoP15I; the endonuclease domain contains two. When modeling the Tr domain, the team found “that these multiple DNA-binding regions are located on the surface, free to interact with DNA,” it writes, adding that “interestingly, the positions of the DNA-binding regions are conserved among Type III restriction endonucleases.”
In another paper published online in advance, an international team led by investigators at the Institute for Systems Biology in Seattle presents RNASEQR, an RNA-seq analysis program. Compared with similar programs, the team says RNASEQR “yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants.”
The University of Ottawa’s Ilona Sylvia Skerjanc and her colleagues show that the Gli2 and MEF2C factors activate one another’s expression while enhancing cardiomyogenesis in differentiating P19 EC cells. “We propose a model whereby Gli2 and MEF2C bind each other's regulatory elements, activate each other's expression and form a protein complex that synergistically activates transcription, enhancing cardiac muscle development,” Skerjanc et al. write.
An academic research team led by scientists at the University of London says that “normalized Affymetrix expression data are biased by G-quadruplex formation.” For a specific microarray data set using the Human HG_U133A Affymetrix GeneChip and RMA normalization, the team found around 14 percent of the probes sets were directly affected by this bias, and that “these effects grow more pronounced as the number of G-stack probes in a probe set increases,” the authors write.