In an advance, online publication of Nature this week, a bicoastal research collaboration led by investigators in Boston reports on the significance of the "epigenetic memory" of induced pluripotent stem cells. Specifically, iPSCs "derived by factor-based reprogramming of adult murine tissues harbor residual DNA methylation signatures characteristic of their somatic tissue of origin, which favors their differentiation along lineages related to the donor cell, while restricting alternative cell fates," the authors write. The team also suggests that "nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin."
A team led by investigators at Princeton University suggests in Nature this week that phenotypic robustness is conferred by redundant transcriptional enhancers, a finding they’ve deduced in a Drosophila model. "Secondary enhancers contribute to phenotypic robustness in the face of environmental and genetic variability," the team concludes.
In Nature Biotechnology this week, investigators at the University of Colorado describe the "rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides" in a method called trackable multiplex recombineering, or TRMR. "In a single day we modified the expression of [more than] 95 percent of the genes in Escherichia coli by inserting synthetic DNA cassettes and molecular barcodes upstream of each gene," the authors say of the technique's efficacy. Within a week, the authors write that they were able to map "thousands of genes that affect E. coli growth in various media ... and in the presence of several growth inhibitors."
And in the most recent issue of Nature Methods, Ting Ni and colleagues at Duke University describe their "paired-end sequencing strategy to map the complex landscape of transcription initiation." Using their approach, the team examined transcription initiation in the Drosophila embryo, and "found that fly promoters exhibited distinct initiation patterns, which were linked to specific promoter sequence motifs," they write. Ni et al. suggest that their paired-end TSS analysis is a "powerful method to uncover the transcriptional complexity of eukaryotic genomes."